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The issue with --apptainer-prefix and -d #3248

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jmzhang1911 opened this issue Jan 11, 2025 · 0 comments
Open

The issue with --apptainer-prefix and -d #3248

jmzhang1911 opened this issue Jan 11, 2025 · 0 comments
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bug Something isn't working

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@jmzhang1911
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Snakemake version

8.27.1

Describe the bug

When I try to specify --apptainer-prefix and -d, Snakemake does not look for the sif file in the location I specified.
The location Snakemake should be looking for is: /share/zhangjm/workflows/bioinfor-workflows/modules/test/config/r-ggplot2_latest.sif, not the path that contains the results (/share/zhangjm/workflows/bioinfor-workflows/modules/test/config/results/r-ggplot2_latest.sif).

I’m not sure why it’s like this, please forgive me for not understanding it.

snakemake -s ../test2.smk --configfile config.yml \
    -d results  \
    --use-apptainer --apptainer-prefix /share/zhangjm/workflows/bioinfor-workflows/modules/test/config \
    --apptainer-args "--bind /share:/share"

Logs

FATAL:   
While checking container encryption: could not open image \
/share/zhangjm/workflows/bioinfor-workflows/modules/test/config/results/r-ggplot2_latest.sif: \
failed to retrieve path for /share/zhangjm/workflows/bioinfor-workflows/modules/test/config/results/r-ggplot2_latest.sif: lstat /share/zhangjm/workflows/bioinfor-workflows/modules/test/config/results/r-ggplot2_latest.sif: no such file or directory

Minimal example

Additional context
@jmzhang1911 jmzhang1911 added the bug Something isn't working label Jan 11, 2025
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@jmzhang1911