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new sif images not in cache #181

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kelly-sovacool opened this issue Dec 2, 2024 · 1 comment · Fixed by #182
Closed

new sif images not in cache #181

kelly-sovacool opened this issue Dec 2, 2024 · 1 comment · Fixed by #182
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@kelly-sovacool
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kelly-sovacool commented Dec 2, 2024

RENEE reports that these images which we updated recently are not in the shared cache

RENEE_DIR=/data/CCBR_Pipeliner/Pipelines/RENEE/renee-dev-sovacool
module load ccbrpipeliner/7
${RENEE_DIR}/bin/renee run \
    --input ${RENEE_DIR}/.tests/*.R?.fastq.gz \
    --output /data/$USER/renee_test_arriba-hg38 \
    --genome hg38_45 \
    --mode slurm \
    --sif-cache /data/CCBR_Pipeliner/SIFS
Python version: 3.11.3
RENEE (v2.6.3-dev)
Thank you for running RENEE on BIOWULF!
Warning: Local image "/data/CCBR_Pipeliner/SIFS/ccbr_ubuntu_22.04_v4.sif" does not exist in singularity cache
Warning: Local image "/data/CCBR_Pipeliner/SIFS/ccbr_multiqc_1.15_v2.sif" does not exist in singularity cache
Warning: Local image "/data/CCBR_Pipeliner/SIFS/ccbr_rseqc_4.0.0_v3.sif" does not exist in singularity cache

but the cache command claims it is up to date

${RENEE_DIR}/bin/renee cache --sif-cache /data/CCBR_Pipeliner/SIFs
Python version: 3.11.3
RENEE (v2.6.3-dev)
Singularity image cache is already up to update!
@kelly-sovacool kelly-sovacool self-assigned this Dec 2, 2024
@kopardev kopardev added the RENEE RepoName label Dec 2, 2024
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just realized there's a discrepancy -- sometimes the directory is spelled SIFs with a lowercase "s" at the end and sometimes it is SIFS in all caps.

kelly-sovacool added a commit to CCBR/Tools that referenced this issue Dec 2, 2024
kelly-sovacool added a commit to CCBR/CHAMPAGNE that referenced this issue Dec 2, 2024
kelly-sovacool added a commit to CCBR/CRISPIN that referenced this issue Dec 2, 2024
kelly-sovacool added a commit that referenced this issue Dec 2, 2024
kelly-sovacool added a commit to CCBR/Tools that referenced this issue Dec 2, 2024
* fix: lowercase SIFs dir

see CCBR/RENEE#181

* refactor: make singularity_sif_dir a dynamic property

* test: sif cache logic

* test: hpc class repr

* chore: update CHANGELOG.md

* ci: 🤖 render readme

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
kelly-sovacool added a commit that referenced this issue Dec 2, 2024
* fix: lowercase SIFs dir

see #181

* chore: update CHANGELOG.md
@kelly-sovacool kelly-sovacool added this to the 2024-12 milestone Dec 23, 2024
kelly-sovacool added a commit to CCBR/CRISPIN that referenced this issue Dec 23, 2024
* fix: lowercase SIFs dir

see CCBR/RENEE#181

* chore: update CHANGELOG.md
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