Set chmod when rsyncing genomicsdb and genomes

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/ReferenceGenomeManager.java

@@ -117,7 +117,7 @@ public void cacheGenomeLocally(ReferenceGenome genome, Logger log) throws Pipeli
 
         //Note: neither source nor dest have trailing slashes, so the entire source (i.e '128', gets synced into a subdir of dest)
         new SimpleScriptWrapper(log).execute(Arrays.asList(
-                "rsync", "-r", "-a", "--delete", "--no-owner", "--no-group", sourceDir.getPath(), localCacheDir.getPath()
+                "rsync", "-r", "-a", "--delete", "--no-owner", "--no-group", "--chmod=D2770,F660", sourceDir.getPath(), localCacheDir.getPath()
         ));
 
         File lastUpdate = getLocalUpdateFile(genome);

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/AbstractGenomicsDBImportHandler.java

@@ -711,7 +711,7 @@ private void copyWorkspace(JobContext ctx, File sourceWorkspace, File destinatio
                     ctx.getLogger().debug("Copying directory with rsync: " + sourceFolder.getPath());
                     //NOTE: since neither path will end in slashes, rsync to the parent folder should result in the correct placement
                     new SimpleScriptWrapper(ctx.getLogger()).execute(Arrays.asList(
-                            "rsync", "-r", "-a", "--delete", "--no-owner", "--no-group", "--no-perms", sourceFolder.getPath(), destContigFolder.getParentFile().getPath()
+                            "rsync", "-r", "-a", "--delete", "--no-owner", "--no-group", "--no-perms", "--chmod=D2770,F660", sourceFolder.getPath(), destContigFolder.getParentFile().getPath()
                     ));
                 }
 

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/GenotypeGVCFsWrapper.java

@@ -199,7 +199,7 @@ else if (f.isDirectory() && doneFile.exists())
                                 //NOTE: since neither path will end in slashes, rsync to the parent folder should result in the correct placement
                                 ctx.getLogger().debug("Copying directory with rsync: " + movedFile.getPath());
                                 new SimpleScriptWrapper(ctx.getLogger()).execute(Arrays.asList(
-                                    "rsync", "-r", "-a", "--delete", "--no-owner", "--no-group", f.getPath(), movedFile.getParentFile().getPath()
+                                    "rsync", "-r", "-a", "--delete", "--no-owner", "--no-group", "--chmod=D2770,F660", f.getPath(), movedFile.getParentFile().getPath()
                                 ));
                             }