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fixes handling singularity cache for docker images #333

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Merged
martenson merged 1 commit into from
Jun 5, 2026
+14 −2
Merged

fixes handling singularity cache for docker images #333

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3 changes: 2 additions & 1 deletion files/repeatexplorer-elixir.cerit-sc.cz/tpv_rules_local.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -173,7 +173,7 @@ tools:
context:
scratch: 64
walltime: 168

# ReapeatExplorer tools http://toolshed.g2.bx.psu.edu/repos/petr-novak/repeatexplorer2_testing
toolshed.g2.bx.psu.edu/repos/petr-novak/repeatexplorer2_testing/repeatexplorer2/.*:
cores: 10
Expand All @@ -186,6 +186,7 @@ tools:
- conda
require:
- singularity
- repex
container_resolvers:
- type: cached_explicit_singularity
cache_directory: "$SINGULARITY_CACHEDIR"
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13 changes: 12 additions & 1 deletion templates/galaxy/config/tpv_rules_meta.yml.j2
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Expand Up @@ -374,7 +374,7 @@ destinations:
--env JAVA_OPTS="-Xmx{int(mem)}g -Djava.io.tmpdir=$SCRATCHDIR"
--env JAVA_TOOL_OPTIONS="-Xmx{int(mem)}g -Djava.io.tmpdir=$SCRATCHDIR"
env:
SINGULARITY_CACHEDIR: "/cvmfs/singularity.galaxyproject.org/all/"
SINGULARITY_CACHEDIR: $SCRATCHDIR
SINGULARITY_TMPDIR: $SCRATCHDIR
XDG_CACHE_HOME: $SCRATCHDIR
scheduling:
Expand Down Expand Up @@ -456,3 +456,14 @@ destinations:
scheduling:
require:
- alphafold
tpv_pulsar_repex:
inherits: tpv_pulsar
env:
SINGULARITY_CACHEDIR: "/storage/brno11-elixir/home/galaxyelixir/pulsar-re/files/singularity_cache"
container_resolvers:
- type: explicit_singularity
- cache_directory: "$SINGULARITY_CACHEDIR"
type: cached_mulled_singularity
scheduling:
require:
- repex