diff --git a/src/org/labkey/targetedms/SkylineDocImporter.java b/src/org/labkey/targetedms/SkylineDocImporter.java
index 5e6f30648..004e7fa4d 100644
--- a/src/org/labkey/targetedms/SkylineDocImporter.java
+++ b/src/org/labkey/targetedms/SkylineDocImporter.java
@@ -71,6 +71,7 @@
 import org.labkey.targetedms.query.ReplicateManager;
 import org.labkey.targetedms.query.RepresentativeStateManager;
 import org.labkey.targetedms.query.SkylineListManager;
+import org.labkey.vfs.FileLike;
 
 import javax.xml.stream.XMLStreamException;
 import java.io.ByteArrayInputStream;
@@ -239,17 +240,17 @@ public TargetedMSRun importRun(RunInfo runInfo, PipelineJob job) throws IOExcept
 
         try
         {
-            File inputFile = getInputFile();
+            FileLike inputFile = getInputFile();
             if (null == inputFile)
                 throw new FileNotFoundException();
 
             // Set the size of the Skyline document (.sky.zip) file.
-            run.setDocumentSize(Files.size(inputFile.toPath()));
+            run.setDocumentSize(inputFile.getSize());
             saveRunDocumentSize(run);
 
             updateRunStatus(IMPORT_STARTED);
             _log.info("Starting to import Skyline document from " + run.getFileName());
-            importSkylineDoc(run, inputFile);
+            importSkylineDoc(run, inputFile.toNioPathForRead().toFile());
             _log.info("Completed import of Skyline document from " + run.getFileName());
 
             updateRunStatus(IMPORT_SUCCEEDED, STATUS_SUCCESS);
@@ -2725,10 +2726,10 @@ private RegressionFit getRegressionFit(QuantificationSettings quantificationSett
     }
 
     @Nullable
-    private File getInputFile()
+    private FileLike getInputFile()
     {
         if (_expData.hasFileScheme())
-            return _expData.getFile();
+            return _expData.getFileLike();
 
         if (null == _pipeRoot || null == _localDirectory)
             return null;
diff --git a/src/org/labkey/targetedms/chromlib/ChromatogramLibraryUtils.java b/src/org/labkey/targetedms/chromlib/ChromatogramLibraryUtils.java
index b6ebe713e..5a39d9823 100644
--- a/src/org/labkey/targetedms/chromlib/ChromatogramLibraryUtils.java
+++ b/src/org/labkey/targetedms/chromlib/ChromatogramLibraryUtils.java
@@ -33,6 +33,7 @@
 import org.labkey.targetedms.TargetedMSManager;
 import org.labkey.targetedms.TargetedMSRun;
 import org.labkey.targetedms.query.ConflictResultsManager;
+import org.labkey.vfs.FileLike;
 import org.sqlite.SQLiteConfig;
 
 import java.io.File;
@@ -182,14 +183,14 @@ public static Integer parseChromLibRevision(@NotNull String chromLibFileName)
         return null;
     }
 
-    public static Path getChromLibTempFile(Container container, LocalDirectory localDirectory, int revision) throws IOException
+    public static FileLike getChromLibTempFile(Container container, LocalDirectory localDirectory, int revision) throws IOException
     {
         // Temp file in LocalDirectory (guaranteed to be local File dir)
-        File localDir = localDirectory.getLocalDirectoryFile();
-        Path chromLibDir = localDir.toPath().resolve(CHROM_LIB_FILE_DIR);
-        if(!Files.exists(chromLibDir))
+        FileLike localDir = localDirectory.getLocalDirectoryFile();
+        FileLike chromLibDir = localDir.resolveChild(CHROM_LIB_FILE_DIR);
+        if(!chromLibDir.exists())
             FileUtil.createDirectory(chromLibDir);
-        return chromLibDir.resolve(
+        return chromLibDir.resolveChild(
                         FileUtil.makeFileNameWithTimestamp(CHROM_LIB_FILE_BASE_NAME+"_"+container.getRowId()+"_rev"+revision,
                                                            CHROM_LIB_FILE_EXT));
     }
diff --git a/src/org/labkey/targetedms/chromlib/ContainerChromatogramLibraryWriter.java b/src/org/labkey/targetedms/chromlib/ContainerChromatogramLibraryWriter.java
index 7572ce206..f6c69901c 100644
--- a/src/org/labkey/targetedms/chromlib/ContainerChromatogramLibraryWriter.java
+++ b/src/org/labkey/targetedms/chromlib/ContainerChromatogramLibraryWriter.java
@@ -113,7 +113,7 @@ public ContainerChromatogramLibraryWriter(String panoramaServer, Container conta
 
     public String writeLibrary(LocalDirectory localDirectory, int libraryRevision) throws SQLException, IOException
     {
-        Path tempChromLibFile = ChromatogramLibraryUtils.getChromLibTempFile(_container, localDirectory, libraryRevision);
+        Path tempChromLibFile = ChromatogramLibraryUtils.getChromLibTempFile(_container, localDirectory, libraryRevision).toNioPathForWrite();
 
         try
         {
diff --git a/src/org/labkey/targetedms/parser/speclib/LibSpectrumReader.java b/src/org/labkey/targetedms/parser/speclib/LibSpectrumReader.java
index af6d489b4..fcf7f2e7b 100644
--- a/src/org/labkey/targetedms/parser/speclib/LibSpectrumReader.java
+++ b/src/org/labkey/targetedms/parser/speclib/LibSpectrumReader.java
@@ -29,6 +29,8 @@
 import org.labkey.api.util.Pair;
 import org.labkey.targetedms.parser.Peptide;
 import org.labkey.targetedms.view.spectrum.LibrarySpectrumMatchGetter;
+import org.labkey.vfs.FileLike;
+import org.labkey.vfs.FileSystemLike;
 import org.sqlite.SQLiteConfig;
 
 import java.io.File;
@@ -161,9 +163,9 @@ private static String getLibCacheKey(@NotNull Container container, String pathSt
             Path remotePath = pair.second;
             if (null != container && null != remotePath)
             {
-                File file = LocalDirectory.copyToContainerDirectory(container, remotePath, LOG);
+                FileLike file = LocalDirectory.copyToContainerDirectory(container, FileSystemLike.wrapFile(remotePath), LOG);
                 if (null != file)
-                    return file.getAbsolutePath();
+                    return file.toNioPathForRead().toFile().getAbsolutePath();
             }
         }
         return null;
diff --git a/src/org/labkey/targetedms/pipeline/TargetedMSImportPipelineJob.java b/src/org/labkey/targetedms/pipeline/TargetedMSImportPipelineJob.java
index 04b966e11..ec0cde2df 100644
--- a/src/org/labkey/targetedms/pipeline/TargetedMSImportPipelineJob.java
+++ b/src/org/labkey/targetedms/pipeline/TargetedMSImportPipelineJob.java
@@ -68,7 +68,7 @@ public TargetedMSImportPipelineJob(ViewBackgroundInfo info, ExpData expData, Sky
             throw new RuntimeException("Cannot process ExpData when its schema does not match root URI scheme.");
 
         LocalDirectory localDirectory = LocalDirectory.create(root, baseLogFileName,
-                null != _expData.getFile() ? _expData.getFile().getParentFile().getPath() : FileUtil.getTempDirectory().getPath());
+                null != _expData.getFile() ? _expData.getFileLike().getParent() : FileUtil.getTempDirectoryFileLike());
         setLocalDirectory(localDirectory);
         setLogFile(localDirectory.determineLogFile());
     }