Fix quoting of $TMPDIR in NCBI FCS-GX

galaxyproject · Nov 20, 2024 · d345b73 · d345b73
1 parent f657597
commit d345b73
Showing 1 changed file with 5 additions and 5 deletions.
diff --git a/tools/ncbi_fcs_gx/ncbi_fcs_gx.xml b/tools/ncbi_fcs_gx/ncbi_fcs_gx.xml
@@ -12,11 +12,11 @@
         #set manifest_pathname = $mode.config_tag.fields.source_manifest
     #end if
     ## skip checksumming the database if the db_state_file exists
-    if [ ! -e '\${TMPDIR}/sync-files-completed.txt' ]; then
+    if [ ! -e "\${TMPDIR}/sync-files-completed.txt" ]; then
         ## copy data to local storage
-        mkdir -p '\${TMPDIR}' &&
-        sync_files.py get --mft '$manifest_pathname' --dir '\${TMPDIR}' > /dev/null 2>&1 &&
-        touch '\${TMPDIR}/sync-files-completed.txt';
+        mkdir -p "\${TMPDIR}" &&
+        sync_files.py get --mft '$manifest_pathname' --dir "\${TMPDIR}" > /dev/null 2>&1 &&
+        touch "\${TMPDIR}/sync-files-completed.txt";
     fi &&
     ## run gx
     GX_NUM_CORES=\${GALAXY_SLOTS:-2} run_gx.py
@@ -37,7 +37,7 @@
     #if $mode.screen_adv.div:
         --div '$mode.screen_adv.div'
     #end if
-        --gx-db '\${TMPDIR}'
+        --gx-db "\${TMPDIR}"
         --out-basename output
         --action-report true
         --generate-logfile false