From 54ff24165ebe7e5e93f5bab98d556b4c9d56eae2 Mon Sep 17 00:00:00 2001
From: Konrad Rokicki <rokickik@janelia.hhmi.org>
Date: Mon, 23 Feb 2026 17:03:36 -0500
Subject: [PATCH 01/20] fix alembic migration

---
 fileglancer/alembic.ini | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fileglancer/alembic.ini b/fileglancer/alembic.ini
index 2b2d7ac5..2583713a 100644
--- a/fileglancer/alembic.ini
+++ b/fileglancer/alembic.ini
@@ -2,7 +2,7 @@
 
 [alembic]
 # path to migration scripts
-script_location = alembic
+script_location = fileglancer/alembic
 
 # template used to generate migration file names; The default value is %%(rev)s_%%(slug)s
 # Uncomment the line below if you want the files to be prepended with date and time

From e8f0f82ed1f7eb759bee17ec7f16c95a28bbf634 Mon Sep 17 00:00:00 2001
From: Konrad Rokicki <rokickik@janelia.hhmi.org>
Date: Mon, 23 Feb 2026 17:04:49 -0500
Subject: [PATCH 02/20] added service apps

---
 ...e8a3f21c76_add_entry_point_type_to_jobs.py | 24 ++++++
 fileglancer/apps.py                           | 41 ++++++++++-
 fileglancer/database.py                       |  3 +
 fileglancer/model.py                          |  3 +
 fileglancer/server.py                         |  2 +
 frontend/src/components/AppLaunch.tsx         | 22 ++++--
 frontend/src/components/JobDetail.tsx         | 73 ++++++++++++++++++-
 .../components/ui/AppsPage/AppLaunchForm.tsx  |  4 +-
 .../components/ui/Table/appsJobsColumns.tsx   | 21 +++++-
 frontend/src/shared.types.ts                  |  3 +
 pixi.lock                                     |  2 +-
 pyproject.toml                                |  4 +-
 12 files changed, 184 insertions(+), 18 deletions(-)
 create mode 100644 fileglancer/alembic/versions/b5e8a3f21c76_add_entry_point_type_to_jobs.py

diff --git a/fileglancer/alembic/versions/b5e8a3f21c76_add_entry_point_type_to_jobs.py b/fileglancer/alembic/versions/b5e8a3f21c76_add_entry_point_type_to_jobs.py
new file mode 100644
index 00000000..c8f529fc
--- /dev/null
+++ b/fileglancer/alembic/versions/b5e8a3f21c76_add_entry_point_type_to_jobs.py
@@ -0,0 +1,24 @@
+"""add entry_point_type to jobs
+
+Revision ID: b5e8a3f21c76
+Revises: a3f7c2e19d04
+Create Date: 2026-02-23 00:00:00.000000
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = 'b5e8a3f21c76'
+down_revision = 'a3f7c2e19d04'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    op.add_column('jobs', sa.Column('entry_point_type', sa.String(), nullable=False, server_default='job'))
+
+
+def downgrade() -> None:
+    op.drop_column('jobs', 'entry_point_type')
diff --git a/fileglancer/apps.py b/fileglancer/apps.py
index cf05a9be..63c2818c 100644
--- a/fileglancer/apps.py
+++ b/fileglancer/apps.py
@@ -627,6 +627,7 @@ async def submit_job(
             app_name=manifest.name,
             entry_point_id=entry_point.id,
             entry_point_name=entry_point.name,
+            entry_point_type=entry_point.type,
             parameters=parameters,
             resources=resources_dict,
             manifest_path=manifest_path,
@@ -798,8 +799,37 @@ def _make_file_info(file_path: str, exists: bool) -> dict:
     }
 
 
+def get_service_url(db_job: db.JobDB) -> Optional[str]:
+    """Read the service URL from a job's work directory.
+
+    Only returns a URL when the job is a service type and is currently RUNNING.
+    The service writes its URL to a plain text file named 'service_url' in the
+    job's work directory.
+    """
+    if getattr(db_job, 'entry_point_type', 'job') != 'service':
+        return None
+    if db_job.status != 'RUNNING':
+        return None
+
+    work_dir = _resolve_work_dir(db_job)
+    url_file = work_dir / "service_url"
+
+    if not url_file.is_file():
+        return None
+
+    try:
+        url = url_file.read_text().strip()
+    except OSError:
+        return None
+
+    if not url.startswith(("http://", "https://")):
+        return None
+
+    return url
+
+
 def get_job_file_paths(db_job: db.JobDB) -> dict[str, dict]:
-    """Return file path info for a job's files (script, stdout, stderr).
+    """Return file path info for a job's files (script, stdout, stderr, service_url).
 
     Returns a dict keyed by file type with path and existence info.
     """
@@ -812,12 +842,19 @@ def get_job_file_paths(db_job: db.JobDB) -> dict[str, dict]:
     stdout_path = work_dir / "stdout.log"
     stderr_path = work_dir / "stderr.log"
 
-    return {
+    files = {
         "script": _make_file_info(script_path, len(scripts) > 0),
         "stdout": _make_file_info(str(stdout_path), stdout_path.is_file()),
         "stderr": _make_file_info(str(stderr_path), stderr_path.is_file()),
     }
 
+    # Include service_url file info for service-type jobs
+    if getattr(db_job, 'entry_point_type', 'job') == 'service':
+        service_url_path = work_dir / "service_url"
+        files["service_url"] = _make_file_info(str(service_url_path), service_url_path.is_file())
+
+    return files
+
 
 async def get_job_file_content(job_id: int, username: str, file_type: str) -> Optional[str]:
     """Read the content of a job file (script, stdout, or stderr).
diff --git a/fileglancer/database.py b/fileglancer/database.py
index 5feb0c92..7adfdb63 100644
--- a/fileglancer/database.py
+++ b/fileglancer/database.py
@@ -148,6 +148,7 @@ class JobDB(Base):
     manifest_path = Column(String, nullable=False, server_default="")
     entry_point_id = Column(String, nullable=False)
     entry_point_name = Column(String, nullable=False)
+    entry_point_type = Column(String, nullable=False, server_default="job")
     parameters = Column(JSON, nullable=False)
     status = Column(String, nullable=False, default="PENDING")
     exit_code = Column(Integer, nullable=True)
@@ -828,6 +829,7 @@ def delete_expired_sessions(session: Session):
 def create_job(session: Session, username: str, app_url: str, app_name: str,
                entry_point_id: str, entry_point_name: str, parameters: Dict,
                resources: Optional[Dict] = None, manifest_path: str = "",
+               entry_point_type: str = "job",
                env: Optional[Dict] = None, pre_run: Optional[str] = None,
                post_run: Optional[str] = None, pull_latest: bool = False) -> JobDB:
     """Create a new job record"""
@@ -839,6 +841,7 @@ def create_job(session: Session, username: str, app_url: str, app_name: str,
         manifest_path=manifest_path,
         entry_point_id=entry_point_id,
         entry_point_name=entry_point_name,
+        entry_point_type=entry_point_type,
         parameters=parameters,
         resources=resources,
         env=env,
diff --git a/fileglancer/model.py b/fileglancer/model.py
index 7cf897a9..45fde4b5 100644
--- a/fileglancer/model.py
+++ b/fileglancer/model.py
@@ -382,6 +382,7 @@ class AppEntryPoint(BaseModel):
     """An entry point (command) within an app"""
     id: str = Field(description="Unique identifier for the entry point")
     name: str = Field(description="Display name of the entry point")
+    type: Literal["job", "service"] = Field(description="Whether this is a batch job or long-running service", default="job")
     description: Optional[str] = Field(description="Description of the entry point", default=None)
     command: str = Field(description="The base CLI command to execute")
     parameters: List[AppParameterItem] = Field(description="Parameters for this entry point", default=[])
@@ -489,6 +490,7 @@ class Job(BaseModel):
     manifest_path: str = Field(description="Relative manifest path within the app repo", default="")
     entry_point_id: str = Field(description="Entry point that was executed")
     entry_point_name: str = Field(description="Display name of the entry point")
+    entry_point_type: str = Field(description="Whether this is a batch job or long-running service", default="job")
     parameters: Dict = Field(description="Parameters used for the job")
     status: str = Field(description="Job status (PENDING, RUNNING, DONE, FAILED, KILLED)")
     exit_code: Optional[int] = Field(description="Exit code of the job", default=None)
@@ -498,6 +500,7 @@ class Job(BaseModel):
     post_run: Optional[str] = Field(description="Script run after the main command", default=None)
     pull_latest: bool = Field(description="Whether pull latest was enabled", default=False)
     cluster_job_id: Optional[str] = Field(description="Cluster-assigned job ID", default=None)
+    service_url: Optional[str] = Field(description="URL of the running service (for service-type jobs)", default=None)
     created_at: datetime = Field(description="When the job was created")
     started_at: Optional[datetime] = Field(description="When the job started running", default=None)
     finished_at: Optional[datetime] = Field(description="When the job finished", default=None)
diff --git a/fileglancer/server.py b/fileglancer/server.py
index 0b771f94..b82d95a2 100644
--- a/fileglancer/server.py
+++ b/fileglancer/server.py
@@ -1728,6 +1728,7 @@ def _convert_job(db_job: db.JobDB, include_files: bool = False) -> Job:
             manifest_path=db_job.manifest_path,
             entry_point_id=db_job.entry_point_id,
             entry_point_name=db_job.entry_point_name,
+            entry_point_type=getattr(db_job, 'entry_point_type', 'job'),
             parameters=db_job.parameters,
             status=db_job.status,
             exit_code=db_job.exit_code,
@@ -1737,6 +1738,7 @@ def _convert_job(db_job: db.JobDB, include_files: bool = False) -> Job:
             post_run=db_job.post_run,
             pull_latest=db_job.pull_latest,
             cluster_job_id=db_job.cluster_job_id,
+            service_url=apps_module.get_service_url(db_job),
             created_at=db_job.created_at,
             started_at=db_job.started_at,
             finished_at=db_job.finished_at,
diff --git a/frontend/src/components/AppLaunch.tsx b/frontend/src/components/AppLaunch.tsx
index 7aac1214..a3cae782 100644
--- a/frontend/src/components/AppLaunch.tsx
+++ b/frontend/src/components/AppLaunch.tsx
@@ -119,7 +119,8 @@ export default function AppLaunch() {
         pre_run: preRun,
         post_run: postRun
       });
-      toast.success('Job submitted');
+      const isService = selectedEntryPoint.type === 'service';
+      toast.success(isService ? 'Service started' : 'Job submitted');
       navigate('/apps/jobs');
     } catch (error) {
       const message =
@@ -244,12 +245,19 @@ export default function AppLaunch() {
                 key={ep.id}
               >
                 <div className="flex-1 min-w-0">
-                  <Typography
-                    className="text-foreground font-medium"
-                    type="small"
-                  >
-                    {ep.name}
-                  </Typography>
+                  <div className="flex items-center gap-2">
+                    <Typography
+                      className="text-foreground font-medium"
+                      type="small"
+                    >
+                      {ep.name}
+                    </Typography>
+                    {ep.type === 'service' ? (
+                      <span className="inline-flex items-center px-1.5 py-0.5 rounded text-[10px] font-medium bg-info/10 text-info border border-info/30">
+                        Service
+                      </span>
+                    ) : null}
+                  </div>
                   {ep.description ? (
                     <Typography className="text-secondary mt-1" type="small">
                       {ep.description}
diff --git a/frontend/src/components/JobDetail.tsx b/frontend/src/components/JobDetail.tsx
index 06cae847..e08b6014 100644
--- a/frontend/src/components/JobDetail.tsx
+++ b/frontend/src/components/JobDetail.tsx
@@ -5,7 +5,9 @@ import { Button, Tabs, Typography } from '@material-tailwind/react';
 import {
   HiOutlineArrowLeft,
   HiOutlineDownload,
-  HiOutlineRefresh
+  HiOutlineExternalLink,
+  HiOutlineRefresh,
+  HiOutlineStop
 } from 'react-icons/hi';
 import { Prism as SyntaxHighlighter } from 'react-syntax-highlighter';
 import {
@@ -22,7 +24,11 @@ import {
 } from '@/utils/pathHandling';
 import { usePreferencesContext } from '@/contexts/PreferencesContext';
 import { useZoneAndFspMapContext } from '@/contexts/ZonesAndFspMapContext';
-import { useJobQuery, useJobFileQuery } from '@/queries/jobsQueries';
+import {
+  useJobQuery,
+  useJobFileQuery,
+  useCancelJobMutation
+} from '@/queries/jobsQueries';
 
 function FilePreview({
   content,
@@ -140,6 +146,11 @@ export default function JobDetail() {
   const scriptQuery = useJobFileQuery(id, 'script');
   const stdoutQuery = useJobFileQuery(id, 'stdout');
   const stderrQuery = useJobFileQuery(id, 'stderr');
+  const cancelMutation = useCancelJobMutation();
+
+  const isService = jobQuery.data?.entry_point_type === 'service';
+  const isActive =
+    jobQuery.data?.status === 'PENDING' || jobQuery.data?.status === 'RUNNING';
 
   useEffect(() => {
     const checkDarkMode = () => {
@@ -260,6 +271,64 @@ export default function JobDetail() {
             </div>
           </div>
 
+          {/* Service URL banner */}
+          {isService && job.status === 'RUNNING' ? (
+            job.service_url ? (
+              <div className="mb-4 p-3 flex items-center gap-3 border border-success rounded-lg bg-success/10">
+                <span className="relative flex h-3 w-3">
+                  <span className="animate-ping absolute inline-flex h-full w-full rounded-full bg-success opacity-75" />
+                  <span className="relative inline-flex rounded-full h-3 w-3 bg-success" />
+                </span>
+                <Typography className="text-foreground flex-1" type="small">
+                  Service is running at{' '}
+                  <a
+                    className="text-primary-light hover:underline font-mono"
+                    href={job.service_url}
+                    rel="noopener noreferrer"
+                    target="_blank"
+                  >
+                    {job.service_url}
+                  </a>
+                </Typography>
+                <a
+                  className="inline-flex items-center gap-1 px-3 py-1.5 text-sm font-medium rounded-md bg-success text-white hover:bg-success/90 transition-colors"
+                  href={job.service_url}
+                  rel="noopener noreferrer"
+                  target="_blank"
+                >
+                  <HiOutlineExternalLink className="h-4 w-4" />
+                  Open Service
+                </a>
+              </div>
+            ) : (
+              <div className="mb-4 p-3 flex items-center gap-3 border border-warning rounded-lg bg-warning/10">
+                <span className="relative flex h-3 w-3">
+                  <span className="animate-ping absolute inline-flex h-full w-full rounded-full bg-warning opacity-75" />
+                  <span className="relative inline-flex rounded-full h-3 w-3 bg-warning" />
+                </span>
+                <Typography className="text-foreground flex-1" type="small">
+                  Service is starting up...
+                </Typography>
+              </div>
+            )
+          ) : null}
+
+          {/* Stop Service button for active services */}
+          {isService && isActive ? (
+            <div className="mb-4">
+              <Button
+                className="!rounded-md"
+                color="error"
+                disabled={cancelMutation.isPending}
+                onClick={() => cancelMutation.mutate(job.id)}
+                variant="outline"
+              >
+                <HiOutlineStop className="icon-small mr-2" />
+                {cancelMutation.isPending ? 'Stopping...' : 'Stop Service'}
+              </Button>
+            </div>
+          ) : null}
+
           {/* Tabs */}
           <Tabs onValueChange={setActiveTab} value={activeTab}>
             <Tabs.List className="justify-start items-stretch shrink-0 min-w-fit w-full py-2 bg-surface dark:bg-surface-light">
diff --git a/frontend/src/components/ui/AppsPage/AppLaunchForm.tsx b/frontend/src/components/ui/AppsPage/AppLaunchForm.tsx
index 56ffe025..76fd95e3 100644
--- a/frontend/src/components/ui/AppsPage/AppLaunchForm.tsx
+++ b/frontend/src/components/ui/AppsPage/AppLaunchForm.tsx
@@ -845,7 +845,9 @@ export default function AppLaunchForm({
           ? 'Validating...'
           : submitting
             ? 'Submitting...'
-            : 'Submit Job'}
+            : entryPoint.type === 'service'
+              ? 'Start Service'
+              : 'Submit Job'}
       </Button>
     </div>
   );
diff --git a/frontend/src/components/ui/Table/appsJobsColumns.tsx b/frontend/src/components/ui/Table/appsJobsColumns.tsx
index 9c211ee1..2ccce696 100644
--- a/frontend/src/components/ui/Table/appsJobsColumns.tsx
+++ b/frontend/src/components/ui/Table/appsJobsColumns.tsx
@@ -97,11 +97,25 @@ export function createAppsJobsColumns(
     {
       accessorKey: 'status',
       header: 'Status',
-      cell: ({ getValue }) => {
+      cell: ({ getValue, row }) => {
         const status = getValue() as Job['status'];
+        const job = row.original;
+        const hasServiceUrl =
+          job.entry_point_type === 'service' && job.service_url;
         return (
-          <div className="flex items-center h-full">
+          <div className="flex items-center gap-2 h-full">
             <JobStatusBadge status={status} />
+            {hasServiceUrl ? (
+              <a
+                className="text-xs text-primary hover:underline"
+                href={job.service_url}
+                onClick={e => e.stopPropagation()}
+                rel="noopener noreferrer"
+                target="_blank"
+              >
+                Open
+              </a>
+            ) : null}
           </div>
         );
       },
@@ -148,6 +162,7 @@ export function createAppsJobsColumns(
         const job = row.original;
         const canCancel = job.status === 'PENDING' || job.status === 'RUNNING';
 
+        const isService = job.entry_point_type === 'service';
         const menuItems: MenuItem<JobRowActionProps>[] = [
           {
             name: 'View Details',
@@ -158,7 +173,7 @@ export function createAppsJobsColumns(
             action: props => props.onRelaunch(props.job)
           },
           {
-            name: 'Cancel',
+            name: isService ? 'Stop Service' : 'Cancel',
             action: props => props.onCancel(props.job.id),
             shouldShow: canCancel
           },
diff --git a/frontend/src/shared.types.ts b/frontend/src/shared.types.ts
index 68b4cd5d..f0cb6f1c 100644
--- a/frontend/src/shared.types.ts
+++ b/frontend/src/shared.types.ts
@@ -108,6 +108,7 @@ type AppResourceDefaults = {
 type AppEntryPoint = {
   id: string;
   name: string;
+  type?: 'job' | 'service';
   description?: string;
   command: string;
   parameters: AppParameterItem[];
@@ -147,6 +148,7 @@ type Job = {
   manifest_path: string;
   entry_point_id: string;
   entry_point_name: string;
+  entry_point_type?: 'job' | 'service';
   parameters: Record<string, unknown>;
   status: 'PENDING' | 'RUNNING' | 'DONE' | 'FAILED' | 'KILLED';
   exit_code?: number;
@@ -156,6 +158,7 @@ type Job = {
   post_run?: string;
   pull_latest: boolean;
   cluster_job_id?: string;
+  service_url?: string;
   created_at: string;
   started_at?: string;
   finished_at?: string;
diff --git a/pixi.lock b/pixi.lock
index bb5fb65e..bdec2561 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -3839,7 +3839,7 @@ packages:
 - pypi: ./
   name: fileglancer
   version: 2.5.0
-  sha256: 2449456fb11db97fa768b4228f62867e530fc3d28f0ec1810a59007173d1c8a3
+  sha256: 51e22bdacfdcf2069b48aebcd73d234991bcdecf87da989cd5cd343d506a8bd5
   requires_dist:
   - aiosqlite>=0.21.0
   - alembic>=1.17.0
diff --git a/pyproject.toml b/pyproject.toml
index bfc32ae3..ec1c9683 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -147,8 +147,8 @@ dev-launch = "pixi run uvicorn fileglancer.server:app --no-access-log --port 787
 dev-launch-remote = "pixi run uvicorn fileglancer.server:app --host 0.0.0.0 --port 7878 --reload --ssl-keyfile /opt/certs/cert.key --ssl-certfile /opt/certs/cert.crt"
 prod-launch-remote = "pixi run uvicorn fileglancer.server:app --workers 10 --host 0.0.0.0 --port 7878 --ssl-keyfile /opt/certs/cert.key --ssl-certfile /opt/certs/cert.crt"
 dev-launch-secure = "python fileglancer/dev_launch.py"
-migrate = "alembic upgrade head"
-migrate-create = "alembic revision --autogenerate"
+migrate = "alembic -c fileglancer/alembic.ini upgrade head"
+migrate-create = "alembic -c fileglancer/alembic.ini revision --autogenerate"
 stamp-db = "python -m fileglancer.stamp_db"
 container-rebuild = "npx @devcontainers/cli up --workspace-folder . --remove-existing-container"
 container-shell = "npx @devcontainers/cli exec --workspace-folder . bash"

From f0f6a4ed725ac63139a5ffc2d8b236c350640b69 Mon Sep 17 00:00:00 2001
From: Konrad Rokicki <rokickik@janelia.hhmi.org>
Date: Mon, 23 Feb 2026 18:08:12 -0500
Subject: [PATCH 03/20] service app development

---
 fileglancer/apps.py          | 24 +++++++++++++++---------
 frontend/src/shared.types.ts |  2 ++
 2 files changed, 17 insertions(+), 9 deletions(-)

diff --git a/fileglancer/apps.py b/fileglancer/apps.py
index 63c2818c..bbca2839 100644
--- a/fileglancer/apps.py
+++ b/fileglancer/apps.py
@@ -648,16 +648,13 @@ async def submit_job(
         tool_repo_dir = await _ensure_repo_cache(manifest.repo_url, pull=pull_latest)
         repo_link = work_dir / "repo"
         repo_link.symlink_to(tool_repo_dir)
-        cd_target = repo_link
+        cd_suffix = "repo"
     else:
         # Tool code is in the discovery repo — cd into manifest's subdirectory
         repo_dir = await _ensure_repo_cache(app_url, pull=pull_latest)
         repo_link = work_dir / "repo"
         repo_link.symlink_to(repo_dir)
-        if manifest_path:
-            cd_target = repo_link / manifest_path
-        else:
-            cd_target = repo_link
+        cd_suffix = f"repo/{manifest_path}" if manifest_path else "repo"
 
     # Build environment variable export lines
     env_lines = ""
@@ -669,10 +666,19 @@ async def submit_job(
             parts.append(f"export {var_name}={shlex.quote(var_value)}")
         env_lines = "\n".join(parts) + "\n"
 
-    # Wrap command with cd into the repo symlink
-    # Unset PIXI_PROJECT_MANIFEST so pixi uses the repo's own manifest
-    # instead of inheriting fileglancer's from the dev server environment
-    script_parts = [f"unset PIXI_PROJECT_MANIFEST\ncd {cd_target}"]
+    # Set up the script preamble:
+    # - FG_WORK_DIR: the job's working directory (used by subsequent variables)
+    # - Unset PIXI_PROJECT_MANIFEST so pixi uses the repo's own manifest
+    # - SERVICE_URL_PATH: for service-type jobs, where to write the service URL
+    # - cd into the repo so commands can find project files (pixi.toml, scripts, etc.)
+    preamble_lines = [
+        "unset PIXI_PROJECT_MANIFEST",
+        f"export FG_WORK_DIR={shlex.quote(str(work_dir))}",
+    ]
+    if entry_point.type == "service":
+        preamble_lines.append('export SERVICE_URL_PATH="$FG_WORK_DIR/service_url"')
+    preamble_lines.append(f'cd "$FG_WORK_DIR/{cd_suffix}"')
+    script_parts = ["\n".join(preamble_lines)]
     if env_lines:
         script_parts.append(env_lines.rstrip())
     if effective_pre_run:
diff --git a/frontend/src/shared.types.ts b/frontend/src/shared.types.ts
index f0cb6f1c..6b6c5c0e 100644
--- a/frontend/src/shared.types.ts
+++ b/frontend/src/shared.types.ts
@@ -139,6 +139,8 @@ type UserApp = {
 type JobFileInfo = {
   path: string;
   exists: boolean;
+  fsp_name?: string;
+  subpath?: string;
 };
 
 type Job = {

From 6e9651c0b2f991a1cf966d5343f4930360b8b153 Mon Sep 17 00:00:00 2001
From: Konrad Rokicki <rokickik@janelia.hhmi.org>
Date: Mon, 23 Feb 2026 18:18:26 -0500
Subject: [PATCH 04/20] remove open link

---
 .../src/components/ui/Table/appsJobsColumns.tsx  | 16 +---------------
 1 file changed, 1 insertion(+), 15 deletions(-)

diff --git a/frontend/src/components/ui/Table/appsJobsColumns.tsx b/frontend/src/components/ui/Table/appsJobsColumns.tsx
index 2ccce696..c5c30042 100644
--- a/frontend/src/components/ui/Table/appsJobsColumns.tsx
+++ b/frontend/src/components/ui/Table/appsJobsColumns.tsx
@@ -97,25 +97,11 @@ export function createAppsJobsColumns(
     {
       accessorKey: 'status',
       header: 'Status',
-      cell: ({ getValue, row }) => {
+      cell: ({ getValue }) => {
         const status = getValue() as Job['status'];
-        const job = row.original;
-        const hasServiceUrl =
-          job.entry_point_type === 'service' && job.service_url;
         return (
           <div className="flex items-center gap-2 h-full">
             <JobStatusBadge status={status} />
-            {hasServiceUrl ? (
-              <a
-                className="text-xs text-primary hover:underline"
-                href={job.service_url}
-                onClick={e => e.stopPropagation()}
-                rel="noopener noreferrer"
-                target="_blank"
-              >
-                Open
-              </a>
-            ) : null}
           </div>
         );
       },

From cdeba46d9d45e9471a3e0ff86636b67ba0f1243b Mon Sep 17 00:00:00 2001
From: Konrad Rokicki <rokickik@janelia.hhmi.org>
Date: Mon, 23 Feb 2026 18:25:26 -0500
Subject: [PATCH 05/20] improve UI

---
 frontend/src/components/AppLaunch.tsx | 10 -----
 frontend/src/components/JobDetail.tsx | 59 +++++++++++++++++++++++----
 2 files changed, 50 insertions(+), 19 deletions(-)

diff --git a/frontend/src/components/AppLaunch.tsx b/frontend/src/components/AppLaunch.tsx
index a3cae782..735e219d 100644
--- a/frontend/src/components/AppLaunch.tsx
+++ b/frontend/src/components/AppLaunch.tsx
@@ -202,16 +202,6 @@ export default function AppLaunch() {
         </div>
       ) : manifest && selectedEntryPoint ? (
         <>
-          {manifest.runnables.length > 1 ? (
-            <Button
-              className="!rounded-md mb-4"
-              onClick={() => setSelectedEntryPoint(null)}
-              variant="outline"
-            >
-              <HiOutlineArrowLeft className="icon-small mr-2" />
-              Choose a different entry point
-            </Button>
-          ) : null}
           <AppLaunchForm
             entryPoint={selectedEntryPoint}
             initialEnv={relaunchEnv}
diff --git a/frontend/src/components/JobDetail.tsx b/frontend/src/components/JobDetail.tsx
index e08b6014..d8b01679 100644
--- a/frontend/src/components/JobDetail.tsx
+++ b/frontend/src/components/JobDetail.tsx
@@ -15,6 +15,7 @@ import {
   coy
 } from 'react-syntax-highlighter/dist/esm/styles/prism';
 
+import FgDialog from '@/components/ui/Dialogs/FgDialog';
 import type { JobFileInfo, FileSharePath } from '@/shared.types';
 import JobStatusBadge from '@/components/ui/AppsPage/JobStatusBadge';
 import { formatDateString, buildRelaunchPath, parseGithubUrl } from '@/utils';
@@ -137,6 +138,7 @@ export default function JobDetail() {
   const navigate = useNavigate();
   const [isDarkMode, setIsDarkMode] = useState(false);
   const [activeTab, setActiveTab] = useState('parameters');
+  const [showStopConfirm, setShowStopConfirm] = useState(false);
 
   const { pathPreference } = usePreferencesContext();
   const { zonesAndFspQuery } = useZoneAndFspMapContext();
@@ -149,8 +151,6 @@ export default function JobDetail() {
   const cancelMutation = useCancelJobMutation();
 
   const isService = jobQuery.data?.entry_point_type === 'service';
-  const isActive =
-    jobQuery.data?.status === 'PENDING' || jobQuery.data?.status === 'RUNNING';
 
   useEffect(() => {
     const checkDarkMode = () => {
@@ -290,6 +290,17 @@ export default function JobDetail() {
                     {job.service_url}
                   </a>
                 </Typography>
+                <Button
+                  className="!rounded-md"
+                  color="error"
+                  disabled={cancelMutation.isPending}
+                  onClick={() => setShowStopConfirm(true)}
+                  size="sm"
+                  variant="outline"
+                >
+                  <HiOutlineStop className="icon-small mr-1" />
+                  {cancelMutation.isPending ? 'Stopping...' : 'Stop Service'}
+                </Button>
                 <a
                   className="inline-flex items-center gap-1 px-3 py-1.5 text-sm font-medium rounded-md bg-success text-white hover:bg-success/90 transition-colors"
                   href={job.service_url}
@@ -309,25 +320,55 @@ export default function JobDetail() {
                 <Typography className="text-foreground flex-1" type="small">
                   Service is starting up...
                 </Typography>
+                <Button
+                  className="!rounded-md"
+                  color="error"
+                  disabled={cancelMutation.isPending}
+                  onClick={() => setShowStopConfirm(true)}
+                  size="sm"
+                  variant="outline"
+                >
+                  <HiOutlineStop className="icon-small mr-1" />
+                  {cancelMutation.isPending ? 'Stopping...' : 'Stop Service'}
+                </Button>
               </div>
             )
           ) : null}
 
-          {/* Stop Service button for active services */}
-          {isService && isActive ? (
-            <div className="mb-4">
+          {/* Stop Service confirmation dialog */}
+          <FgDialog
+            onClose={() => setShowStopConfirm(false)}
+            open={showStopConfirm}
+          >
+            <Typography className="text-foreground font-bold mb-2" type="h6">
+              Stop Service
+            </Typography>
+            <Typography className="text-secondary mb-4" type="small">
+              Are you sure you want to stop this service? It will be terminated
+              and the URL will no longer be accessible.
+            </Typography>
+            <div className="flex justify-end gap-2">
+              <Button
+                className="!rounded-md"
+                onClick={() => setShowStopConfirm(false)}
+                variant="outline"
+              >
+                Cancel
+              </Button>
               <Button
                 className="!rounded-md"
                 color="error"
                 disabled={cancelMutation.isPending}
-                onClick={() => cancelMutation.mutate(job.id)}
-                variant="outline"
+                onClick={() => {
+                  cancelMutation.mutate(job.id);
+                  setShowStopConfirm(false);
+                }}
               >
-                <HiOutlineStop className="icon-small mr-2" />
+                <HiOutlineStop className="icon-small mr-1" />
                 {cancelMutation.isPending ? 'Stopping...' : 'Stop Service'}
               </Button>
             </div>
-          ) : null}
+          </FgDialog>
 
           {/* Tabs */}
           <Tabs onValueChange={setActiveTab} value={activeTab}>

From e7d6fbd7cea49396a02f8cc8c910ca6847dc7d00 Mon Sep 17 00:00:00 2001
From: Konrad Rokicki <rokickik@janelia.hhmi.org>
Date: Mon, 23 Feb 2026 20:32:07 -0500
Subject: [PATCH 06/20] added docs

---
 docs/AuthoringApps.md | 106 +++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 105 insertions(+), 1 deletion(-)

diff --git a/docs/AuthoringApps.md b/docs/AuthoringApps.md
index 082d8316..11ea5a4a 100644
--- a/docs/AuthoringApps.md
+++ b/docs/AuthoringApps.md
@@ -80,6 +80,7 @@ Each runnable defines a single command that users can launch. If the manifest ha
 |-------|------|----------|-------------|
 | `id` | string | yes | Unique identifier (used in CLI flags and URLs, should be URL-safe) |
 | `name` | string | yes | Display name shown in the UI |
+| `type` | string | no | `"job"` (default) for batch jobs or `"service"` for long-running services (see [Services](#services)) |
 | `description` | string | no | Longer description of what this runnable does |
 | `command` | string | yes | Base shell command to execute (see [Command Building](#command-building)) |
 | `parameters` | list of objects | no | Parameter definitions (see [Parameters](#parameters)) |
@@ -219,8 +220,9 @@ Users can override these in the UI. If a user provides their own pre/post-run sc
 The generated job script has the following structure:
 
 ```bash
+export FG_WORK_DIR='/home/user/.fileglancer/jobs/42-MyApp-convert'
 unset PIXI_PROJECT_MANIFEST
-cd /path/to/repo
+cd "$FG_WORK_DIR/repo"
 
 # Environment variables
 export JAVA_HOME='/opt/java'
@@ -238,6 +240,8 @@ nextflow run main.nf \
 echo "Conversion complete"
 ```
 
+`FG_WORK_DIR` is always exported and points to the job's working directory. See [Environment Variables Set by Fileglancer](#environment-variables-set-by-fileglancer) for the full list.
+
 ## Command Building
 
 When a job is submitted, Fileglancer constructs the full shell command from the runnable's `command` field and the user-provided parameter values using a two-pass approach:
@@ -314,6 +318,106 @@ When a user submits a job:
 
 Users can view logs, relaunch with the same parameters, or cancel running jobs from the Fileglancer UI.
 
+## Services
+
+A **service** is a long-running process (web server, notebook, API, viewer) that runs until the user explicitly stops it. Services are declared with `type: service` on the runnable:
+
+```yaml
+runnables:
+  - id: notebook
+    name: JupyterLab
+    type: service
+    command: jupyter lab --no-browser --ip=0.0.0.0 --port=0
+    resources:
+      cpus: 4
+      memory: "32 GB"
+      walltime: "08:00"
+```
+
+### How It Works
+
+From the cluster's perspective, a service is just a long-running batch job. The difference is in how Fileglancer communicates the service URL to the user:
+
+1. User launches a service-type runnable → job enters PENDING state
+2. Cluster picks it up → RUNNING
+3. The service starts, binds a port, and writes its URL to the file at `SERVICE_URL_PATH`
+4. On the next poll (every few seconds), Fileglancer reads the file and displays the URL in the UI
+5. User clicks "Open Service" → service opens in a new browser tab
+6. When done, user clicks "Stop Service" → job is killed and the URL disappears
+
+### Writing the Service URL
+
+For service-type runnables, Fileglancer exports `SERVICE_URL_PATH` — the absolute path to a file where your service should write its URL. Your service must write its URL (e.g. `http://hostname:port`) to this file once it is ready to accept connections.
+
+Example in Python:
+
+```python
+import os, socket
+
+url = f"http://{socket.gethostname()}:{port}"
+service_url_path = os.environ.get("SERVICE_URL_PATH")
+if service_url_path:
+    with open(service_url_path, "w") as f:
+        f.write(url)
+```
+
+Example in Bash:
+
+```bash
+echo "http://$(hostname):${PORT}" > "$SERVICE_URL_PATH"
+```
+
+The URL must start with `http://` or `https://`. Fileglancer validates this before displaying it. If the file doesn't exist or contains an invalid URL, no link is shown.
+
+### Service Lifecycle
+
+- **Startup**: The service should write its URL to `SERVICE_URL_PATH` as soon as it is ready. Until the file exists, the UI shows "Service is starting up..."
+- **Running**: Fileglancer reads the URL file on each poll. If the URL changes (e.g. port rebind), the UI updates automatically.
+- **Shutdown**: When the user clicks "Stop Service", Fileglancer sends a SIGTERM to the job. Services should handle this signal for graceful shutdown. Cleaning up the URL file on exit is good practice but not required — Fileglancer only reads it while the job status is RUNNING.
+
+### Tips
+
+- **Port selection**: Use port 0 or auto-detection to avoid conflicts when multiple services run on the same node
+- **Walltime**: Set a generous walltime — services run until stopped, but the cluster will kill them if walltime expires. Consider `"08:00"` or longer for interactive sessions
+- **Flush output**: If running under a batch scheduler like LSF, Python's stdout may be buffered. Use `flush=True` on print statements or set `PYTHONUNBUFFERED=1` so logs appear in real time
+
+### Service Example
+
+```yaml
+name: My Viewer
+description: Interactive data viewer
+version: "1.0"
+
+runnables:
+  - id: view
+    name: Start Viewer
+    type: service
+    description: Launch an interactive viewer for browsing datasets
+    command: pixi run python start_viewer.py
+    parameters:
+      - flag: --data-dir
+        name: Data Directory
+        type: directory
+        description: Directory containing datasets to view
+        required: true
+
+    resources:
+      cpus: 2
+      memory: "8 GB"
+      walltime: "08:00"
+```
+
+## Environment Variables Set by Fileglancer
+
+Fileglancer exports the following environment variables in every job script:
+
+| Variable | Availability | Description |
+|----------|-------------|-------------|
+| `FG_WORK_DIR` | All jobs | Absolute path to the job's working directory (contains `repo/` symlink, log files, etc.) |
+| `SERVICE_URL_PATH` | Service-type jobs only | Absolute path where the service should write its URL. Equivalent to `$FG_WORK_DIR/service_url` |
+
+These are available to `pre_run` scripts, the main command, and `post_run` scripts.
+
 ## Full Example
 
 ```yaml

From df3dc20af1ea96b907c604494b25ddc5dcd50216 Mon Sep 17 00:00:00 2001
From: Konrad Rokicki <rokickik@janelia.hhmi.org>
Date: Mon, 23 Feb 2026 20:38:33 -0500
Subject: [PATCH 07/20] ensure git is run without prompts

---
 fileglancer/apps.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/fileglancer/apps.py b/fileglancer/apps.py
index bbca2839..61721aa0 100644
--- a/fileglancer/apps.py
+++ b/fileglancer/apps.py
@@ -67,12 +67,14 @@ async def _run_git(args: list[str], timeout: int = 60):
 
     Raises ValueError with a readable message on failure.
     """
+    env = {**os.environ, "GIT_TERMINAL_PROMPT": "0"}
     try:
         proc = await asyncio.wait_for(
             asyncio.create_subprocess_exec(
                 *args,
                 stdout=asyncio.subprocess.PIPE,
                 stderr=asyncio.subprocess.PIPE,
+                env=env,
             ),
             timeout=timeout,
         )

From 869fbd92b212149b5f7b857ba6015a0319ab926d Mon Sep 17 00:00:00 2001
From: Konrad Rokicki <rokickik@janelia.hhmi.org>
Date: Mon, 23 Feb 2026 20:47:04 -0500
Subject: [PATCH 08/20] fix timezone bug

---
 .../src/components/ui/Table/appsJobsColumns.tsx   | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/frontend/src/components/ui/Table/appsJobsColumns.tsx b/frontend/src/components/ui/Table/appsJobsColumns.tsx
index c5c30042..752c440d 100644
--- a/frontend/src/components/ui/Table/appsJobsColumns.tsx
+++ b/frontend/src/components/ui/Table/appsJobsColumns.tsx
@@ -7,12 +7,19 @@ import { formatDateString } from '@/utils';
 import type { MenuItem } from '@/components/ui/Menus/FgMenuItems';
 import type { Job } from '@/shared.types';
 
+function parseAsUtc(dateStr: string): number {
+  // Server timestamps are UTC but may lack a "Z" suffix
+  if (!/Z$|[+-]\d{2}:\d{2}$/.test(dateStr)) {
+    return new Date(dateStr + 'Z').getTime();
+  }
+  return new Date(dateStr).getTime();
+}
+
 function formatDuration(job: Job): string {
   const start = job.started_at || job.created_at;
-  const end = job.finished_at || new Date().toISOString();
-  const startDate = new Date(start);
-  const endDate = new Date(end);
-  const diffMs = endDate.getTime() - startDate.getTime();
+  const startMs = parseAsUtc(start);
+  const endMs = job.finished_at ? parseAsUtc(job.finished_at) : Date.now();
+  const diffMs = endMs - startMs;
 
   if (diffMs < 0) {
     return '-';

From 957c64f8a638de36d93ec278d7c83cb9334650a6 Mon Sep 17 00:00:00 2001
From: Konrad Rokicki <rokickik@janelia.hhmi.org>
Date: Mon, 23 Feb 2026 21:50:13 -0500
Subject: [PATCH 09/20] fix timestamp bugs

---
 fileglancer/apps.py                           |  8 +++--
 fileglancer/server.py                         | 19 +++++++++--
 .../components/ui/Table/appsJobsColumns.tsx   | 18 ++++------
 pixi.lock                                     | 34 +++++++++----------
 pyproject.toml                                |  2 +-
 5 files changed, 47 insertions(+), 34 deletions(-)

diff --git a/fileglancer/apps.py b/fileglancer/apps.py
index 61721aa0..76a9e72a 100644
--- a/fileglancer/apps.py
+++ b/fileglancer/apps.py
@@ -502,11 +502,15 @@ async def _reconcile_jobs(settings):
             # Terminal transitions are handled by the on_exit callback.
             new_status = _map_status(tracked.status)
             if new_status != db_job.status:
+                # Only store finished_at for terminal states. LSF may report
+                # a FINISH_TIME for running jobs (projected walltime end),
+                # which we must not store as an actual finish time.
+                is_terminal = new_status in ("DONE", "FAILED", "KILLED")
                 db.update_job_status(
                     session, db_job.id, new_status,
-                    exit_code=tracked.exit_code,
+                    exit_code=tracked.exit_code if is_terminal else None,
                     started_at=tracked.start_time,
-                    finished_at=tracked.finish_time,
+                    finished_at=tracked.finish_time if is_terminal else None,
                 )
                 logger.info(f"Job {db_job.id} status updated: {db_job.status} -> {new_status}")
 
diff --git a/fileglancer/server.py b/fileglancer/server.py
index b82d95a2..7b26d39c 100644
--- a/fileglancer/server.py
+++ b/fileglancer/server.py
@@ -1716,6 +1716,19 @@ async def get_job_file(job_id: int,
         except ValueError as e:
             raise HTTPException(status_code=404, detail=str(e))
 
+    def _ensure_utc(dt: Optional[datetime]) -> Optional[datetime]:
+        """Re-attach UTC timezone to naive datetimes from the DB.
+
+        SQLAlchemy's DateTime column strips tzinfo, so datetimes come back
+        naive even though they were stored as UTC. Re-attaching ensures
+        Pydantic serializes with '+00:00' so JS parses them correctly.
+        """
+        if dt is None:
+            return None
+        if dt.tzinfo is None:
+            return dt.replace(tzinfo=UTC)
+        return dt
+
     def _convert_job(db_job: db.JobDB, include_files: bool = False) -> Job:
         """Convert a database JobDB to a Pydantic Job model."""
         files = None
@@ -1739,9 +1752,9 @@ def _convert_job(db_job: db.JobDB, include_files: bool = False) -> Job:
             pull_latest=db_job.pull_latest,
             cluster_job_id=db_job.cluster_job_id,
             service_url=apps_module.get_service_url(db_job),
-            created_at=db_job.created_at,
-            started_at=db_job.started_at,
-            finished_at=db_job.finished_at,
+            created_at=_ensure_utc(db_job.created_at),
+            started_at=_ensure_utc(db_job.started_at),
+            finished_at=_ensure_utc(db_job.finished_at),
             files=files,
         )
 
diff --git a/frontend/src/components/ui/Table/appsJobsColumns.tsx b/frontend/src/components/ui/Table/appsJobsColumns.tsx
index 752c440d..6fa523dc 100644
--- a/frontend/src/components/ui/Table/appsJobsColumns.tsx
+++ b/frontend/src/components/ui/Table/appsJobsColumns.tsx
@@ -7,18 +7,14 @@ import { formatDateString } from '@/utils';
 import type { MenuItem } from '@/components/ui/Menus/FgMenuItems';
 import type { Job } from '@/shared.types';
 
-function parseAsUtc(dateStr: string): number {
-  // Server timestamps are UTC but may lack a "Z" suffix
-  if (!/Z$|[+-]\d{2}:\d{2}$/.test(dateStr)) {
-    return new Date(dateStr + 'Z').getTime();
-  }
-  return new Date(dateStr).getTime();
-}
-
 function formatDuration(job: Job): string {
-  const start = job.started_at || job.created_at;
-  const startMs = parseAsUtc(start);
-  const endMs = job.finished_at ? parseAsUtc(job.finished_at) : Date.now();
+  if (!job.started_at) {
+    return '-';
+  }
+  const startMs = new Date(job.started_at).getTime();
+  const endMs = job.finished_at
+    ? new Date(job.finished_at).getTime()
+    : new Date().getTime();
   const diffMs = endMs - startMs;
 
   if (diffMs < 0) {
diff --git a/pixi.lock b/pixi.lock
index bdec2561..54e6333a 100644
--- a/pixi.lock
+++ b/pixi.lock
@@ -170,7 +170,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/a7/b2/fabede9fafd976b991e9f1b9c8c873ed86f202889b864756f240ce6dd855/frozenlist-1.8.0-cp314-cp314-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl
       - pypi: https://files.pythonhosted.org/packages/fe/3b/8ec5074bcfc450fe84273713b4b0a0dd47c0249358f5d82eb8104ffe2520/multidict-6.7.1-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
       - pypi: https://files.pythonhosted.org/packages/b2/f2/889ad4b2408f72fe1a4f6a19491177b30ea7bf1a0fd5f17050ca08cfc882/propcache-0.4.1-cp314-cp314-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl
-      - pypi: https://files.pythonhosted.org/packages/e1/b5/226661a1ca70b1b06500f4c4cc004a90d6bc421fb8bb2446d012511f2578/py_cluster_api-0.2.3-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/58/07/0bf2e004d397f3beca035a53d193e5ed08f37372cac92f5017f9afac0439/py_cluster_api-0.2.4-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/48/a2/87a0b61a3078be07ab04ec574ef6c683c764590ed0d2a50d00cbb23aeae7/pydantic_settings_yaml-0.2.0-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/fc/51/727abb13f44c1fcf6d145979e1535a35794db0f6e450a0cb46aa24732fe2/s3transfer-0.16.0-py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/bc/4b/5079831d1b4f37caa13a994f50a9f9d943eef44ea04aa2a2f53d49abbd32/x2s3-1.1.1-py3-none-any.whl
@@ -337,7 +337,7 @@ environments:
       - pypi: https://files.pythonhosted.org/packages/3a/3b/d9b1e0b0eed36e70477ffb8360c49c85c8ca8ef9700a4e6711f39a6e8b45/frozenlist-1.8.0-cp314-cp314-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl
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   - psycopg2-binary>=2.9.10,<3
-  - py-cluster-api>=0.2.3
+  - py-cluster-api>=0.2.4
   - pydantic-settings>=2.11.0
   - pydantic>=2.10.6
   - python-jose>=3.5.0,<4
@@ -7452,10 +7452,10 @@ packages:
   - pkg:pypi/pure-eval?source=hash-mapping
   size: 16668
   timestamp: 1733569518868
-- pypi: https://files.pythonhosted.org/packages/e1/b5/226661a1ca70b1b06500f4c4cc004a90d6bc421fb8bb2446d012511f2578/py_cluster_api-0.2.3-py3-none-any.whl
+- pypi: https://files.pythonhosted.org/packages/58/07/0bf2e004d397f3beca035a53d193e5ed08f37372cac92f5017f9afac0439/py_cluster_api-0.2.4-py3-none-any.whl
   name: py-cluster-api
-  version: 0.2.3
-  sha256: 44c129325e8b440ff3c2735e044dd88af0191839ece3c587a23d0d53bce9021f
+  version: 0.2.4
+  sha256: 6f0554394e2b36429641a40ddb8391636a87033c67f12ad5af515a5ede1ba0df
   requires_dist:
   - pyyaml
   - build ; extra == 'release'
diff --git a/pyproject.toml b/pyproject.toml
index ec1c9683..16e92507 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -44,7 +44,7 @@ dependencies = [
     "sqlalchemy >=2.0.44",
     "uvicorn >=0.38.0",
     "x2s3 >=1.1.1",
-    "py-cluster-api >=0.2.3"
+    "py-cluster-api >=0.2.4"
 ]
 
 [project.scripts]

From 7c841a86064eefcc022c9f2af9dbe5972b37a662 Mon Sep 17 00:00:00 2001
From: Konrad Rokicki <rokickik@janelia.hhmi.org>
Date: Tue, 24 Feb 2026 07:56:42 -0500
Subject: [PATCH 10/20] default to local executor

---
 docs/config.yaml.template | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/config.yaml.template b/docs/config.yaml.template
index 5f44863f..9b9fe167 100644
--- a/docs/config.yaml.template
+++ b/docs/config.yaml.template
@@ -129,8 +129,8 @@ session_cookie_secure: true
 # Mirrors py-cluster-api ClusterConfig - all fields are optional
 # See: https://github.com/JaneliaSciComp/py-cluster-api
 #
-# cluster:
-#   executor: local            # "local" or "lsf"
+cluster:
+  executor: local            # "local" or "lsf"
 #   job_name_prefix: fg        # Prefix for cluster job names. REQUIRED for job
 #                              # reconnection after server restarts. Without this,
 #                              # active jobs will not be re-tracked and will

From 247402ad254124b3dfb4bafb18df109560478a94 Mon Sep 17 00:00:00 2001
From: Konrad Rokicki <rokickik@janelia.hhmi.org>
Date: Tue, 24 Feb 2026 11:46:47 -0500
Subject: [PATCH 11/20] added more cluster options, override for extra args

---
 fileglancer/apps.py                           |  18 +-
 fileglancer/model.py                          |   2 +
 fileglancer/server.py                         |   8 +
 frontend/src/components/AppLaunch.tsx         |  33 ++--
 frontend/src/components/Preferences.tsx       |   2 +
 .../components/ui/AppsPage/AppLaunchForm.tsx  | 155 ++++++++++++++++--
 .../ui/PreferencesPage/JobOptions.tsx         |  61 +++++++
 frontend/src/contexts/PreferencesContext.tsx  |  18 ++
 frontend/src/queries/jobsQueries.ts           |  37 +++++
 frontend/src/queries/preferencesQueries.ts    |   5 +-
 frontend/src/shared.types.ts                  |   2 +
 11 files changed, 312 insertions(+), 29 deletions(-)
 create mode 100644 frontend/src/components/ui/PreferencesPage/JobOptions.tsx

diff --git a/fileglancer/apps.py b/fileglancer/apps.py
index 76a9e72a..cb9d5557 100644
--- a/fileglancer/apps.py
+++ b/fileglancer/apps.py
@@ -573,6 +573,7 @@ async def submit_job(
     entry_point_id: str,
     parameters: dict,
     resources: Optional[dict] = None,
+    extra_args: Optional[str] = None,
     pull_latest: bool = False,
     manifest_path: str = "",
     env: Optional[dict] = None,
@@ -605,8 +606,11 @@ async def submit_job(
     # Build command
     command = build_command(entry_point, parameters)
 
-    # Build resource spec
-    resource_spec = _build_resource_spec(entry_point, resources, settings)
+    # Build resource spec (extra_args passed separately, not from manifest)
+    overrides = dict(resources) if resources else {}
+    if extra_args is not None:
+        overrides["extra_args"] = extra_args
+    resource_spec = _build_resource_spec(entry_point, overrides or None, settings)
 
     # Merge env/pre_run/post_run: manifest defaults overridden by user values
     merged_env = dict(entry_point.env or {})
@@ -623,6 +627,7 @@ async def submit_job(
             "memory": resource_spec.memory,
             "walltime": resource_spec.walltime,
             "queue": resource_spec.queue,
+            "extra_args": " ".join(resource_spec.extra_args) if resource_spec.extra_args else None,
         }
 
     with db.get_db_session(settings.db_url) as session:
@@ -739,8 +744,12 @@ def _build_resource_spec(entry_point: AppEntryPoint, overrides: Optional[dict],
             memory = entry_point.resources.memory
         if entry_point.resources.walltime is not None:
             walltime = entry_point.resources.walltime
+        if entry_point.resources.queue is not None:
+            queue = entry_point.resources.queue
 
     # Apply user overrides
+    # Note: extra_args replaces (not extends) config defaults via ResourceSpec
+    extra_args = None
     if overrides:
         if overrides.get("cpus") is not None:
             cpus = overrides["cpus"]
@@ -748,12 +757,17 @@ def _build_resource_spec(entry_point: AppEntryPoint, overrides: Optional[dict],
             memory = overrides["memory"]
         if overrides.get("walltime") is not None:
             walltime = overrides["walltime"]
+        if overrides.get("queue") is not None:
+            queue = overrides["queue"]
+        if overrides.get("extra_args") is not None:
+            extra_args = [overrides["extra_args"]]
 
     return ResourceSpec(
         cpus=cpus,
         memory=memory,
         walltime=walltime,
         queue=queue,
+        extra_args=extra_args,
     )
 
 
diff --git a/fileglancer/model.py b/fileglancer/model.py
index 45fde4b5..4609c04d 100644
--- a/fileglancer/model.py
+++ b/fileglancer/model.py
@@ -376,6 +376,7 @@ class AppResourceDefaults(BaseModel):
     cpus: Optional[int] = Field(description="Number of CPUs", default=None)
     memory: Optional[str] = Field(description="Memory allocation (e.g. '16 GB')", default=None)
     walltime: Optional[str] = Field(description="Wall time limit (e.g. '04:00')", default=None)
+    queue: Optional[str] = Field(description="Cluster queue/partition name", default=None)
 
 
 class AppEntryPoint(BaseModel):
@@ -514,6 +515,7 @@ class JobSubmitRequest(BaseModel):
     entry_point_id: str = Field(description="Entry point to execute")
     parameters: Dict = Field(description="Parameter values keyed by parameter key")
     resources: Optional[AppResourceDefaults] = Field(description="Resource overrides", default=None)
+    extra_args: Optional[str] = Field(description="Extra CLI args for the submit command (replaces config defaults)", default=None)
     pull_latest: bool = Field(
         description="Pull latest code from GitHub before running",
         default=False,
diff --git a/fileglancer/server.py b/fileglancer/server.py
index 7b26d39c..4711e326 100644
--- a/fileglancer/server.py
+++ b/fileglancer/server.py
@@ -1634,6 +1634,13 @@ async def validate_paths(body: PathValidationRequest,
                 errors[param_key] = f"Path is not accessible: {normalized}"
         return PathValidationResponse(errors=errors)
 
+    @app.get("/api/cluster-defaults",
+             description="Get cluster configuration defaults")
+    async def get_cluster_defaults():
+        return {
+            "extra_args": " ".join(settings.cluster.extra_args),
+        }
+
     @app.post("/api/jobs", response_model=Job,
               description="Submit a new job")
     async def submit_job(body: JobSubmitRequest,
@@ -1649,6 +1656,7 @@ async def submit_job(body: JobSubmitRequest,
                 entry_point_id=body.entry_point_id,
                 parameters=body.parameters,
                 resources=resources_dict,
+                extra_args=body.extra_args,
                 pull_latest=body.pull_latest,
                 manifest_path=body.manifest_path,
                 env=body.env,
diff --git a/frontend/src/components/AppLaunch.tsx b/frontend/src/components/AppLaunch.tsx
index 735e219d..222e8d37 100644
--- a/frontend/src/components/AppLaunch.tsx
+++ b/frontend/src/components/AppLaunch.tsx
@@ -58,6 +58,10 @@ export default function AppLaunch() {
   const relaunchResources = relaunchState?.resources as
     | AppResourceDefaults
     | undefined;
+  // extra_args stored in resources dict from previous job
+  const relaunchExtraArgs = relaunchState?.resources?.extra_args as
+    | string
+    | undefined;
   const relaunchEnv = relaunchState?.env;
   const relaunchPreRun = relaunchState?.pre_run;
   const relaunchPostRun = relaunchState?.post_run;
@@ -99,6 +103,7 @@ export default function AppLaunch() {
   const handleSubmit = async (
     parameters: Record<string, unknown>,
     resources?: AppResourceDefaults,
+    extraArgs?: string,
     pullLatest?: boolean,
     env?: Record<string, string>,
     preRun?: string,
@@ -114,6 +119,7 @@ export default function AppLaunch() {
         entry_point_id: selectedEntryPoint.id,
         parameters,
         resources,
+        extra_args: extraArgs,
         pull_latest: pullLatest,
         env,
         pre_run: preRun,
@@ -201,20 +207,19 @@ export default function AppLaunch() {
           {manifestMutation.error?.message || 'Unknown error'}
         </div>
       ) : manifest && selectedEntryPoint ? (
-        <>
-          <AppLaunchForm
-            entryPoint={selectedEntryPoint}
-            initialEnv={relaunchEnv}
-            initialPostRun={relaunchPostRun}
-            initialPreRun={relaunchPreRun}
-            initialPullLatest={relaunchPullLatest}
-            initialResources={relaunchResources}
-            initialValues={relaunchParameters}
-            manifest={manifest}
-            onSubmit={handleSubmit}
-            submitting={submitJobMutation.isPending}
-          />
-        </>
+        <AppLaunchForm
+          entryPoint={selectedEntryPoint}
+          initialEnv={relaunchEnv}
+          initialExtraArgs={relaunchExtraArgs}
+          initialPostRun={relaunchPostRun}
+          initialPreRun={relaunchPreRun}
+          initialPullLatest={relaunchPullLatest}
+          initialResources={relaunchResources}
+          initialValues={relaunchParameters}
+          manifest={manifest}
+          onSubmit={handleSubmit}
+          submitting={submitJobMutation.isPending}
+        />
       ) : manifest ? (
         <div className="max-w-2xl">
           <Typography className="text-foreground font-bold mb-1" type="h5">
diff --git a/frontend/src/components/Preferences.tsx b/frontend/src/components/Preferences.tsx
index c4d553f2..7961f59c 100644
--- a/frontend/src/components/Preferences.tsx
+++ b/frontend/src/components/Preferences.tsx
@@ -5,6 +5,7 @@ import toast from 'react-hot-toast';
 import { usePreferencesContext } from '@/contexts/PreferencesContext';
 import DataLinkOptions from '@/components/ui/PreferencesPage/DataLinkOptions';
 import DisplayOptions from '@/components/ui/PreferencesPage/DisplayOptions';
+import JobOptions from '@/components/ui/PreferencesPage/JobOptions';
 import NeuroglancerOptions from '@/components/ui/PreferencesPage/NeuroglancerOptions';
 
 export default function Preferences() {
@@ -122,6 +123,7 @@ export default function Preferences() {
           <DisplayOptions />
           <DataLinkOptions />
           <NeuroglancerOptions />
+          <JobOptions />
         </Card.Body>
       </Card>
     </>
diff --git a/frontend/src/components/ui/AppsPage/AppLaunchForm.tsx b/frontend/src/components/ui/AppsPage/AppLaunchForm.tsx
index 76fd95e3..d11a7f44 100644
--- a/frontend/src/components/ui/AppsPage/AppLaunchForm.tsx
+++ b/frontend/src/components/ui/AppsPage/AppLaunchForm.tsx
@@ -10,7 +10,9 @@ import {
 } from 'react-icons/hi';
 
 import FileSelectorButton from '@/components/ui/BrowsePage/FileSelector/FileSelectorButton';
+import { usePreferencesContext } from '@/contexts/PreferencesContext';
 import { validatePaths } from '@/queries/appsQueries';
+import { useClusterDefaultsQuery } from '@/queries/jobsQueries';
 import { convertBackToForwardSlash } from '@/utils/pathHandling';
 import { flattenParameters, isParameterSection } from '@/shared.types';
 import type {
@@ -27,6 +29,7 @@ interface AppLaunchFormProps {
   readonly onSubmit: (
     parameters: Record<string, unknown>,
     resources?: AppResourceDefaults,
+    extraArgs?: string,
     pullLatest?: boolean,
     env?: Record<string, string>,
     preRun?: string,
@@ -35,6 +38,7 @@ interface AppLaunchFormProps {
   readonly submitting: boolean;
   readonly initialValues?: Record<string, unknown>;
   readonly initialResources?: AppResourceDefaults;
+  readonly initialExtraArgs?: string;
   readonly initialEnv?: Record<string, string>;
   readonly initialPreRun?: string;
   readonly initialPostRun?: string;
@@ -411,6 +415,61 @@ function ResourcesSectionContent({
   );
 }
 
+function SubmitOptionsSectionContent({
+  resources,
+  setResources,
+  extraArgs,
+  setExtraArgs
+}: {
+  readonly resources: AppResourceDefaults;
+  readonly setResources: Dispatch<SetStateAction<AppResourceDefaults>>;
+  readonly extraArgs: string;
+  readonly setExtraArgs: Dispatch<SetStateAction<string>>;
+}) {
+  const inputClass =
+    'w-full p-2 text-foreground border rounded-sm focus:outline-none bg-background border-primary-light focus:border-primary';
+
+  return (
+    <div className="space-y-4">
+      <div>
+        <label className="block text-foreground text-sm font-medium mb-1">
+          Queue
+        </label>
+        <Typography className="text-secondary mb-1" type="small">
+          Cluster queue/partition to submit the job to
+        </Typography>
+        <input
+          className={inputClass}
+          onChange={e =>
+            setResources(prev => ({
+              ...prev,
+              queue: e.target.value || undefined
+            }))
+          }
+          placeholder="e.g. normal"
+          type="text"
+          value={resources.queue ?? ''}
+        />
+      </div>
+      <div>
+        <label className="block text-foreground text-sm font-medium mb-1">
+          Extra Arguments
+        </label>
+        <Typography className="text-secondary mb-1" type="small">
+          Additional CLI arguments for the submit command
+        </Typography>
+        <input
+          className={`max-w-md ${inputClass} font-mono text-sm`}
+          onChange={e => setExtraArgs(e.target.value)}
+          placeholder='e.g. -P your_project -R "select[mem>8000]"'
+          type="text"
+          value={extraArgs}
+        />
+      </div>
+    </div>
+  );
+}
+
 function EnvironmentTabContent({
   envVars,
   setEnvVars,
@@ -418,8 +477,6 @@ function EnvironmentTabContent({
   setPreRun,
   postRun,
   setPostRun,
-  resources,
-  setResources,
   openEnvSections,
   setOpenEnvSections
 }: {
@@ -429,8 +486,6 @@ function EnvironmentTabContent({
   readonly setPreRun: Dispatch<SetStateAction<string>>;
   readonly postRun: string;
   readonly setPostRun: Dispatch<SetStateAction<string>>;
-  readonly resources: AppResourceDefaults;
-  readonly setResources: Dispatch<SetStateAction<AppResourceDefaults>>;
   readonly openEnvSections: string[];
   readonly setOpenEnvSections: Dispatch<SetStateAction<string[]>>;
 }) {
@@ -444,7 +499,7 @@ function EnvironmentTabContent({
     >
       <Accordion.Item value="environment">
         <Accordion.Trigger className="flex w-full items-center justify-between py-3 border-b border-primary-light">
-          <div className="text-foreground font-medium text-sm">Environment</div>
+          <div className="text-foreground font-bold text-sm">Environment</div>
           <HiChevronDown
             className={`h-4 w-4 text-secondary transition-transform ${
               openEnvSections.includes('environment') ? 'rotate-180' : ''
@@ -462,13 +517,39 @@ function EnvironmentTabContent({
           />
         </Accordion.Content>
       </Accordion.Item>
+    </Accordion>
+  );
+}
 
+function ClusterTabContent({
+  resources,
+  setResources,
+  extraArgs,
+  setExtraArgs,
+  openClusterSections,
+  setOpenClusterSections
+}: {
+  readonly resources: AppResourceDefaults;
+  readonly setResources: Dispatch<SetStateAction<AppResourceDefaults>>;
+  readonly extraArgs: string;
+  readonly setExtraArgs: Dispatch<SetStateAction<string>>;
+  readonly openClusterSections: string[];
+  readonly setOpenClusterSections: Dispatch<SetStateAction<string[]>>;
+}) {
+  return (
+    <Accordion
+      onValueChange={
+        setOpenClusterSections as Dispatch<SetStateAction<string | string[]>>
+      }
+      type="multiple"
+      value={openClusterSections}
+    >
       <Accordion.Item value="resources">
         <Accordion.Trigger className="flex w-full items-center justify-between py-3 border-b border-primary-light">
-          <div className="text-foreground font-medium text-sm">Resources</div>
+          <div className="text-foreground font-bold text-sm">Resources</div>
           <HiChevronDown
             className={`h-4 w-4 text-secondary transition-transform ${
-              openEnvSections.includes('resources') ? 'rotate-180' : ''
+              openClusterSections.includes('resources') ? 'rotate-180' : ''
             }`}
           />
         </Accordion.Trigger>
@@ -479,6 +560,27 @@ function EnvironmentTabContent({
           />
         </Accordion.Content>
       </Accordion.Item>
+
+      <Accordion.Item value="submitOptions">
+        <Accordion.Trigger className="flex w-full items-center justify-between py-3 border-b border-primary-light">
+          <div className="text-foreground font-bold text-sm">
+            Submit Options
+          </div>
+          <HiChevronDown
+            className={`h-4 w-4 text-secondary transition-transform ${
+              openClusterSections.includes('submitOptions') ? 'rotate-180' : ''
+            }`}
+          />
+        </Accordion.Trigger>
+        <Accordion.Content className="pt-4 pb-2 pl-4">
+          <SubmitOptionsSectionContent
+            extraArgs={extraArgs}
+            resources={resources}
+            setExtraArgs={setExtraArgs}
+            setResources={setResources}
+          />
+        </Accordion.Content>
+      </Accordion.Item>
     </Accordion>
   );
 }
@@ -490,11 +592,14 @@ export default function AppLaunchForm({
   submitting,
   initialValues: externalValues,
   initialResources,
+  initialExtraArgs: externalExtraArgs,
   initialEnv,
   initialPreRun,
   initialPostRun,
   initialPullLatest
 }: AppLaunchFormProps) {
+  const { defaultExtraArgs } = usePreferencesContext();
+  const clusterDefaultsQuery = useClusterDefaultsQuery();
   const allParams = flattenParameters(entryPoint.parameters);
 
   // Initialize parameter values: external values override defaults
@@ -513,6 +618,11 @@ export default function AppLaunchForm({
     .filter(item => isParameterSection(item) && !item.collapsed)
     .map(item => (item as AppParameterSection).section);
 
+  // extra_args priority: relaunch > user preference > config.yaml
+  const configExtraArgs = clusterDefaultsQuery.data?.extra_args ?? '';
+  const resolvedExtraArgs =
+    externalExtraArgs ?? (defaultExtraArgs || configExtraArgs);
+
   const [values, setValues] = useState<Record<string, unknown>>(startingValues);
   const [errors, setErrors] = useState<Record<string, string>>({});
   const [activeTab, setActiveTab] = useState('parameters');
@@ -523,9 +633,11 @@ export default function AppLaunchForm({
     initialResources ?? {
       cpus: entryPoint.resources?.cpus,
       memory: entryPoint.resources?.memory,
-      walltime: entryPoint.resources?.walltime
+      walltime: entryPoint.resources?.walltime,
+      queue: entryPoint.resources?.queue
     }
   );
+  const [extraArgs, setExtraArgs] = useState<string>(resolvedExtraArgs);
 
   // Environment tab state — relaunch values override entry point defaults
   const [envVars, setEnvVars] = useState<EnvVar[]>(() => {
@@ -542,8 +654,11 @@ export default function AppLaunchForm({
     initialPostRun ?? entryPoint.post_run ?? ''
   );
   const [openEnvSections, setOpenEnvSections] = useState<string[]>([
-    'environment',
-    'resources'
+    'environment'
+  ]);
+  const [openClusterSections, setOpenClusterSections] = useState<string[]>([
+    'resources',
+    'submitOptions'
   ]);
 
   const handleChange = (paramId: string, value: unknown) => {
@@ -671,7 +786,10 @@ export default function AppLaunchForm({
 
     // Only pass resources if user provided values
     const hasResourceOverrides =
-      resources.cpus || resources.memory || resources.walltime;
+      resources.cpus ||
+      resources.memory ||
+      resources.walltime ||
+      resources.queue;
 
     // Convert envVars array to Record, filtering empty keys
     const envRecord: Record<string, string> = {};
@@ -685,6 +803,7 @@ export default function AppLaunchForm({
     await onSubmit(
       params,
       hasResourceOverrides ? resources : undefined,
+      extraArgs.trim() || undefined,
       pullLatest,
       hasEnv ? envRecord : undefined,
       preRun.trim() || undefined,
@@ -718,6 +837,9 @@ export default function AppLaunchForm({
           <Tabs.Trigger className="!text-foreground h-full" value="environment">
             Environment
           </Tabs.Trigger>
+          <Tabs.Trigger className="!text-foreground h-full" value="cluster">
+            Cluster
+          </Tabs.Trigger>
           <Tabs.TriggerIndicator className="h-full" />
         </Tabs.List>
 
@@ -817,11 +939,20 @@ export default function AppLaunchForm({
             openEnvSections={openEnvSections}
             postRun={postRun}
             preRun={preRun}
-            resources={resources}
             setEnvVars={setEnvVars}
             setOpenEnvSections={setOpenEnvSections}
             setPostRun={setPostRun}
             setPreRun={setPreRun}
+          />
+        </Tabs.Panel>
+
+        <Tabs.Panel className="pt-4 max-w-2xl" value="cluster">
+          <ClusterTabContent
+            extraArgs={extraArgs}
+            openClusterSections={openClusterSections}
+            resources={resources}
+            setExtraArgs={setExtraArgs}
+            setOpenClusterSections={setOpenClusterSections}
             setResources={setResources}
           />
         </Tabs.Panel>
diff --git a/frontend/src/components/ui/PreferencesPage/JobOptions.tsx b/frontend/src/components/ui/PreferencesPage/JobOptions.tsx
new file mode 100644
index 00000000..f6317eff
--- /dev/null
+++ b/frontend/src/components/ui/PreferencesPage/JobOptions.tsx
@@ -0,0 +1,61 @@
+import { useState } from 'react';
+
+import { Typography } from '@material-tailwind/react';
+import toast from 'react-hot-toast';
+
+import { usePreferencesContext } from '@/contexts/PreferencesContext';
+
+export default function JobOptions() {
+  const { defaultExtraArgs, updateDefaultExtraArgs } = usePreferencesContext();
+
+  const [localValue, setLocalValue] = useState(defaultExtraArgs);
+  const [saving, setSaving] = useState(false);
+
+  // Track whether the local value differs from the saved preference
+  const isDirty = localValue !== defaultExtraArgs;
+
+  const handleSave = async () => {
+    setSaving(true);
+    const result = await updateDefaultExtraArgs(localValue.trim());
+    setSaving(false);
+    if (result.success) {
+      toast.success('Default extra arguments saved');
+    } else {
+      toast.error(result.error);
+    }
+  };
+
+  return (
+    <div>
+      <Typography className="font-semibold">Jobs</Typography>
+      <div className="pl-4 mt-2">
+        <label
+          className="block text-foreground text-sm mb-1"
+          htmlFor="default-extra-args"
+        >
+          Default extra arguments
+        </label>
+        <Typography className="text-secondary mb-2" type="small">
+          Additional CLI arguments appended to every job submit command. Can be
+          overridden per job on the Cluster tab.
+        </Typography>
+        <input
+          className="max-w-md w-full p-2 text-foreground border rounded-sm focus:outline-none bg-background border-primary-light focus:border-primary font-mono text-sm"
+          id="default-extra-args"
+          onChange={e => setLocalValue(e.target.value)}
+          placeholder="e.g. -P your_project"
+          type="text"
+          value={localValue}
+        />
+        <button
+          className="mt-2 block px-3 py-1 text-sm rounded bg-primary text-white hover:bg-primary-dark transition-colors disabled:opacity-50"
+          disabled={!isDirty || saving}
+          onClick={handleSave}
+          type="button"
+        >
+          {saving ? 'Saving...' : 'Save'}
+        </button>
+      </div>
+    </div>
+  );
+}
diff --git a/frontend/src/contexts/PreferencesContext.tsx b/frontend/src/contexts/PreferencesContext.tsx
index 877e484f..3c75c28d 100644
--- a/frontend/src/contexts/PreferencesContext.tsx
+++ b/frontend/src/contexts/PreferencesContext.tsx
@@ -53,6 +53,7 @@ type PreferencesContextType = {
   useLegacyMultichannelApproach: boolean;
   isFilteredByGroups: boolean;
   showTutorial: boolean;
+  defaultExtraArgs: string;
 
   // Favorites
   zoneFavorites: Zone[];
@@ -80,6 +81,7 @@ type PreferencesContextType = {
   toggleUseLegacyMultichannelApproach: () => Promise<Result<void>>;
   toggleFilterByGroups: () => Promise<Result<void>>;
   toggleShowTutorial: () => Promise<Result<void>>;
+  updateDefaultExtraArgs: (args: string) => Promise<Result<void>>;
   handleFavoriteChange: (
     item: Zone | FileSharePath | FolderFavorite,
     type: 'zone' | 'fileSharePath' | 'folder'
@@ -242,6 +244,20 @@ export const PreferencesProvider = ({
     );
   };
 
+  const updateDefaultExtraArgs = async (
+    args: string
+  ): Promise<Result<void>> => {
+    try {
+      await updatePreferenceMutation.mutateAsync({
+        key: 'defaultExtraArgs',
+        value: args
+      });
+      return createSuccess(undefined);
+    } catch (error) {
+      return handleError(error);
+    }
+  };
+
   function updatePreferenceList<T>(
     key: string,
     itemToUpdate: T,
@@ -500,6 +516,7 @@ export const PreferencesProvider = ({
       preferencesQuery.data?.useLegacyMultichannelApproach || false,
     isFilteredByGroups: preferencesQuery.data?.isFilteredByGroups ?? true,
     showTutorial: preferencesQuery.data?.showTutorial ?? true,
+    defaultExtraArgs: preferencesQuery.data?.defaultExtraArgs || '',
 
     // Favorites
     zoneFavorites: preferencesQuery.data?.zoneFavorites || [],
@@ -526,6 +543,7 @@ export const PreferencesProvider = ({
     toggleUseLegacyMultichannelApproach,
     toggleFilterByGroups,
     toggleShowTutorial,
+    updateDefaultExtraArgs,
     handleFavoriteChange,
     handleContextMenuFavorite
   };
diff --git a/frontend/src/queries/jobsQueries.ts b/frontend/src/queries/jobsQueries.ts
index c53cc319..87b8ed10 100644
--- a/frontend/src/queries/jobsQueries.ts
+++ b/frontend/src/queries/jobsQueries.ts
@@ -8,8 +8,18 @@ import {
 } from '@/queries/queryUtils';
 import type { Job, JobSubmitRequest } from '@/shared.types';
 
+// --- Types ---
+
+type ClusterDefaults = {
+  extra_args: string;
+};
+
 // --- Query Keys ---
 
+export const clusterDefaultsQueryKeys = {
+  all: ['cluster-defaults'] as const
+};
+
 export const jobsQueryKeys = {
   all: ['cluster-jobs'] as const,
   list: () => ['cluster-jobs', 'list'] as const,
@@ -18,6 +28,22 @@ export const jobsQueryKeys = {
 
 // --- Fetch Helpers ---
 
+async function fetchClusterDefaults(
+  signal?: AbortSignal
+): Promise<ClusterDefaults> {
+  const response = await sendFetchRequest(
+    '/api/cluster-defaults',
+    'GET',
+    undefined,
+    { signal }
+  );
+  const data = await getResponseJsonOrError(response);
+  if (!response.ok) {
+    throwResponseNotOkError(response, data);
+  }
+  return data as ClusterDefaults;
+}
+
 async function fetchJobs(signal?: AbortSignal): Promise<Job[]> {
   const response = await sendFetchRequest('/api/jobs', 'GET', undefined, {
     signal
@@ -67,6 +93,17 @@ async function fetchJobFile(
 
 // --- Query Hooks ---
 
+export function useClusterDefaultsQuery(): UseQueryResult<
+  ClusterDefaults,
+  Error
+> {
+  return useQuery({
+    queryKey: clusterDefaultsQueryKeys.all,
+    queryFn: ({ signal }) => fetchClusterDefaults(signal),
+    staleTime: 1000 * 60 * 60 // 1 hour — cluster config rarely changes
+  });
+}
+
 export function useJobsQuery(): UseQueryResult<Job[], Error> {
   return useQuery({
     queryKey: jobsQueryKeys.list(),
diff --git a/frontend/src/queries/preferencesQueries.ts b/frontend/src/queries/preferencesQueries.ts
index a5962069..a1aa9bec 100644
--- a/frontend/src/queries/preferencesQueries.ts
+++ b/frontend/src/queries/preferencesQueries.ts
@@ -38,6 +38,7 @@ type PreferencesApiResponse = {
   useLegacyMultichannelApproach?: { value: boolean };
   isFilteredByGroups?: { value: boolean };
   showTutorial?: { value: boolean };
+  defaultExtraArgs?: { value: string };
   zone?: { value: ZonePreference[] };
   fileSharePath?: { value: FileSharePathPreference[] };
   folder?: { value: FolderPreference[] };
@@ -68,6 +69,7 @@ export type PreferencesQueryData = {
   useLegacyMultichannelApproach: boolean;
   isFilteredByGroups: boolean;
   showTutorial: boolean;
+  defaultExtraArgs: string;
 };
 
 /**
@@ -232,7 +234,8 @@ const createTransformPreferences = (
       useLegacyMultichannelApproach:
         rawData.useLegacyMultichannelApproach?.value || false,
       isFilteredByGroups: rawData.isFilteredByGroups?.value ?? true,
-      showTutorial: rawData.showTutorial?.value ?? true
+      showTutorial: rawData.showTutorial?.value ?? true,
+      defaultExtraArgs: rawData.defaultExtraArgs?.value || ''
     };
   };
 };
diff --git a/frontend/src/shared.types.ts b/frontend/src/shared.types.ts
index 6b6c5c0e..635b0004 100644
--- a/frontend/src/shared.types.ts
+++ b/frontend/src/shared.types.ts
@@ -103,6 +103,7 @@ type AppResourceDefaults = {
   cpus?: number;
   memory?: string;
   walltime?: string;
+  queue?: string;
 };
 
 type AppEntryPoint = {
@@ -173,6 +174,7 @@ type JobSubmitRequest = {
   entry_point_id: string;
   parameters: Record<string, unknown>;
   resources?: AppResourceDefaults;
+  extra_args?: string;
   pull_latest?: boolean;
   env?: Record<string, string>;
   pre_run?: string;

From d5215e7861ae441b7a380d5ca0440a8dc7981b52 Mon Sep 17 00:00:00 2001
From: Konrad Rokicki <rokickik@janelia.hhmi.org>
Date: Wed, 25 Feb 2026 11:06:51 -0500
Subject: [PATCH 12/20] fixed _MANIFEST_FILENAME bug

---
 fileglancer/server.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fileglancer/server.py b/fileglancer/server.py
index 4711e326..c6418aa9 100644
--- a/fileglancer/server.py
+++ b/fileglancer/server.py
@@ -1520,7 +1520,7 @@ async def add_user_app(body: AppAddRequest,
             raise HTTPException(status_code=400, detail=f"Failed to clone or scan repo: {str(e)}")
 
         if not discovered:
-            filenames = ", ".join(apps_module._MANIFEST_FILENAMES)
+            filenames = apps_module._MANIFEST_FILENAME
             raise HTTPException(
                 status_code=404,
                 detail=f"No manifest files found ({filenames}). "

From e29288eee824816c0c1bb75f17fdd1670e04eee1 Mon Sep 17 00:00:00 2001
From: Konrad Rokicki <rokickik@janelia.hhmi.org>
Date: Thu, 26 Feb 2026 16:10:58 -0500
Subject: [PATCH 13/20] added conda support for apps

---
 docs/AuthoringApps.md        |  49 ++++++++-
 fileglancer/apps.py          |  13 +++
 fileglancer/model.py         |  28 +++++-
 frontend/src/shared.types.ts |   1 +
 tests/test_apps.py           | 188 +++++++++++++++++++++++++++++++++++
 5 files changed, 276 insertions(+), 3 deletions(-)
 create mode 100644 tests/test_apps.py

diff --git a/docs/AuthoringApps.md b/docs/AuthoringApps.md
index 11ea5a4a..eb1f14ad 100644
--- a/docs/AuthoringApps.md
+++ b/docs/AuthoringApps.md
@@ -64,9 +64,10 @@ requirements:
   - "pixi>=0.40"
   - npm
   - "maven>=3.9"
+  - miniforge
 ```
 
-**Supported tools:** `pixi`, `npm`, `maven`
+**Supported tools:** `pixi`, `npm`, `maven`, `miniforge`
 
 **Supported version operators:** `>=`, `<=`, `!=`, `==`, `>`, `<`
 
@@ -88,6 +89,7 @@ Each runnable defines a single command that users can launch. If the manifest ha
 | `env` | object | no | Default environment variables to export (see [Environment Variables](#environment-variables)) |
 | `pre_run` | string | no | Shell script to run before the main command (see [Pre/Post-Run Scripts](#prepost-run-scripts)) |
 | `post_run` | string | no | Shell script to run after the main command (see [Pre/Post-Run Scripts](#prepost-run-scripts)) |
+| `conda_env` | string | no | Conda environment name or absolute path to activate before running (see [Conda Environments](#conda-environments)) |
 
 ### Parameters
 
@@ -220,10 +222,14 @@ Users can override these in the UI. If a user provides their own pre/post-run sc
 The generated job script has the following structure:
 
 ```bash
-export FG_WORK_DIR='/home/user/.fileglancer/jobs/42-MyApp-convert'
 unset PIXI_PROJECT_MANIFEST
+export FG_WORK_DIR='/home/user/.fileglancer/jobs/42-MyApp-convert'
 cd "$FG_WORK_DIR/repo"
 
+# Conda activation (if conda_env is set)
+eval "$(conda shell.bash hook)"
+conda activate myenv
+
 # Environment variables
 export JAVA_HOME='/opt/java'
 export NXF_SINGULARITY_CACHEDIR='/scratch/singularity'
@@ -242,6 +248,45 @@ echo "Conversion complete"
 
 `FG_WORK_DIR` is always exported and points to the job's working directory. See [Environment Variables Set by Fileglancer](#environment-variables-set-by-fileglancer) for the full list.
 
+### Conda Environments
+
+The `conda_env` field specifies a conda environment to activate before running the command. This requires `miniforge` (or any conda distribution providing the `conda` binary) in the `requirements` list.
+
+The value can be either:
+- **An environment name** (e.g. `myenv`): must match `[a-zA-Z0-9_.-]+`
+- **An absolute path** (e.g. `/opt/envs/myenv`): must not contain shell metacharacters
+
+```yaml
+name: My Analysis Tool
+requirements:
+  - miniforge
+runnables:
+  - id: analyze
+    name: Run Analysis
+    command: python analyze.py
+    conda_env: my-analysis-env
+    parameters:
+      - flag: --input
+        name: Input
+        type: file
+        required: true
+```
+
+When `conda_env` is set, the generated script initializes conda and activates the environment before any env vars, pre_run, or the main command:
+
+```bash
+eval "$(conda shell.bash hook)"
+conda activate my-analysis-env
+```
+
+> **Tip:** If the conda environment needs to be created before use (e.g. from an `environment.yml`), use `pre_run` to create it first:
+>
+> ```yaml
+> conda_env: my-tool-env
+> pre_run: |
+>   conda env create -f environment.yml -n my-tool-env --yes 2>/dev/null || true
+> ```
+
 ## Command Building
 
 When a job is submitted, Fileglancer constructs the full shell command from the runnable's `command` field and the user-provided parameter values using a two-pass approach:
diff --git a/fileglancer/apps.py b/fileglancer/apps.py
index cb9d5557..b6a4c916 100644
--- a/fileglancer/apps.py
+++ b/fileglancer/apps.py
@@ -188,6 +188,10 @@ async def fetch_app_manifest(url: str, manifest_path: str = "") -> AppManifest:
         "version_args": ["mvn", "--version"],
         "version_pattern": r"Apache Maven (\S+)",
     },
+    "miniforge": {
+        "version_args": ["conda", "--version"],
+        "version_pattern": r"conda (\S+)",
+    },
 }
 
 _REQ_PATTERN = re.compile(r"^([a-zA-Z][a-zA-Z0-9_-]*)\s*((?:>=|<=|!=|==|>|<)\s*\S+)?$")
@@ -690,6 +694,15 @@ async def submit_job(
         preamble_lines.append('export SERVICE_URL_PATH="$FG_WORK_DIR/service_url"')
     preamble_lines.append(f'cd "$FG_WORK_DIR/{cd_suffix}"')
     script_parts = ["\n".join(preamble_lines)]
+
+    # Conda environment activation
+    if entry_point.conda_env:
+        conda_activation = (
+            'eval "$(conda shell.bash hook)"\n'
+            f'conda activate {shlex.quote(entry_point.conda_env)}'
+        )
+        script_parts.append(conda_activation)
+
     if env_lines:
         script_parts.append(env_lines.rstrip())
     if effective_pre_run:
diff --git a/fileglancer/model.py b/fileglancer/model.py
index 4609c04d..da74d2e3 100644
--- a/fileglancer/model.py
+++ b/fileglancer/model.py
@@ -391,6 +391,29 @@ class AppEntryPoint(BaseModel):
     env: Optional[Dict[str, str]] = Field(description="Default environment variables", default=None)
     pre_run: Optional[str] = Field(description="Script to run before the main command", default=None)
     post_run: Optional[str] = Field(description="Script to run after the main command", default=None)
+    conda_env: Optional[str] = Field(
+        description="Conda environment name or path to activate before running",
+        default=None,
+    )
+
+    @field_validator("conda_env")
+    @classmethod
+    def validate_conda_env(cls, v):
+        if v is None:
+            return v
+        if v.startswith("/"):
+            # Absolute path: reject shell metacharacters
+            if _CONDA_ENV_PATH_FORBIDDEN.search(v):
+                raise ValueError(
+                    f"conda_env path contains forbidden characters: {v!r}"
+                )
+        else:
+            # Name: must be alphanumeric, dots, dashes, underscores
+            if not _CONDA_ENV_NAME_PATTERN.match(v):
+                raise ValueError(
+                    f"conda_env name must match [a-zA-Z0-9_.-]+, got: {v!r}"
+                )
+        return v
 
     def flat_parameters(self) -> List[AppParameter]:
         """Return a flat list of all parameters, traversing sections."""
@@ -421,7 +444,10 @@ def generate_parameter_keys(self):
         return self
 
 
-SUPPORTED_TOOLS = {"pixi", "npm", "maven"}
+SUPPORTED_TOOLS = {"pixi", "npm", "maven", "miniforge"}
+
+_CONDA_ENV_NAME_PATTERN = re.compile(r'^[a-zA-Z0-9_.-]+$')
+_CONDA_ENV_PATH_FORBIDDEN = re.compile(r'[;&|`$(){}!<>\n\r]')
 
 
 class AppManifest(BaseModel):
diff --git a/frontend/src/shared.types.ts b/frontend/src/shared.types.ts
index 635b0004..28661734 100644
--- a/frontend/src/shared.types.ts
+++ b/frontend/src/shared.types.ts
@@ -117,6 +117,7 @@ type AppEntryPoint = {
   env?: Record<string, string>;
   pre_run?: string;
   post_run?: string;
+  conda_env?: string;
 };
 
 type AppManifest = {
diff --git a/tests/test_apps.py b/tests/test_apps.py
new file mode 100644
index 00000000..23776248
--- /dev/null
+++ b/tests/test_apps.py
@@ -0,0 +1,188 @@
+"""Tests for apps module: miniforge requirement and conda_env support."""
+
+import subprocess
+from unittest.mock import patch, MagicMock
+
+import pytest
+from pydantic import ValidationError
+
+from fileglancer.model import SUPPORTED_TOOLS, AppEntryPoint
+from fileglancer.apps import _TOOL_REGISTRY, verify_requirements
+
+
+# --- Model tests ---
+
+class TestSupportedTools:
+    def test_miniforge_in_supported_tools(self):
+        assert "miniforge" in SUPPORTED_TOOLS
+
+    def test_miniforge_in_tool_registry(self):
+        assert "miniforge" in _TOOL_REGISTRY
+        entry = _TOOL_REGISTRY["miniforge"]
+        assert entry["version_args"] == ["conda", "--version"]
+        assert entry["version_pattern"] == r"conda (\S+)"
+
+
+class TestCondaEnvValidation:
+    def test_valid_name(self):
+        ep = AppEntryPoint(id="t", name="T", command="echo", conda_env="myenv")
+        assert ep.conda_env == "myenv"
+
+    def test_valid_name_with_dots_dashes(self):
+        ep = AppEntryPoint(id="t", name="T", command="echo", conda_env="my.env-2_test")
+        assert ep.conda_env == "my.env-2_test"
+
+    def test_valid_absolute_path(self):
+        ep = AppEntryPoint(id="t", name="T", command="echo", conda_env="/opt/envs/myenv")
+        assert ep.conda_env == "/opt/envs/myenv"
+
+    def test_none_is_allowed(self):
+        ep = AppEntryPoint(id="t", name="T", command="echo", conda_env=None)
+        assert ep.conda_env is None
+
+    def test_default_is_none(self):
+        ep = AppEntryPoint(id="t", name="T", command="echo")
+        assert ep.conda_env is None
+
+    def test_rejects_name_with_spaces(self):
+        with pytest.raises(ValidationError, match="conda_env name must match"):
+            AppEntryPoint(id="t", name="T", command="echo", conda_env="my env")
+
+    def test_rejects_name_with_semicolon(self):
+        with pytest.raises(ValidationError, match="conda_env name must match"):
+            AppEntryPoint(id="t", name="T", command="echo", conda_env="env;rm")
+
+    def test_rejects_path_with_semicolon(self):
+        with pytest.raises(ValidationError, match="forbidden characters"):
+            AppEntryPoint(id="t", name="T", command="echo", conda_env="/opt/envs;rm -rf /")
+
+    def test_rejects_path_with_backtick(self):
+        with pytest.raises(ValidationError, match="forbidden characters"):
+            AppEntryPoint(id="t", name="T", command="echo", conda_env="/opt/`whoami`/env")
+
+    def test_rejects_path_with_dollar(self):
+        with pytest.raises(ValidationError, match="forbidden characters"):
+            AppEntryPoint(id="t", name="T", command="echo", conda_env="/opt/$HOME/env")
+
+    def test_rejects_path_with_pipe(self):
+        with pytest.raises(ValidationError, match="forbidden characters"):
+            AppEntryPoint(id="t", name="T", command="echo", conda_env="/opt/env|bad")
+
+
+# --- verify_requirements tests ---
+
+class TestVerifyRequirementsMiniforge:
+    @patch("fileglancer.apps.shutil.which")
+    def test_miniforge_found_via_conda(self, mock_which):
+        """miniforge binary doesn't exist, but conda does — should pass."""
+        def which_side_effect(name):
+            if name == "miniforge":
+                return None
+            if name == "conda":
+                return "/usr/bin/conda"
+            return None
+        mock_which.side_effect = which_side_effect
+
+        # No version constraint, so just checking binary existence
+        verify_requirements(["miniforge"])
+
+    @patch("fileglancer.apps.shutil.which")
+    def test_miniforge_not_found(self, mock_which):
+        mock_which.return_value = None
+        with pytest.raises(ValueError, match="not installed or not on PATH"):
+            verify_requirements(["miniforge"])
+
+    @patch("fileglancer.apps.subprocess.run")
+    @patch("fileglancer.apps.shutil.which")
+    def test_miniforge_version_check(self, mock_which, mock_run):
+        def which_side_effect(name):
+            if name == "miniforge":
+                return None
+            if name == "conda":
+                return "/usr/bin/conda"
+            return None
+        mock_which.side_effect = which_side_effect
+
+        mock_run.return_value = MagicMock(
+            stdout="conda 24.7.1", stderr="", returncode=0
+        )
+        verify_requirements(["miniforge>=24.0"])
+
+    @patch("fileglancer.apps.subprocess.run")
+    @patch("fileglancer.apps.shutil.which")
+    def test_miniforge_version_too_old(self, mock_which, mock_run):
+        def which_side_effect(name):
+            if name == "miniforge":
+                return None
+            if name == "conda":
+                return "/usr/bin/conda"
+            return None
+        mock_which.side_effect = which_side_effect
+
+        mock_run.return_value = MagicMock(
+            stdout="conda 23.1.0", stderr="", returncode=0
+        )
+        with pytest.raises(ValueError, match="does not satisfy"):
+            verify_requirements(["miniforge>=24.0"])
+
+
+# --- Script generation tests ---
+
+class TestCondaActivationInScript:
+    """Test that conda activation appears in the generated script."""
+
+    @pytest.fixture
+    def _make_entry_point(self):
+        def factory(**kwargs):
+            defaults = dict(
+                id="test", name="Test", command="python run.py", parameters=[]
+            )
+            defaults.update(kwargs)
+            return AppEntryPoint(**defaults)
+        return factory
+
+    def test_script_includes_conda_activation(self, _make_entry_point):
+        """When conda_env is set, script should contain conda activation lines."""
+        import shlex
+        ep = _make_entry_point(conda_env="myenv")
+
+        # Simulate the script building logic from submit_job
+        script_parts = ["# preamble"]
+        if ep.conda_env:
+            conda_activation = (
+                'eval "$(conda shell.bash hook)"\n'
+                f'conda activate {shlex.quote(ep.conda_env)}'
+            )
+            script_parts.append(conda_activation)
+        script_parts.append(ep.command)
+        full_script = "\n\n".join(script_parts)
+
+        assert 'eval "$(conda shell.bash hook)"' in full_script
+        assert "conda activate myenv" in full_script
+        # Activation should come before the command
+        hook_pos = full_script.index('eval "$(conda shell.bash hook)"')
+        cmd_pos = full_script.index("python run.py")
+        assert hook_pos < cmd_pos
+
+    def test_script_omits_conda_when_not_set(self, _make_entry_point):
+        """When conda_env is None, script should not contain conda activation."""
+        ep = _make_entry_point(conda_env=None)
+
+        script_parts = ["# preamble"]
+        if ep.conda_env:
+            script_parts.append("conda activate something")
+        script_parts.append(ep.command)
+        full_script = "\n\n".join(script_parts)
+
+        assert "conda" not in full_script
+
+    def test_conda_env_path_is_quoted(self, _make_entry_point):
+        """Absolute paths should be shell-quoted in the script."""
+        import shlex
+        ep = _make_entry_point(conda_env="/opt/conda/envs/my env")
+        # This would fail validation (spaces in path name, not absolute path forbidden chars)
+        # but let's test with a valid path containing special-but-allowed chars
+        ep2 = _make_entry_point(conda_env="/opt/conda/envs/myenv")
+
+        activation = f'conda activate {shlex.quote(ep2.conda_env)}'
+        assert activation == "conda activate /opt/conda/envs/myenv"

From 817ae5aeb85a3de2ead7310625ce1d25da8b04c3 Mon Sep 17 00:00:00 2001
From: Konrad Rokicki <rokickik@janelia.hhmi.org>
Date: Sat, 28 Feb 2026 19:21:07 -0500
Subject: [PATCH 14/20] added container support

---
 docs/AuthoringApps.md                         |  68 ++++++-
 .../483b2e31b85e_add_container_args_column.py |  26 +++
 fileglancer/apps.py                           |  72 ++++++++
 fileglancer/database.py                       |   8 +-
 fileglancer/model.py                          |  52 +++++-
 fileglancer/server.py                         |   4 +
 frontend/src/components/AppJobs.tsx           |   4 +-
 frontend/src/components/AppLaunch.tsx         |  14 +-
 frontend/src/components/JobDetail.tsx         |   4 +-
 .../components/ui/AppsPage/AppLaunchForm.tsx  |  90 ++++++++-
 frontend/src/shared.types.ts                  |   6 +
 tests/test_apps.py                            | 174 +++++++++++++++++-
 12 files changed, 506 insertions(+), 16 deletions(-)
 create mode 100644 fileglancer/alembic/versions/483b2e31b85e_add_container_args_column.py

diff --git a/docs/AuthoringApps.md b/docs/AuthoringApps.md
index eb1f14ad..b9988fd9 100644
--- a/docs/AuthoringApps.md
+++ b/docs/AuthoringApps.md
@@ -67,7 +67,7 @@ requirements:
   - miniforge
 ```
 
-**Supported tools:** `pixi`, `npm`, `maven`, `miniforge`
+**Supported tools:** `pixi`, `npm`, `maven`, `miniforge`, `apptainer`
 
 **Supported version operators:** `>=`, `<=`, `!=`, `==`, `>`, `<`
 
@@ -90,6 +90,9 @@ Each runnable defines a single command that users can launch. If the manifest ha
 | `pre_run` | string | no | Shell script to run before the main command (see [Pre/Post-Run Scripts](#prepost-run-scripts)) |
 | `post_run` | string | no | Shell script to run after the main command (see [Pre/Post-Run Scripts](#prepost-run-scripts)) |
 | `conda_env` | string | no | Conda environment name or absolute path to activate before running (see [Conda Environments](#conda-environments)) |
+| `container` | string | no | Container image URL for Apptainer (see [Containers](#containers-apptainer)) |
+| `bind_paths` | list of strings | no | Additional paths to bind-mount into the container (requires `container`) |
+| `container_args` | string | no | Default extra arguments for container exec (e.g. `--nv`), overridable at launch time |
 
 ### Parameters
 
@@ -287,6 +290,69 @@ conda activate my-analysis-env
 >   conda env create -f environment.yml -n my-tool-env --yes 2>/dev/null || true
 > ```
 
+### Containers (Apptainer)
+
+The `container` field specifies a container image to run the command inside using [Apptainer](https://apptainer.org/) (formerly Singularity). This requires `apptainer` in the `requirements` list.
+
+The value is a container image URL, typically from a Docker/OCI registry:
+
+- `ghcr.io/org/image:tag` — GitHub Container Registry
+- `docker://ghcr.io/org/image:tag` — explicit Docker protocol prefix (added automatically if absent)
+
+```yaml
+name: Lolcow
+requirements:
+  - apptainer
+runnables:
+  - id: say
+    name: Cow Say
+    command: cowsay
+    container: godlovedc/lolcow
+    parameters:
+      - name: Message
+        type: string
+        description: What the cow should say
+        required: true
+        default: "Hello from Fileglancer!"
+```
+
+When `container` is set, the generated script:
+
+1. Creates a SIF cache directory at `$APPTAINER_CACHEDIR` (defaults to `~/.apptainer/cache/fileglancer/`)
+2. Pulls the image to a `.sif` file if not already cached
+3. Runs the command inside the container via `apptainer exec`
+
+```bash
+# Apptainer container setup
+APPTAINER_CACHE_DIR="${APPTAINER_CACHEDIR:-$HOME/.apptainer/cache/fileglancer}"
+mkdir -p "$APPTAINER_CACHE_DIR"
+SIF_PATH="$APPTAINER_CACHE_DIR/godlovedc_lolcow.sif"
+if [ ! -f "$SIF_PATH" ]; then
+  apptainer pull "$SIF_PATH" 'docker://godlovedc/lolcow'
+fi
+apptainer exec --bind /home/user/.fileglancer/jobs/1-lolcow-say "$SIF_PATH" \
+  cowsay \
+  'Hello from Fileglancer!'
+```
+
+**Bind mounts** are auto-detected from file and directory parameters. The job's working directory is always bound. Use `bind_paths` to add extra paths:
+
+```yaml
+container: ghcr.io/org/image:tag
+bind_paths:
+  - /shared/reference-data
+  - /scratch
+```
+
+**Extra Apptainer arguments** can be set as defaults in the manifest with `container_args`, and overridden by the user at launch time through the UI's Environment tab:
+
+```yaml
+container: ghcr.io/org/cuda-tool:latest
+container_args: "--nv"
+```
+
+> **Important:** `conda_env` and `container` are mutually exclusive — you cannot use both on the same entry point.
+
 ## Command Building
 
 When a job is submitted, Fileglancer constructs the full shell command from the runnable's `command` field and the user-provided parameter values using a two-pass approach:
diff --git a/fileglancer/alembic/versions/483b2e31b85e_add_container_args_column.py b/fileglancer/alembic/versions/483b2e31b85e_add_container_args_column.py
new file mode 100644
index 00000000..3c9c1d7f
--- /dev/null
+++ b/fileglancer/alembic/versions/483b2e31b85e_add_container_args_column.py
@@ -0,0 +1,26 @@
+"""add container and container_args columns
+
+Revision ID: 483b2e31b85e
+Revises: b5e8a3f21c76
+Create Date: 2026-02-28 16:39:39.385514
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '483b2e31b85e'
+down_revision = 'b5e8a3f21c76'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    op.add_column('jobs', sa.Column('container', sa.String(), nullable=True))
+    op.add_column('jobs', sa.Column('container_args', sa.String(), nullable=True))
+
+
+def downgrade() -> None:
+    op.drop_column('jobs', 'container_args')
+    op.drop_column('jobs', 'container')
diff --git a/fileglancer/apps.py b/fileglancer/apps.py
index b6a4c916..6764beea 100644
--- a/fileglancer/apps.py
+++ b/fileglancer/apps.py
@@ -192,6 +192,10 @@ async def fetch_app_manifest(url: str, manifest_path: str = "") -> AppManifest:
         "version_args": ["conda", "--version"],
         "version_pattern": r"conda (\S+)",
     },
+    "apptainer": {
+        "version_args": ["apptainer", "--version"],
+        "version_pattern": r"apptainer version (\S+)",
+    },
 }
 
 _REQ_PATTERN = re.compile(r"^([a-zA-Z][a-zA-Z0-9_-]*)\s*((?:>=|<=|!=|==|>|<)\s*\S+)?$")
@@ -564,6 +568,46 @@ def _sanitize_for_path(s: str) -> str:
     return re.sub(r'[^a-zA-Z0-9._-]', '_', s)
 
 
+_CONTAINER_SIF_SAFE = re.compile(r'[^a-zA-Z0-9._-]')
+
+
+def _container_sif_name(container_url: str) -> str:
+    """Derive a safe SIF filename from a container URL."""
+    url = container_url.removeprefix("docker://")
+    return _CONTAINER_SIF_SAFE.sub('_', url) + ".sif"
+
+
+def _build_container_script(
+    container_url: str,
+    command: str,
+    work_dir: str,
+    bind_paths: list[str],
+    container_args: Optional[str] = None,
+) -> str:
+    """Build shell script for running a command inside an Apptainer container."""
+    sif_name = _container_sif_name(container_url)
+    docker_url = container_url if container_url.startswith("docker://") else f"docker://{container_url}"
+
+    # Deduplicate and sort bind paths
+    all_binds = sorted(set([work_dir] + bind_paths))
+    bind_flags = " ".join(f"--bind {shlex.quote(p)}" for p in all_binds)
+
+    extra = f" {container_args}" if container_args else ""
+
+    lines = [
+        "# Apptainer container setup",
+        'APPTAINER_CACHE_DIR="${APPTAINER_CACHEDIR:-$HOME/.apptainer/cache/fileglancer}"',
+        'mkdir -p "$APPTAINER_CACHE_DIR"',
+        f'SIF_PATH="$APPTAINER_CACHE_DIR/{sif_name}"',
+        'if [ ! -f "$SIF_PATH" ]; then',
+        f'  apptainer pull "$SIF_PATH" {shlex.quote(docker_url)}',
+        'fi',
+        f'apptainer exec {bind_flags}{extra} "$SIF_PATH" \\',
+        f'  {command}',
+    ]
+    return "\n".join(lines)
+
+
 def _build_work_dir(job_id: int, app_name: str, entry_point_id: str) -> Path:
     """Build a working directory path under ~/.fileglancer/jobs/."""
     safe_app = _sanitize_for_path(app_name)
@@ -583,6 +627,8 @@ async def submit_job(
     env: Optional[dict] = None,
     pre_run: Optional[str] = None,
     post_run: Optional[str] = None,
+    container: Optional[str] = None,
+    container_args: Optional[str] = None,
 ) -> db.JobDB:
     """Submit a new job to the cluster.
 
@@ -622,6 +668,8 @@ async def submit_job(
         merged_env.update(env)
     effective_pre_run = pre_run if pre_run is not None else (entry_point.pre_run or None)
     effective_post_run = post_run if post_run is not None else (entry_point.post_run or None)
+    effective_container = container if container is not None else (entry_point.container or None)
+    effective_container_args = container_args if container_args is not None else (entry_point.container_args or None)
 
     # Create DB record first to get job ID for the work directory
     resources_dict = None
@@ -650,6 +698,8 @@ async def submit_job(
             pre_run=effective_pre_run,
             post_run=effective_post_run,
             pull_latest=pull_latest,
+            container=effective_container,
+            container_args=effective_container_args,
         )
         job_id = db_job.id
 
@@ -703,6 +753,28 @@ async def submit_job(
         )
         script_parts.append(conda_activation)
 
+    # If container is defined, wrap command in apptainer exec
+    if effective_container:
+        bind_paths = []
+        for param in entry_point.flat_parameters():
+            if param.type in ("file", "directory") and param.key in parameters:
+                path_val = str(parameters[param.key])
+                expanded = os.path.expanduser(path_val)
+                if param.type == "directory":
+                    bind_paths.append(expanded)
+                else:
+                    bind_paths.append(str(Path(expanded).parent))
+        if entry_point.bind_paths:
+            bind_paths.extend(entry_point.bind_paths)
+
+        command = _build_container_script(
+            container_url=effective_container,
+            command=command,
+            work_dir=str(work_dir),
+            bind_paths=bind_paths,
+            container_args=effective_container_args,
+        )
+
     if env_lines:
         script_parts.append(env_lines.rstrip())
     if effective_pre_run:
diff --git a/fileglancer/database.py b/fileglancer/database.py
index 7adfdb63..dc495609 100644
--- a/fileglancer/database.py
+++ b/fileglancer/database.py
@@ -156,6 +156,8 @@ class JobDB(Base):
     env = Column(JSON, nullable=True)
     pre_run = Column(String, nullable=True)
     post_run = Column(String, nullable=True)
+    container = Column(String, nullable=True)
+    container_args = Column(String, nullable=True)
     pull_latest = Column(Boolean, nullable=False, default=False)
     created_at = Column(DateTime, nullable=False, default=lambda: datetime.now(UTC))
     started_at = Column(DateTime, nullable=True)
@@ -831,7 +833,9 @@ def create_job(session: Session, username: str, app_url: str, app_name: str,
                resources: Optional[Dict] = None, manifest_path: str = "",
                entry_point_type: str = "job",
                env: Optional[Dict] = None, pre_run: Optional[str] = None,
-               post_run: Optional[str] = None, pull_latest: bool = False) -> JobDB:
+               post_run: Optional[str] = None, pull_latest: bool = False,
+               container: Optional[str] = None,
+               container_args: Optional[str] = None) -> JobDB:
     """Create a new job record"""
     now = datetime.now(UTC)
     job = JobDB(
@@ -847,6 +851,8 @@ def create_job(session: Session, username: str, app_url: str, app_name: str,
         env=env,
         pre_run=pre_run,
         post_run=post_run,
+        container=container,
+        container_args=container_args,
         pull_latest=pull_latest,
         status="PENDING",
         created_at=now
diff --git a/fileglancer/model.py b/fileglancer/model.py
index da74d2e3..2378b7fa 100644
--- a/fileglancer/model.py
+++ b/fileglancer/model.py
@@ -395,6 +395,18 @@ class AppEntryPoint(BaseModel):
         description="Conda environment name or path to activate before running",
         default=None,
     )
+    container: Optional[str] = Field(
+        description="Container image URL for Apptainer (e.g. 'ghcr.io/org/image:tag')",
+        default=None,
+    )
+    bind_paths: Optional[List[str]] = Field(
+        description="Additional paths to bind-mount into the container",
+        default=None,
+    )
+    container_args: Optional[str] = Field(
+        description="Default extra arguments for container exec (e.g. '--nv')",
+        default=None,
+    )
 
     @field_validator("conda_env")
     @classmethod
@@ -415,6 +427,25 @@ def validate_conda_env(cls, v):
                 )
         return v
 
+    @field_validator("container")
+    @classmethod
+    def validate_container(cls, v):
+        if v is None:
+            return v
+        if _SHELL_METACHAR_PATTERN.search(v):
+            raise ValueError(f"container URL contains forbidden characters: {v!r}")
+        return v
+
+    @field_validator("bind_paths")
+    @classmethod
+    def validate_bind_paths(cls, v):
+        if v is None:
+            return v
+        for p in v:
+            if _SHELL_METACHAR_PATTERN.search(p):
+                raise ValueError(f"bind_paths entry contains forbidden characters: {p!r}")
+        return v
+
     def flat_parameters(self) -> List[AppParameter]:
         """Return a flat list of all parameters, traversing sections."""
         result = []
@@ -443,9 +474,18 @@ def generate_parameter_keys(self):
             keys_seen[param.key] = param.name
         return self
 
+    @model_validator(mode='after')
+    def check_conda_container_exclusive(self):
+        if self.conda_env and self.container:
+            raise ValueError("conda_env and container are mutually exclusive — use one or the other")
+        if self.bind_paths and not self.container:
+            raise ValueError("bind_paths requires container to be set")
+        return self
 
-SUPPORTED_TOOLS = {"pixi", "npm", "maven", "miniforge"}
 
+SUPPORTED_TOOLS = {"pixi", "npm", "maven", "miniforge", "apptainer"}
+
+_SHELL_METACHAR_PATTERN = re.compile(r'[;&|`$(){}!<>\n\r]')
 _CONDA_ENV_NAME_PATTERN = re.compile(r'^[a-zA-Z0-9_.-]+$')
 _CONDA_ENV_PATH_FORBIDDEN = re.compile(r'[;&|`$(){}!<>\n\r]')
 
@@ -525,6 +565,8 @@ class Job(BaseModel):
     env: Optional[Dict[str, str]] = Field(description="Environment variables used for the job", default=None)
     pre_run: Optional[str] = Field(description="Script run before the main command", default=None)
     post_run: Optional[str] = Field(description="Script run after the main command", default=None)
+    container: Optional[str] = Field(description="Container image URL used for this job", default=None)
+    container_args: Optional[str] = Field(description="Extra arguments for container exec (e.g. '--nv' for GPU)", default=None)
     pull_latest: bool = Field(description="Whether pull latest was enabled", default=False)
     cluster_job_id: Optional[str] = Field(description="Cluster-assigned job ID", default=None)
     service_url: Optional[str] = Field(description="URL of the running service (for service-type jobs)", default=None)
@@ -549,6 +591,14 @@ class JobSubmitRequest(BaseModel):
     env: Optional[Dict[str, str]] = Field(description="Environment variables to export", default=None)
     pre_run: Optional[str] = Field(description="Script to run before the main command", default=None)
     post_run: Optional[str] = Field(description="Script to run after the main command", default=None)
+    container: Optional[str] = Field(
+        description="Container image URL override (defaults to manifest value)",
+        default=None,
+    )
+    container_args: Optional[str] = Field(
+        description="Extra arguments for container exec (e.g. '--nv' for GPU)",
+        default=None,
+    )
 
 
 class PathValidationRequest(BaseModel):
diff --git a/fileglancer/server.py b/fileglancer/server.py
index c6418aa9..c46d728b 100644
--- a/fileglancer/server.py
+++ b/fileglancer/server.py
@@ -1662,6 +1662,8 @@ async def submit_job(body: JobSubmitRequest,
                 env=body.env,
                 pre_run=body.pre_run,
                 post_run=body.post_run,
+                container=body.container,
+                container_args=body.container_args,
             )
             return _convert_job(db_job)
         except ValueError as e:
@@ -1757,6 +1759,8 @@ def _convert_job(db_job: db.JobDB, include_files: bool = False) -> Job:
             env=db_job.env,
             pre_run=db_job.pre_run,
             post_run=db_job.post_run,
+            container=getattr(db_job, 'container', None),
+            container_args=getattr(db_job, 'container_args', None),
             pull_latest=db_job.pull_latest,
             cluster_job_id=db_job.cluster_job_id,
             service_url=apps_module.get_service_url(db_job),
diff --git a/frontend/src/components/AppJobs.tsx b/frontend/src/components/AppJobs.tsx
index 0410ab55..f458408d 100644
--- a/frontend/src/components/AppJobs.tsx
+++ b/frontend/src/components/AppJobs.tsx
@@ -40,7 +40,9 @@ export default function AppJobs() {
         env: job.env,
         pre_run: job.pre_run,
         post_run: job.post_run,
-        pull_latest: job.pull_latest
+        pull_latest: job.pull_latest,
+        container: job.container,
+        container_args: job.container_args
       }
     });
   };
diff --git a/frontend/src/components/AppLaunch.tsx b/frontend/src/components/AppLaunch.tsx
index 222e8d37..40888a8e 100644
--- a/frontend/src/components/AppLaunch.tsx
+++ b/frontend/src/components/AppLaunch.tsx
@@ -52,6 +52,8 @@ export default function AppLaunch() {
         pre_run?: string;
         post_run?: string;
         pull_latest?: boolean;
+        container?: string;
+        container_args?: string;
       } | null)
     : null;
   const relaunchParameters = relaunchState?.parameters;
@@ -66,6 +68,8 @@ export default function AppLaunch() {
   const relaunchPreRun = relaunchState?.pre_run;
   const relaunchPostRun = relaunchState?.post_run;
   const relaunchPullLatest = relaunchState?.pull_latest;
+  const relaunchContainer = relaunchState?.container;
+  const relaunchContainerArgs = relaunchState?.container_args;
 
   // Check if app is in user's library
   const isInstalled = appsQuery.data?.some(
@@ -107,7 +111,9 @@ export default function AppLaunch() {
     pullLatest?: boolean,
     env?: Record<string, string>,
     preRun?: string,
-    postRun?: string
+    postRun?: string,
+    container?: string,
+    containerArgs?: string
   ) => {
     if (!selectedEntryPoint) {
       return;
@@ -123,7 +129,9 @@ export default function AppLaunch() {
         pull_latest: pullLatest,
         env,
         pre_run: preRun,
-        post_run: postRun
+        post_run: postRun,
+        container,
+        container_args: containerArgs
       });
       const isService = selectedEntryPoint.type === 'service';
       toast.success(isService ? 'Service started' : 'Job submitted');
@@ -209,6 +217,8 @@ export default function AppLaunch() {
       ) : manifest && selectedEntryPoint ? (
         <AppLaunchForm
           entryPoint={selectedEntryPoint}
+          initialContainer={relaunchContainer}
+          initialContainerArgs={relaunchContainerArgs}
           initialEnv={relaunchEnv}
           initialExtraArgs={relaunchExtraArgs}
           initialPostRun={relaunchPostRun}
diff --git a/frontend/src/components/JobDetail.tsx b/frontend/src/components/JobDetail.tsx
index d8b01679..c1706d36 100644
--- a/frontend/src/components/JobDetail.tsx
+++ b/frontend/src/components/JobDetail.tsx
@@ -196,7 +196,9 @@ export default function JobDetail() {
         env: job.env,
         pre_run: job.pre_run,
         post_run: job.post_run,
-        pull_latest: job.pull_latest
+        pull_latest: job.pull_latest,
+        container: job.container,
+        container_args: job.container_args
       }
     });
   };
diff --git a/frontend/src/components/ui/AppsPage/AppLaunchForm.tsx b/frontend/src/components/ui/AppsPage/AppLaunchForm.tsx
index d11a7f44..d3e07e03 100644
--- a/frontend/src/components/ui/AppsPage/AppLaunchForm.tsx
+++ b/frontend/src/components/ui/AppsPage/AppLaunchForm.tsx
@@ -33,7 +33,9 @@ interface AppLaunchFormProps {
     pullLatest?: boolean,
     env?: Record<string, string>,
     preRun?: string,
-    postRun?: string
+    postRun?: string,
+    container?: string,
+    containerArgs?: string
   ) => Promise<void>;
   readonly submitting: boolean;
   readonly initialValues?: Record<string, unknown>;
@@ -43,6 +45,8 @@ interface AppLaunchFormProps {
   readonly initialPreRun?: string;
   readonly initialPostRun?: string;
   readonly initialPullLatest?: boolean;
+  readonly initialContainer?: string;
+  readonly initialContainerArgs?: string;
 }
 
 type EnvVar = { key: string; value: string };
@@ -478,7 +482,12 @@ function EnvironmentTabContent({
   postRun,
   setPostRun,
   openEnvSections,
-  setOpenEnvSections
+  setOpenEnvSections,
+  entryPoint,
+  containerImage,
+  setContainerImage,
+  containerArgs,
+  setContainerArgs
 }: {
   readonly envVars: EnvVar[];
   readonly setEnvVars: Dispatch<SetStateAction<EnvVar[]>>;
@@ -488,7 +497,15 @@ function EnvironmentTabContent({
   readonly setPostRun: Dispatch<SetStateAction<string>>;
   readonly openEnvSections: string[];
   readonly setOpenEnvSections: Dispatch<SetStateAction<string[]>>;
+  readonly entryPoint: AppEntryPoint;
+  readonly containerImage: string;
+  readonly setContainerImage: Dispatch<SetStateAction<string>>;
+  readonly containerArgs: string;
+  readonly setContainerArgs: Dispatch<SetStateAction<string>>;
 }) {
+  const inputClass =
+    'w-full p-2 text-foreground border rounded-sm focus:outline-none bg-background border-primary-light focus:border-primary';
+
   return (
     <Accordion
       onValueChange={
@@ -517,6 +534,50 @@ function EnvironmentTabContent({
           />
         </Accordion.Content>
       </Accordion.Item>
+
+      {entryPoint.container ? (
+        <Accordion.Item value="apptainer">
+          <Accordion.Trigger className="flex w-full items-center justify-between py-3 border-b border-primary-light">
+            <div className="text-foreground font-bold text-sm">Container</div>
+            <HiChevronDown
+              className={`h-4 w-4 text-secondary transition-transform ${
+                openEnvSections.includes('apptainer') ? 'rotate-180' : ''
+              }`}
+            />
+          </Accordion.Trigger>
+          <Accordion.Content className="pt-4 pb-2 pl-4">
+            <div className="space-y-4">
+              <div>
+                <label className="block text-foreground text-sm font-medium mb-1">
+                  Container Image
+                </label>
+                <input
+                  className={`max-w-md ${inputClass} font-mono text-sm`}
+                  onChange={e => setContainerImage(e.target.value)}
+                  placeholder="e.g. ghcr.io/org/image:tag"
+                  type="text"
+                  value={containerImage}
+                />
+              </div>
+              <div>
+                <label className="block text-foreground text-sm font-medium mb-1">
+                  Extra Apptainer Arguments
+                </label>
+                <Typography className="text-secondary mb-1" type="small">
+                  Additional flags passed to apptainer exec
+                </Typography>
+                <input
+                  className={`max-w-md ${inputClass} font-mono text-sm`}
+                  onChange={e => setContainerArgs(e.target.value)}
+                  placeholder="e.g. --nv"
+                  type="text"
+                  value={containerArgs}
+                />
+              </div>
+            </div>
+          </Accordion.Content>
+        </Accordion.Item>
+      ) : null}
     </Accordion>
   );
 }
@@ -596,7 +657,9 @@ export default function AppLaunchForm({
   initialEnv,
   initialPreRun,
   initialPostRun,
-  initialPullLatest
+  initialPullLatest,
+  initialContainer,
+  initialContainerArgs
 }: AppLaunchFormProps) {
   const { defaultExtraArgs } = usePreferencesContext();
   const clusterDefaultsQuery = useClusterDefaultsQuery();
@@ -653,9 +716,15 @@ export default function AppLaunchForm({
   const [postRun, setPostRun] = useState(
     initialPostRun ?? entryPoint.post_run ?? ''
   );
-  const [openEnvSections, setOpenEnvSections] = useState<string[]>([
-    'environment'
-  ]);
+  const [containerImage, setContainerImage] = useState(
+    initialContainer ?? entryPoint.container ?? ''
+  );
+  const [containerArgs, setContainerArgs] = useState(
+    initialContainerArgs ?? entryPoint.container_args ?? ''
+  );
+  const [openEnvSections, setOpenEnvSections] = useState<string[]>(
+    entryPoint.container ? ['environment', 'apptainer'] : ['environment']
+  );
   const [openClusterSections, setOpenClusterSections] = useState<string[]>([
     'resources',
     'submitOptions'
@@ -807,7 +876,9 @@ export default function AppLaunchForm({
       pullLatest,
       hasEnv ? envRecord : undefined,
       preRun.trim() || undefined,
-      postRun.trim() || undefined
+      postRun.trim() || undefined,
+      containerImage.trim() || undefined,
+      containerArgs.trim() || undefined
     );
   };
 
@@ -935,10 +1006,15 @@ export default function AppLaunchForm({
           </div>
 
           <EnvironmentTabContent
+            containerArgs={containerArgs}
+            containerImage={containerImage}
+            entryPoint={entryPoint}
             envVars={envVars}
             openEnvSections={openEnvSections}
             postRun={postRun}
             preRun={preRun}
+            setContainerArgs={setContainerArgs}
+            setContainerImage={setContainerImage}
             setEnvVars={setEnvVars}
             setOpenEnvSections={setOpenEnvSections}
             setPostRun={setPostRun}
diff --git a/frontend/src/shared.types.ts b/frontend/src/shared.types.ts
index 28661734..a923c084 100644
--- a/frontend/src/shared.types.ts
+++ b/frontend/src/shared.types.ts
@@ -118,6 +118,8 @@ type AppEntryPoint = {
   pre_run?: string;
   post_run?: string;
   conda_env?: string;
+  container?: string;
+  container_args?: string;
 };
 
 type AppManifest = {
@@ -160,6 +162,8 @@ type Job = {
   env?: Record<string, string>;
   pre_run?: string;
   post_run?: string;
+  container?: string;
+  container_args?: string;
   pull_latest: boolean;
   cluster_job_id?: string;
   service_url?: string;
@@ -180,6 +184,8 @@ type JobSubmitRequest = {
   env?: Record<string, string>;
   pre_run?: string;
   post_run?: string;
+  container?: string;
+  container_args?: string;
 };
 
 export type {
diff --git a/tests/test_apps.py b/tests/test_apps.py
index 23776248..a7fe1c5a 100644
--- a/tests/test_apps.py
+++ b/tests/test_apps.py
@@ -1,4 +1,4 @@
-"""Tests for apps module: miniforge requirement and conda_env support."""
+"""Tests for apps module: miniforge/apptainer requirements, conda_env, and container support."""
 
 import subprocess
 from unittest.mock import patch, MagicMock
@@ -7,7 +7,12 @@
 from pydantic import ValidationError
 
 from fileglancer.model import SUPPORTED_TOOLS, AppEntryPoint
-from fileglancer.apps import _TOOL_REGISTRY, verify_requirements
+from fileglancer.apps import (
+    _TOOL_REGISTRY,
+    verify_requirements,
+    _container_sif_name,
+    _build_container_script,
+)
 
 
 # --- Model tests ---
@@ -186,3 +191,168 @@ def test_conda_env_path_is_quoted(self, _make_entry_point):
 
         activation = f'conda activate {shlex.quote(ep2.conda_env)}'
         assert activation == "conda activate /opt/conda/envs/myenv"
+
+
+# --- Apptainer / Container tests ---
+
+class TestApptainerRequirement:
+    def test_apptainer_in_supported_tools(self):
+        assert "apptainer" in SUPPORTED_TOOLS
+
+    def test_apptainer_in_tool_registry(self):
+        assert "apptainer" in _TOOL_REGISTRY
+        entry = _TOOL_REGISTRY["apptainer"]
+        assert entry["version_args"] == ["apptainer", "--version"]
+        assert entry["version_pattern"] == r"apptainer version (\S+)"
+
+
+class TestContainerValidation:
+    def test_valid_container_url(self):
+        ep = AppEntryPoint(
+            id="t", name="T", command="echo",
+            container="ghcr.io/org/image:tag"
+        )
+        assert ep.container == "ghcr.io/org/image:tag"
+
+    def test_valid_docker_prefix(self):
+        ep = AppEntryPoint(
+            id="t", name="T", command="echo",
+            container="docker://ghcr.io/org/image:1.0"
+        )
+        assert ep.container == "docker://ghcr.io/org/image:1.0"
+
+    def test_none_is_allowed(self):
+        ep = AppEntryPoint(id="t", name="T", command="echo", container=None)
+        assert ep.container is None
+
+    def test_default_is_none(self):
+        ep = AppEntryPoint(id="t", name="T", command="echo")
+        assert ep.container is None
+
+    def test_rejects_shell_metacharacters(self):
+        with pytest.raises(ValidationError, match="forbidden characters"):
+            AppEntryPoint(
+                id="t", name="T", command="echo",
+                container="ghcr.io/org/image;rm -rf /"
+            )
+
+    def test_rejects_backtick(self):
+        with pytest.raises(ValidationError, match="forbidden characters"):
+            AppEntryPoint(
+                id="t", name="T", command="echo",
+                container="ghcr.io/`whoami`/image:tag"
+            )
+
+    def test_mutual_exclusion_with_conda(self):
+        with pytest.raises(ValidationError, match="mutually exclusive"):
+            AppEntryPoint(
+                id="t", name="T", command="echo",
+                conda_env="myenv",
+                container="ghcr.io/org/image:tag"
+            )
+
+    def test_bind_paths_requires_container(self):
+        with pytest.raises(ValidationError, match="bind_paths requires container"):
+            AppEntryPoint(
+                id="t", name="T", command="echo",
+                bind_paths=["/data"]
+            )
+
+    def test_bind_paths_with_container(self):
+        ep = AppEntryPoint(
+            id="t", name="T", command="echo",
+            container="ghcr.io/org/image:tag",
+            bind_paths=["/data", "/scratch"]
+        )
+        assert ep.bind_paths == ["/data", "/scratch"]
+
+    def test_bind_paths_rejects_metacharacters(self):
+        with pytest.raises(ValidationError, match="forbidden characters"):
+            AppEntryPoint(
+                id="t", name="T", command="echo",
+                container="ghcr.io/org/image:tag",
+                bind_paths=["/data;rm -rf /"]
+            )
+
+
+class TestContainerSifName:
+    def test_simple_url(self):
+        assert _container_sif_name("ghcr.io/org/image:1.0") == "ghcr.io_org_image_1.0.sif"
+
+    def test_docker_prefix_stripped(self):
+        assert _container_sif_name("docker://ghcr.io/org/image:tag") == "ghcr.io_org_image_tag.sif"
+
+    def test_nested_path(self):
+        result = _container_sif_name("godlovedc/lolcow")
+        assert result == "godlovedc_lolcow.sif"
+
+    def test_no_tag(self):
+        result = _container_sif_name("ghcr.io/org/image")
+        assert result == "ghcr.io_org_image.sif"
+
+
+class TestContainerScriptGeneration:
+    def test_basic_script(self):
+        script = _build_container_script(
+            container_url="ghcr.io/org/image:1.0",
+            command="python run.py",
+            work_dir="/home/user/.fileglancer/jobs/1-test-run",
+            bind_paths=[],
+        )
+        assert "apptainer pull" in script
+        assert "apptainer exec" in script
+        assert "docker://ghcr.io/org/image:1.0" in script
+        assert "ghcr.io_org_image_1.0.sif" in script
+        assert "python run.py" in script
+
+    def test_bind_mounts_included(self):
+        script = _build_container_script(
+            container_url="ghcr.io/org/image:1.0",
+            command="echo hello",
+            work_dir="/work",
+            bind_paths=["/data/input", "/data/output"],
+        )
+        assert "--bind /data/input" in script
+        assert "--bind /data/output" in script
+        assert "--bind /work" in script
+
+    def test_bind_mounts_deduplicated(self):
+        script = _build_container_script(
+            container_url="ghcr.io/org/image:1.0",
+            command="echo hello",
+            work_dir="/work",
+            bind_paths=["/work", "/data", "/data"],
+        )
+        # /work should only appear once in bind flags
+        assert script.count("--bind /work") == 1
+        assert script.count("--bind /data") == 1
+
+    def test_extra_args(self):
+        script = _build_container_script(
+            container_url="ghcr.io/org/image:1.0",
+            command="python run.py",
+            work_dir="/work",
+            bind_paths=[],
+            container_args="--nv",
+        )
+        assert "--nv" in script
+
+    def test_pull_conditional(self):
+        script = _build_container_script(
+            container_url="ghcr.io/org/image:1.0",
+            command="echo",
+            work_dir="/work",
+            bind_paths=[],
+        )
+        assert 'if [ ! -f "$SIF_PATH" ]' in script
+
+    def test_docker_prefix_not_doubled(self):
+        script = _build_container_script(
+            container_url="docker://ghcr.io/org/image:1.0",
+            command="echo",
+            work_dir="/work",
+            bind_paths=[],
+        )
+        # Should not have docker://docker://
+        assert "docker://docker://" not in script
+        assert "docker://ghcr.io/org/image:1.0" in script

From d495b78c20f9adaa6acf1a4bd4fbbf8dffd81632 Mon Sep 17 00:00:00 2001
From: Konrad Rokicki <rokickik@janelia.hhmi.org>
Date: Sat, 28 Feb 2026 19:26:25 -0500
Subject: [PATCH 15/20] move apptainer cache and add preference

---
 docs/AuthoringApps.md                         |   4 +-
 fileglancer/apps.py                           |  13 +-
 .../ui/PreferencesPage/JobOptions.tsx         | 120 ++++++++++++------
 frontend/src/contexts/PreferencesContext.tsx  |  18 +++
 frontend/src/queries/preferencesQueries.ts    |   5 +-
 5 files changed, 120 insertions(+), 40 deletions(-)

diff --git a/docs/AuthoringApps.md b/docs/AuthoringApps.md
index b9988fd9..575bac8e 100644
--- a/docs/AuthoringApps.md
+++ b/docs/AuthoringApps.md
@@ -318,13 +318,13 @@ runnables:
 
 When `container` is set, the generated script:
 
-1. Creates a SIF cache directory at `$APPTAINER_CACHEDIR` (defaults to `~/.apptainer/cache/fileglancer/`)
+1. Creates a SIF cache directory (defaults to `~/.fileglancer/apptainer_cache/`, configurable in Preferences)
 2. Pulls the image to a `.sif` file if not already cached
 3. Runs the command inside the container via `apptainer exec`
 
 ```bash
 # Apptainer container setup
-APPTAINER_CACHE_DIR="${APPTAINER_CACHEDIR:-$HOME/.apptainer/cache/fileglancer}"
+APPTAINER_CACHE_DIR=$HOME/.fileglancer/apptainer_cache
 mkdir -p "$APPTAINER_CACHE_DIR"
 SIF_PATH="$APPTAINER_CACHE_DIR/godlovedc_lolcow.sif"
 if [ ! -f "$SIF_PATH" ]; then
diff --git a/fileglancer/apps.py b/fileglancer/apps.py
index 6764beea..ba8d3f50 100644
--- a/fileglancer/apps.py
+++ b/fileglancer/apps.py
@@ -577,12 +577,16 @@ def _container_sif_name(container_url: str) -> str:
     return _CONTAINER_SIF_SAFE.sub('_', url) + ".sif"
 
 
+_DEFAULT_CONTAINER_CACHE_DIR = "$HOME/.fileglancer/apptainer_cache"
+
+
 def _build_container_script(
     container_url: str,
     command: str,
     work_dir: str,
     bind_paths: list[str],
     container_args: Optional[str] = None,
+    cache_dir: Optional[str] = None,
 ) -> str:
     """Build shell script for running a command inside an Apptainer container."""
     sif_name = _container_sif_name(container_url)
@@ -594,9 +598,11 @@ def _build_container_script(
 
     extra = f" {container_args}" if container_args else ""
 
+    resolved_dir = shlex.quote(cache_dir) if cache_dir else _DEFAULT_CONTAINER_CACHE_DIR
+
     lines = [
         "# Apptainer container setup",
-        'APPTAINER_CACHE_DIR="${APPTAINER_CACHEDIR:-$HOME/.apptainer/cache/fileglancer}"',
+        f'APPTAINER_CACHE_DIR={resolved_dir}',
         'mkdir -p "$APPTAINER_CACHE_DIR"',
         f'SIF_PATH="$APPTAINER_CACHE_DIR/{sif_name}"',
         'if [ ! -f "$SIF_PATH" ]; then',
@@ -683,6 +689,10 @@ async def submit_job(
         }
 
     with db.get_db_session(settings.db_url) as session:
+        # Read user's container cache dir preference
+        cache_dir_pref = db.get_user_preference(session, username, "apptainerCacheDir")
+        container_cache_dir = cache_dir_pref.get("value") if cache_dir_pref else None
+
         db_job = db.create_job(
             session=session,
             username=username,
@@ -773,6 +783,7 @@ async def submit_job(
             work_dir=str(work_dir),
             bind_paths=bind_paths,
             container_args=effective_container_args,
+            cache_dir=container_cache_dir,
         )
 
     if env_lines:
diff --git a/frontend/src/components/ui/PreferencesPage/JobOptions.tsx b/frontend/src/components/ui/PreferencesPage/JobOptions.tsx
index f6317eff..ac2575d6 100644
--- a/frontend/src/components/ui/PreferencesPage/JobOptions.tsx
+++ b/frontend/src/components/ui/PreferencesPage/JobOptions.tsx
@@ -6,18 +6,25 @@ import toast from 'react-hot-toast';
 import { usePreferencesContext } from '@/contexts/PreferencesContext';
 
 export default function JobOptions() {
-  const { defaultExtraArgs, updateDefaultExtraArgs } = usePreferencesContext();
+  const {
+    defaultExtraArgs,
+    updateDefaultExtraArgs,
+    apptainerCacheDir,
+    updateApptainerCacheDir
+  } = usePreferencesContext();
 
-  const [localValue, setLocalValue] = useState(defaultExtraArgs);
-  const [saving, setSaving] = useState(false);
+  const [localExtraArgs, setLocalExtraArgs] = useState(defaultExtraArgs);
+  const [savingExtraArgs, setSavingExtraArgs] = useState(false);
+  const isExtraArgsDirty = localExtraArgs !== defaultExtraArgs;
 
-  // Track whether the local value differs from the saved preference
-  const isDirty = localValue !== defaultExtraArgs;
+  const [localCacheDir, setLocalCacheDir] = useState(apptainerCacheDir);
+  const [savingCacheDir, setSavingCacheDir] = useState(false);
+  const isCacheDirDirty = localCacheDir !== apptainerCacheDir;
 
-  const handleSave = async () => {
-    setSaving(true);
-    const result = await updateDefaultExtraArgs(localValue.trim());
-    setSaving(false);
+  const handleSaveExtraArgs = async () => {
+    setSavingExtraArgs(true);
+    const result = await updateDefaultExtraArgs(localExtraArgs.trim());
+    setSavingExtraArgs(false);
     if (result.success) {
       toast.success('Default extra arguments saved');
     } else {
@@ -25,36 +32,77 @@ export default function JobOptions() {
     }
   };
 
+  const handleSaveCacheDir = async () => {
+    setSavingCacheDir(true);
+    const result = await updateApptainerCacheDir(localCacheDir.trim());
+    setSavingCacheDir(false);
+    if (result.success) {
+      toast.success('Container cache directory saved');
+    } else {
+      toast.error(result.error);
+    }
+  };
+
   return (
     <div>
       <Typography className="font-semibold">Jobs</Typography>
-      <div className="pl-4 mt-2">
-        <label
-          className="block text-foreground text-sm mb-1"
-          htmlFor="default-extra-args"
-        >
-          Default extra arguments
-        </label>
-        <Typography className="text-secondary mb-2" type="small">
-          Additional CLI arguments appended to every job submit command. Can be
-          overridden per job on the Cluster tab.
-        </Typography>
-        <input
-          className="max-w-md w-full p-2 text-foreground border rounded-sm focus:outline-none bg-background border-primary-light focus:border-primary font-mono text-sm"
-          id="default-extra-args"
-          onChange={e => setLocalValue(e.target.value)}
-          placeholder="e.g. -P your_project"
-          type="text"
-          value={localValue}
-        />
-        <button
-          className="mt-2 block px-3 py-1 text-sm rounded bg-primary text-white hover:bg-primary-dark transition-colors disabled:opacity-50"
-          disabled={!isDirty || saving}
-          onClick={handleSave}
-          type="button"
-        >
-          {saving ? 'Saving...' : 'Save'}
-        </button>
+      <div className="pl-4 mt-2 space-y-6">
+        <div>
+          <label
+            className="block text-foreground text-sm mb-1"
+            htmlFor="default-extra-args"
+          >
+            Default extra arguments
+          </label>
+          <Typography className="text-secondary mb-2" type="small">
+            Additional CLI arguments appended to every job submit command. Can
+            be overridden per job on the Cluster tab.
+          </Typography>
+          <input
+            className="max-w-md w-full p-2 text-foreground border rounded-sm focus:outline-none bg-background border-primary-light focus:border-primary font-mono text-sm"
+            id="default-extra-args"
+            onChange={e => setLocalExtraArgs(e.target.value)}
+            placeholder="e.g. -P your_project"
+            type="text"
+            value={localExtraArgs}
+          />
+          <button
+            className="mt-2 block px-3 py-1 text-sm rounded bg-primary text-white hover:bg-primary-dark transition-colors disabled:opacity-50"
+            disabled={!isExtraArgsDirty || savingExtraArgs}
+            onClick={handleSaveExtraArgs}
+            type="button"
+          >
+            {savingExtraArgs ? 'Saving...' : 'Save'}
+          </button>
+        </div>
+
+        <div>
+          <label
+            className="block text-foreground text-sm mb-1"
+            htmlFor="apptainer-cache-dir"
+          >
+            Container cache directory
+          </label>
+          <Typography className="text-secondary mb-2" type="small">
+            Directory where Apptainer SIF images are cached. Defaults to <code>~/.fileglancer/apptainer_cache</code> if not set.
+          </Typography>
+          <input
+            className="max-w-md w-full p-2 text-foreground border rounded-sm focus:outline-none bg-background border-primary-light focus:border-primary font-mono text-sm"
+            id="apptainer-cache-dir"
+            onChange={e => setLocalCacheDir(e.target.value)}
+            placeholder="~/.fileglancer/apptainer_cache"
+            type="text"
+            value={localCacheDir}
+          />
+          <button
+            className="mt-2 block px-3 py-1 text-sm rounded bg-primary text-white hover:bg-primary-dark transition-colors disabled:opacity-50"
+            disabled={!isCacheDirDirty || savingCacheDir}
+            onClick={handleSaveCacheDir}
+            type="button"
+          >
+            {savingCacheDir ? 'Saving...' : 'Save'}
+          </button>
+        </div>
       </div>
     </div>
   );
diff --git a/frontend/src/contexts/PreferencesContext.tsx b/frontend/src/contexts/PreferencesContext.tsx
index 3c75c28d..e1c4e8d9 100644
--- a/frontend/src/contexts/PreferencesContext.tsx
+++ b/frontend/src/contexts/PreferencesContext.tsx
@@ -54,6 +54,7 @@ type PreferencesContextType = {
   isFilteredByGroups: boolean;
   showTutorial: boolean;
   defaultExtraArgs: string;
+  apptainerCacheDir: string;
 
   // Favorites
   zoneFavorites: Zone[];
@@ -82,6 +83,7 @@ type PreferencesContextType = {
   toggleFilterByGroups: () => Promise<Result<void>>;
   toggleShowTutorial: () => Promise<Result<void>>;
   updateDefaultExtraArgs: (args: string) => Promise<Result<void>>;
+  updateApptainerCacheDir: (dir: string) => Promise<Result<void>>;
   handleFavoriteChange: (
     item: Zone | FileSharePath | FolderFavorite,
     type: 'zone' | 'fileSharePath' | 'folder'
@@ -258,6 +260,20 @@ export const PreferencesProvider = ({
     }
   };
 
+  const updateApptainerCacheDir = async (
+    dir: string
+  ): Promise<Result<void>> => {
+    try {
+      await updatePreferenceMutation.mutateAsync({
+        key: 'apptainerCacheDir',
+        value: dir
+      });
+      return createSuccess(undefined);
+    } catch (error) {
+      return handleError(error);
+    }
+  };
+
   function updatePreferenceList<T>(
     key: string,
     itemToUpdate: T,
@@ -517,6 +533,7 @@ export const PreferencesProvider = ({
     isFilteredByGroups: preferencesQuery.data?.isFilteredByGroups ?? true,
     showTutorial: preferencesQuery.data?.showTutorial ?? true,
     defaultExtraArgs: preferencesQuery.data?.defaultExtraArgs || '',
+    apptainerCacheDir: preferencesQuery.data?.apptainerCacheDir || '',
 
     // Favorites
     zoneFavorites: preferencesQuery.data?.zoneFavorites || [],
@@ -544,6 +561,7 @@ export const PreferencesProvider = ({
     toggleFilterByGroups,
     toggleShowTutorial,
     updateDefaultExtraArgs,
+    updateApptainerCacheDir,
     handleFavoriteChange,
     handleContextMenuFavorite
   };
diff --git a/frontend/src/queries/preferencesQueries.ts b/frontend/src/queries/preferencesQueries.ts
index a1aa9bec..57f50815 100644
--- a/frontend/src/queries/preferencesQueries.ts
+++ b/frontend/src/queries/preferencesQueries.ts
@@ -39,6 +39,7 @@ type PreferencesApiResponse = {
   isFilteredByGroups?: { value: boolean };
   showTutorial?: { value: boolean };
   defaultExtraArgs?: { value: string };
+  apptainerCacheDir?: { value: string };
   zone?: { value: ZonePreference[] };
   fileSharePath?: { value: FileSharePathPreference[] };
   folder?: { value: FolderPreference[] };
@@ -70,6 +71,7 @@ export type PreferencesQueryData = {
   isFilteredByGroups: boolean;
   showTutorial: boolean;
   defaultExtraArgs: string;
+  apptainerCacheDir: string;
 };
 
 /**
@@ -235,7 +237,8 @@ const createTransformPreferences = (
         rawData.useLegacyMultichannelApproach?.value || false,
       isFilteredByGroups: rawData.isFilteredByGroups?.value ?? true,
       showTutorial: rawData.showTutorial?.value ?? true,
-      defaultExtraArgs: rawData.defaultExtraArgs?.value || ''
+      defaultExtraArgs: rawData.defaultExtraArgs?.value || '',
+      apptainerCacheDir: rawData.apptainerCacheDir?.value || ''
     };
   };
 };

From 8d8e6de19b413c723afb26d0350b6a8158697a1e Mon Sep 17 00:00:00 2001
From: Konrad Rokicki <rokickik@janelia.hhmi.org>
Date: Sun, 1 Mar 2026 06:51:39 -0500
Subject: [PATCH 16/20] added nextflow to supported tools

---
 docs/AuthoringApps.md | 2 +-
 fileglancer/apps.py   | 4 ++++
 fileglancer/model.py  | 2 +-
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/docs/AuthoringApps.md b/docs/AuthoringApps.md
index 575bac8e..95894346 100644
--- a/docs/AuthoringApps.md
+++ b/docs/AuthoringApps.md
@@ -67,7 +67,7 @@ requirements:
   - miniforge
 ```
 
-**Supported tools:** `pixi`, `npm`, `maven`, `miniforge`, `apptainer`
+**Supported tools:** `pixi`, `npm`, `maven`, `miniforge`, `apptainer`, `nextflow`
 
 **Supported version operators:** `>=`, `<=`, `!=`, `==`, `>`, `<`
 
diff --git a/fileglancer/apps.py b/fileglancer/apps.py
index ba8d3f50..3f920906 100644
--- a/fileglancer/apps.py
+++ b/fileglancer/apps.py
@@ -196,6 +196,10 @@ async def fetch_app_manifest(url: str, manifest_path: str = "") -> AppManifest:
         "version_args": ["apptainer", "--version"],
         "version_pattern": r"apptainer version (\S+)",
     },
+    "nextflow": {
+        "version_args": ["nextflow", "-version"],
+        "version_pattern": r"version (\S+)",
+    },
 }
 
 _REQ_PATTERN = re.compile(r"^([a-zA-Z][a-zA-Z0-9_-]*)\s*((?:>=|<=|!=|==|>|<)\s*\S+)?$")
diff --git a/fileglancer/model.py b/fileglancer/model.py
index 2378b7fa..0e2037d7 100644
--- a/fileglancer/model.py
+++ b/fileglancer/model.py
@@ -483,7 +483,7 @@ def check_conda_container_exclusive(self):
         return self
 
 
-SUPPORTED_TOOLS = {"pixi", "npm", "maven", "miniforge", "apptainer"}
+SUPPORTED_TOOLS = {"pixi", "npm", "maven", "miniforge", "apptainer", "nextflow"}
 
 _SHELL_METACHAR_PATTERN = re.compile(r'[;&|`$(){}!<>\n\r]')
 _CONDA_ENV_NAME_PATTERN = re.compile(r'^[a-zA-Z0-9_.-]+$')

From 886fcf4e3ad7c37e4d6ccc0c5aa657c619e9aef7 Mon Sep 17 00:00:00 2001
From: Konrad Rokicki <rokickik@janelia.hhmi.org>
Date: Sun, 1 Mar 2026 07:19:21 -0500
Subject: [PATCH 17/20] extra paths, fixed updates

---
 docs/AuthoringApps.md               | 27 +++++++++++++++++++++++++++
 docs/config.yaml.template           |  3 +++
 fileglancer/apps.py                 | 19 +++++++++++++++++--
 fileglancer/model.py                |  1 +
 fileglancer/server.py               | 26 ++++++++++++++++++++++----
 fileglancer/settings.py             |  1 +
 frontend/src/queries/appsQueries.ts |  4 ++--
 frontend/src/shared.types.ts        |  1 +
 tests/test_apps.py                  |  6 +++---
 9 files changed, 77 insertions(+), 11 deletions(-)

diff --git a/docs/AuthoringApps.md b/docs/AuthoringApps.md
index 95894346..72a1f7d5 100644
--- a/docs/AuthoringApps.md
+++ b/docs/AuthoringApps.md
@@ -529,6 +529,33 @@ Fileglancer exports the following environment variables in every job script:
 
 These are available to `pre_run` scripts, the main command, and `post_run` scripts.
 
+## Server Configuration for Apps
+
+Some aspects of app execution are controlled by the Fileglancer server's `config.yaml`, not by individual app manifests. These settings are managed by the system administrator.
+
+### Extra Paths (`extra_paths`)
+
+The `extra_paths` cluster setting lets administrators add directories to `$PATH` for all job scripts. This is useful for making tools like `nextflow`, `pixi`, or `apptainer` available without requiring users to configure their own environments.
+
+```yaml
+cluster:
+  extra_paths:
+    - /opt/nextflow/bin
+    - /opt/pixi/bin
+    - /usr/local/apptainer/bin
+```
+
+These paths are:
+
+1. **Appended to `$PATH` in every generated job script** — the user's own `$PATH` entries take precedence
+2. **Used when verifying tool requirements** — so `requirements: [nextflow]` can find `/opt/nextflow/bin/nextflow` even if it's not on the server process's default `$PATH`
+
+### Container Cache Directory
+
+By default, Apptainer container images (SIF files) are cached at `~/.fileglancer/apptainer_cache/`. Users can override this per-user in the Preferences page under "Container cache directory".
+
+See the [config.yaml.template](config.yaml.template) for all available cluster settings.
+
 ## Full Example
 
 ```yaml
diff --git a/docs/config.yaml.template b/docs/config.yaml.template
index 9b9fe167..f943ed09 100644
--- a/docs/config.yaml.template
+++ b/docs/config.yaml.template
@@ -149,3 +149,6 @@ cluster:
 #     - "your_project"
 #   script_prologue:            # Commands to run before each job
 #     - "module load java/11"
+#   extra_paths:                # Paths appended to $PATH in every job script
+#     - /opt/nextflow/bin       # and used when verifying tool requirements
+#     - /opt/pixi/bin
diff --git a/fileglancer/apps.py b/fileglancer/apps.py
index 3f920906..a594367e 100644
--- a/fileglancer/apps.py
+++ b/fileglancer/apps.py
@@ -205,6 +205,13 @@ async def fetch_app_manifest(url: str, manifest_path: str = "") -> AppManifest:
 _REQ_PATTERN = re.compile(r"^([a-zA-Z][a-zA-Z0-9_-]*)\s*((?:>=|<=|!=|==|>|<)\s*\S+)?$")
 
 
+def _augmented_path(extra_paths: list[str]) -> str:
+    """Build a PATH string with extra_paths appended (user's PATH takes precedence)."""
+    if not extra_paths:
+        return os.environ.get("PATH", "")
+    return os.environ.get("PATH", "") + os.pathsep + os.pathsep.join(extra_paths)
+
+
 def verify_requirements(requirements: list[str]):
     """Verify that all required tools are available and meet version constraints.
 
@@ -213,6 +220,10 @@ def verify_requirements(requirements: list[str]):
     if not requirements:
         return
 
+    settings = get_settings()
+    search_path = _augmented_path(settings.cluster.extra_paths)
+    env = {**os.environ, "PATH": search_path} if settings.cluster.extra_paths else None
+
     errors = []
 
     for req in requirements:
@@ -225,11 +236,11 @@ def verify_requirements(requirements: list[str]):
         version_spec = match.group(2)
 
         # Check tool exists on PATH
-        if shutil.which(tool) is None:
+        if shutil.which(tool, path=search_path) is None:
             # For maven, the binary is 'mvn' not 'maven'
             registry_entry = _TOOL_REGISTRY.get(tool)
             binary = registry_entry["version_args"][0] if registry_entry else tool
-            if binary != tool and shutil.which(binary) is not None:
+            if binary != tool and shutil.which(binary, path=search_path) is not None:
                 pass  # binary found under alternate name
             else:
                 errors.append(f"Required tool '{tool}' is not installed or not on PATH")
@@ -245,6 +256,7 @@ def verify_requirements(requirements: list[str]):
                 result = subprocess.run(
                     registry_entry["version_args"],
                     capture_output=True, text=True, timeout=10,
+                    env=env,
                 )
                 output = result.stdout.strip() or result.stderr.strip()
                 ver_match = re.search(registry_entry["version_pattern"], output)
@@ -754,6 +766,9 @@ async def submit_job(
         "unset PIXI_PROJECT_MANIFEST",
         f"export FG_WORK_DIR={shlex.quote(str(work_dir))}",
     ]
+    if settings.cluster.extra_paths:
+        path_suffix = os.pathsep.join(shlex.quote(p) for p in settings.cluster.extra_paths)
+        preamble_lines.append(f"export PATH=$PATH:{path_suffix}")
     if entry_point.type == "service":
         preamble_lines.append('export SERVICE_URL_PATH="$FG_WORK_DIR/service_url"')
     preamble_lines.append(f'cd "$FG_WORK_DIR/{cd_suffix}"')
diff --git a/fileglancer/model.py b/fileglancer/model.py
index 0e2037d7..56712f40 100644
--- a/fileglancer/model.py
+++ b/fileglancer/model.py
@@ -522,6 +522,7 @@ class UserApp(BaseModel):
     name: str = Field(description="App name from manifest")
     description: Optional[str] = Field(description="App description from manifest", default=None)
     added_at: datetime = Field(description="When the app was added")
+    updated_at: Optional[datetime] = Field(description="When the app was last updated", default=None)
     manifest: Optional[AppManifest] = Field(description="Cached manifest data", default=None)
 
 
diff --git a/fileglancer/server.py b/fileglancer/server.py
index c46d728b..acc5f107 100644
--- a/fileglancer/server.py
+++ b/fileglancer/server.py
@@ -1492,6 +1492,7 @@ async def get_user_apps(username: str = Depends(get_current_user)):
                 name=app_entry.get("name", "Unknown"),
                 description=app_entry.get("description"),
                 added_at=app_entry.get("added_at", datetime.now(UTC).isoformat()),
+                updated_at=app_entry.get("updated_at"),
             )
             # Try to fetch manifest from local clone
             try:
@@ -1590,30 +1591,47 @@ async def remove_user_app(url: str = Query(..., description="URL of the app to r
 
         return {"message": "App removed"}
 
-    @app.post("/api/apps/update", response_model=AppManifest,
+    @app.post("/api/apps/update", response_model=UserApp,
               description="Pull latest code and re-read the manifest for an app")
     async def update_user_app(body: ManifestFetchRequest,
                               username: str = Depends(get_current_user)):
         try:
             await apps_module._ensure_repo_cache(body.url, pull=True)
+        except Exception as e:
+            raise HTTPException(status_code=400, detail=f"Failed to pull latest code: {str(e)}")
+
+        try:
             manifest = await apps_module.fetch_app_manifest(body.url, body.manifest_path)
         except ValueError as e:
             raise HTTPException(status_code=404, detail=str(e))
         except Exception as e:
-            raise HTTPException(status_code=400, detail=f"Failed to update app: {str(e)}")
+            raise HTTPException(status_code=400, detail=f"Failed to read manifest after update: {str(e)}")
 
-        # Update stored name/description from refreshed manifest
+        now = datetime.now(UTC)
+
+        # Update stored name/description/updated_at from refreshed manifest
         with db.get_db_session(settings.db_url) as session:
             pref = db.get_user_preference(session, username, "apps")
             app_list = pref.get("apps", []) if pref else []
+            added_at = now  # fallback
             for entry in app_list:
                 if entry["url"] == body.url and entry.get("manifest_path", "") == body.manifest_path:
                     entry["name"] = manifest.name
                     entry["description"] = manifest.description
+                    entry["updated_at"] = now.isoformat()
+                    added_at = entry.get("added_at", now.isoformat())
                     break
             db.set_user_preference(session, username, "apps", {"apps": app_list})
 
-        return manifest
+        return UserApp(
+            url=body.url,
+            manifest_path=body.manifest_path,
+            name=manifest.name,
+            description=manifest.description,
+            added_at=added_at,
+            updated_at=now,
+            manifest=manifest,
+        )
 
     @app.post("/api/apps/validate-paths", response_model=PathValidationResponse,
               description="Validate file/directory paths for app parameters")
diff --git a/fileglancer/settings.py b/fileglancer/settings.py
index 149a42d3..29c1ee16 100644
--- a/fileglancer/settings.py
+++ b/fileglancer/settings.py
@@ -32,6 +32,7 @@ class ClusterSettings(BaseModel):
     completed_retention_minutes: float = 10.0
     command_timeout: float = 100.0
     suppress_job_email: bool = True
+    extra_paths: List[str] = []
 
 
 class Settings(BaseSettings):
diff --git a/frontend/src/queries/appsQueries.ts b/frontend/src/queries/appsQueries.ts
index 9bf4ec11..4c167d22 100644
--- a/frontend/src/queries/appsQueries.ts
+++ b/frontend/src/queries/appsQueries.ts
@@ -101,7 +101,7 @@ export async function validatePaths(
 }
 
 export function useUpdateAppMutation(): UseMutationResult<
-  AppManifest,
+  UserApp,
   Error,
   { url: string; manifest_path: string }
 > {
@@ -122,7 +122,7 @@ export function useUpdateAppMutation(): UseMutationResult<
       if (!response.ok) {
         throwResponseNotOkError(response, data);
       }
-      return data as AppManifest;
+      return data as UserApp;
     },
     onSuccess: () => {
       queryClient.invalidateQueries({ queryKey: appsQueryKeys.all });
diff --git a/frontend/src/shared.types.ts b/frontend/src/shared.types.ts
index a923c084..36f181ff 100644
--- a/frontend/src/shared.types.ts
+++ b/frontend/src/shared.types.ts
@@ -137,6 +137,7 @@ type UserApp = {
   name: string;
   description?: string;
   added_at: string;
+  updated_at?: string;
   manifest?: AppManifest;
 };
 
diff --git a/tests/test_apps.py b/tests/test_apps.py
index a7fe1c5a..89c2184d 100644
--- a/tests/test_apps.py
+++ b/tests/test_apps.py
@@ -80,7 +80,7 @@ class TestVerifyRequirementsMiniforge:
     @patch("fileglancer.apps.shutil.which")
     def test_miniforge_found_via_conda(self, mock_which):
         """miniforge binary doesn't exist, but conda does — should pass."""
-        def which_side_effect(name):
+        def which_side_effect(name, **kwargs):
             if name == "miniforge":
                 return None
             if name == "conda":
@@ -100,7 +100,7 @@ def test_miniforge_not_found(self, mock_which):
     @patch("fileglancer.apps.subprocess.run")
     @patch("fileglancer.apps.shutil.which")
     def test_miniforge_version_check(self, mock_which, mock_run):
-        def which_side_effect(name):
+        def which_side_effect(name, **kwargs):
             if name == "miniforge":
                 return None
             if name == "conda":
@@ -116,7 +116,7 @@ def which_side_effect(name):
     @patch("fileglancer.apps.subprocess.run")
     @patch("fileglancer.apps.shutil.which")
     def test_miniforge_version_too_old(self, mock_which, mock_run):
-        def which_side_effect(name):
+        def which_side_effect(name, **kwargs):
             if name == "miniforge":
                 return None
             if name == "conda":

From 30325140c5993a98040a676d176a989fc6f1f7e7 Mon Sep 17 00:00:00 2001
From: Konrad Rokicki <rokickik@janelia.hhmi.org>
Date: Sun, 1 Mar 2026 07:35:07 -0500
Subject: [PATCH 18/20] fixed output refresh

---
 frontend/src/components/JobDetail.tsx              |  5 +++--
 .../src/components/ui/AppsPage/AppLaunchForm.tsx   | 14 +++++++++++++-
 frontend/src/queries/jobsQueries.ts                | 10 ++++++----
 3 files changed, 22 insertions(+), 7 deletions(-)

diff --git a/frontend/src/components/JobDetail.tsx b/frontend/src/components/JobDetail.tsx
index c1706d36..429c3dd3 100644
--- a/frontend/src/components/JobDetail.tsx
+++ b/frontend/src/components/JobDetail.tsx
@@ -145,9 +145,10 @@ export default function JobDetail() {
 
   const id = jobId ? parseInt(jobId) : 0;
   const jobQuery = useJobQuery(id);
+  const jobStatus = jobQuery.data?.status;
   const scriptQuery = useJobFileQuery(id, 'script');
-  const stdoutQuery = useJobFileQuery(id, 'stdout');
-  const stderrQuery = useJobFileQuery(id, 'stderr');
+  const stdoutQuery = useJobFileQuery(id, 'stdout', jobStatus);
+  const stderrQuery = useJobFileQuery(id, 'stderr', jobStatus);
   const cancelMutation = useCancelJobMutation();
 
   const isService = jobQuery.data?.entry_point_type === 'service';
diff --git a/frontend/src/components/ui/AppsPage/AppLaunchForm.tsx b/frontend/src/components/ui/AppsPage/AppLaunchForm.tsx
index d3e07e03..f34c9a4c 100644
--- a/frontend/src/components/ui/AppsPage/AppLaunchForm.tsx
+++ b/frontend/src/components/ui/AppsPage/AppLaunchForm.tsx
@@ -1,4 +1,4 @@
-import { useState } from 'react';
+import { useEffect, useState } from 'react';
 import type { Dispatch, SetStateAction } from 'react';
 
 import { Accordion, Button, Tabs, Typography } from '@material-tailwind/react';
@@ -702,6 +702,18 @@ export default function AppLaunchForm({
   );
   const [extraArgs, setExtraArgs] = useState<string>(resolvedExtraArgs);
 
+  // Update extraArgs when async data (preferences or cluster defaults) arrives,
+  // but only if not a relaunch and the user hasn't modified the field yet
+  useEffect(() => {
+    if (externalExtraArgs !== undefined) {
+      return; // relaunch value takes priority, don't overwrite
+    }
+    const resolved = defaultExtraArgs || configExtraArgs;
+    if (resolved) {
+      setExtraArgs(prev => (prev === '' ? resolved : prev));
+    }
+  }, [defaultExtraArgs, configExtraArgs, externalExtraArgs]);
+
   // Environment tab state — relaunch values override entry point defaults
   const [envVars, setEnvVars] = useState<EnvVar[]>(() => {
     const source = initialEnv ?? entryPoint.env;
diff --git a/frontend/src/queries/jobsQueries.ts b/frontend/src/queries/jobsQueries.ts
index 87b8ed10..3c8a51ab 100644
--- a/frontend/src/queries/jobsQueries.ts
+++ b/frontend/src/queries/jobsQueries.ts
@@ -140,14 +140,16 @@ export function useJobQuery(jobId: number): UseQueryResult<Job, Error> {
 
 export function useJobFileQuery(
   jobId: number,
-  fileType: string
+  fileType: string,
+  jobStatus?: string
 ): UseQueryResult<string | null, Error> {
+  const isActive = jobStatus === 'PENDING' || jobStatus === 'RUNNING';
   return useQuery({
     queryKey: [...jobsQueryKeys.detail(jobId), 'file', fileType],
     queryFn: ({ signal }) => fetchJobFile(jobId, fileType, signal),
-    refetchInterval: query => {
-      // Only auto-refresh if file doesn't exist yet (null) - it may appear later
-      return query.state.data === null ? 10000 : false;
+    refetchInterval: () => {
+      // Auto-refresh while job is active, or if file doesn't exist yet
+      return isActive ? 5000 : false;
     }
   });
 }

From fefcd9530b6be8476bcc19b3719d83db929d3249 Mon Sep 17 00:00:00 2001
From: Konrad Rokicki <rokickik@janelia.hhmi.org>
Date: Sun, 1 Mar 2026 10:08:44 -0500
Subject: [PATCH 19/20] add positional args last

---
 fileglancer/apps.py | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/fileglancer/apps.py b/fileglancer/apps.py
index a594367e..0b4e3040 100644
--- a/fileglancer/apps.py
+++ b/fileglancer/apps.py
@@ -391,29 +391,29 @@ def build_command(entry_point: AppEntryPoint, parameters: dict) -> str:
     # Start with the base command
     parts = [entry_point.command]
 
-    # Pass 1: Positional args in declaration order
+    # Pass 1: Flagged args in declaration order
     for param in flat_params:
-        if param.flag is not None:
+        if param.flag is None:
             continue
         if param.key not in effective:
             continue
         p, value = effective[param.key]
         validated = _validate_parameter_value(p, value)
-        parts.append(shlex.quote(validated))
+        if p.type == "boolean":
+            if value is True:
+                parts.append(p.flag)
+        else:
+            parts.append(f"{p.flag} {shlex.quote(validated)}")
 
-    # Pass 2: Flagged args in declaration order
+    # Pass 2: Positional args in declaration order
     for param in flat_params:
-        if param.flag is None:
+        if param.flag is not None:
             continue
         if param.key not in effective:
             continue
         p, value = effective[param.key]
         validated = _validate_parameter_value(p, value)
-        if p.type == "boolean":
-            if value is True:
-                parts.append(p.flag)
-        else:
-            parts.append(f"{p.flag} {shlex.quote(validated)}")
+        parts.append(shlex.quote(validated))
 
     return (" \\\n  ").join(parts)
 
@@ -840,7 +840,7 @@ async def submit_job(
         db_job = db.get_job(session, job_id, username)
         session.expunge(db_job)
 
-    logger.info(f"Job {db_job.id} submitted for user {username} in {work_dir}: {command}")
+    logger.info(f"Job {db_job.id} submitted for user {username} in {work_dir}")
     return db_job
 
 

From 42b5acfcc1ad2daf24d555182c11787c24d44e17 Mon Sep 17 00:00:00 2001
From: Konrad Rokicki <rokickik@janelia.hhmi.org>
Date: Sun, 1 Mar 2026 10:38:25 -0500
Subject: [PATCH 20/20] fix lint errors

---
 frontend/src/components/ui/PreferencesPage/JobOptions.tsx | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/frontend/src/components/ui/PreferencesPage/JobOptions.tsx b/frontend/src/components/ui/PreferencesPage/JobOptions.tsx
index ac2575d6..adc82b3f 100644
--- a/frontend/src/components/ui/PreferencesPage/JobOptions.tsx
+++ b/frontend/src/components/ui/PreferencesPage/JobOptions.tsx
@@ -84,7 +84,8 @@ export default function JobOptions() {
             Container cache directory
           </label>
           <Typography className="text-secondary mb-2" type="small">
-            Directory where Apptainer SIF images are cached. Defaults to <code>~/.fileglancer/apptainer_cache</code> if not set.
+            Directory where Apptainer SIF images are cached. Defaults to{' '}
+            <code>~/.fileglancer/apptainer_cache</code> if not set.
           </Typography>
           <input
             className="max-w-md w-full p-2 text-foreground border rounded-sm focus:outline-none bg-background border-primary-light focus:border-primary font-mono text-sm"