add HDF5_USE_FILE_LOCKING ENV and set it to false in TPV tool defaults

usegalaxy-eu · Nov 28, 2024 · 92f5773 · 92f5773
1 parent 5a65d85
commit 92f5773
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Showing 2 changed files with 4 additions and 6 deletions.
diff --git a/files/galaxy/tpv/tool_defaults.yml b/files/galaxy/tpv/tool_defaults.yml
@@ -8,7 +8,10 @@ tools:
     mem: cores * 3.8
     gpus: 0
     env:
-      GALAXY_MEMORY_MB: "{int(mem * 1024)}" # set 5/2023 might be moved to runner or tool wrappers, related to Galaxy issue 15952
+      - name: GALAXY_MEMORY_MB
+        value: "{int(mem * 1024)}" # set 5/2023 might be moved to runner or tool wrappers, related to Galaxy issue 15952
+      - name: HDF5_USE_FILE_LOCKING
+        value: "FALSE"
     params:
       metadata_strategy: "extended"
       tmp_dir: true

diff --git a/files/galaxy/tpv/tools.yml b/files/galaxy/tpv/tools.yml
@@ -207,11 +207,6 @@ tools:
       prefer:
         - condor-tpv
 
-  toolshed.g2.bx.psu.edu/repos/lldelisle/cooler_cload_tabix/cooler_cload_tabix/.*:
-    env:
-      - name: HDF5_USE_FILE_LOCKING
-        value: "FALSE"
-
   toolshed.g2.bx.psu.edu/repos/iuc/fasta_stats/fasta-stats/.*:
     rules:
       - if: input_size >= 0.01