move check for file existence to the shell code

galaxyproject · Sep 26, 2024 · fa57643 · fa57643
1 parent 56fbde1
commit fa57643
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/tools/ncbi_fcs_gx/ncbi_fcs_gx.xml b/tools/ncbi_fcs_gx/ncbi_fcs_gx.xml
@@ -15,12 +15,12 @@ GX_NUM_CORES=\${GALAXY_SLOTS:-2}
     ## skip checksumming the database if the db_state_file exists
     #import os
     #set db_state_file = os.path.join($mode.config_tag.fields.node_cache_dir, "sync-files-completed.txt")
-    #if not os.path.exists($db_state_file)
+    if [ ! -e '$db_state_file' ]; then
         ## copy data to local storage
         mkdir -p '$mode.config_tag.fields.node_cache_dir' &&
         sync_files.py get --mft '$manifest_pathname' --dir '$mode.config_tag.fields.node_cache_dir' > /dev/null 2>&1 &&
         touch '$db_state_file' &&
-    #end if
+    fi
     ## run gx
     run_gx.py
     #if $mode.config_tag.fields.phone_home == "1"