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fix: correct xavier base path for cache subcommand #124

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merged 4 commits into from
Nov 5, 2024
Merged

fix: correct xavier base path for cache subcommand #124

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f3131f8
fix: correct xavier base path for cache subcommand
kelly-sovacool Nov 4, 2024
eec2786
chore: update CHANGELOG.md
kelly-sovacool Nov 4, 2024
0a38af7
chore: Merge branch 'main' into fix-cache
kelly-sovacool Nov 4, 2024
75101f4
Merge branch 'main' into fix-cache
kelly-sovacool Nov 5, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

- Fix minor bug in `assess_significance.R` script associated with rule `freec_exome_somatic`. (#120, @samarth8392)
- Fix bug in multiqc docker container, which caused an error when running xavier from ccbrpipeliner/7. (#123, @kelly-sovacool)
- Fix `cache` subcommand to correctly read the container images config file. (#124, @kelly-sovacool)

## XAVIER 3.1.1

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5 changes: 2 additions & 3 deletions src/xavier/__main__.py
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Expand Up @@ -92,8 +92,7 @@ def cache(sub_args):

sif_cache = sub_args.sif_cache
# Get absolute PATH to templates in XAVIER git repo
repo_path = os.path.dirname(os.path.abspath(__file__))
images = os.path.join(repo_path, "config", "containers", "images.json")
images = xavier_base("config", "containers", "images.json")

# Create image cache
if not exists(sif_cache):
Expand Down Expand Up @@ -135,7 +134,7 @@ def cache(sub_args):
# Quote user provided values to avoid shell injections
masterjob = subprocess.Popen(
"sbatch --parsable -J pl:cache --gres=lscratch:200 --time=10:00:00 --mail-type=BEGIN,END,FAIL "
+ str(os.path.join(repo_path, "resources", "cacher"))
+ xavier_base("resources", "cacher")
+ " slurm "
+ " -s '{}' ".format(sif_cache)
+ " -i '{}' ".format(",".join(pull))
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