Merge pull request #1254 from mira-miracoli/tmp-tmp-fix

Trying with docker tmpfs mount

files/galaxy/tpv/tools.yml

@@ -324,6 +324,11 @@ tools:
     inherits: basic_docker_tool
   toolshed.g2.bx.psu.edu/repos/artbio/manta/manta/.*:
     inherits: basic_docker_tool
+  toolshed.g2.bx.psu.edu/repos/goeckslab/squidpy/squidpy_spatial/*:
+    inherits: basic_docker_tool
+    mem: 6
+    params:
+      docker_run_extra_arguments: "--mount type=tmpfs,tmpfs-size=2147483648,destination=/tmp"
   toolshed.g2.bx.psu.edu/repos/goeckslab/gate_finder/gate_finder/.*:
     inherits: basic_docker_tool
   toolshed.g2.bx.psu.edu/repos/goeckslab/vitessce_spatial/vitessce_spatial/.*:
@@ -1305,17 +1310,15 @@ tools:
         - singularity
 
   toolshed.g2.bx.psu.edu/repos/iuc/funannotate_annotate/funannotate_annotate/.*:
+    inherits: basic_docker_tool
     cores: 8
-    mem: 40
-    env:
-      SINGULARITY_WRITABLE_TMPFS: 1
+    mem: 42
+    params:
+      docker_run_extra_arguments: "--mount type=tmpfs,tmpfs-size=2147483648,destination=/tmp"
     rules:
       - id: funannotate_annotate_large_input
         if: input_size > 3.2
         mem: 62
-    scheduling:
-      require:
-        - singularity
 
   toolshed.g2.bx.psu.edu/repos/iuc/funannotate_clean/funannotate_clean/.*:
     cores: 8