Docker img doesnt work - Githubissues

hello,

tried to pull the docker img docker://gridss/gridss:latest into a singularity (v 3.6.4) container to run gridss but encountered the following problem:

singularity build gridss.sif docker://gridss/gridss:latest
singularity exec -B /computer \
                 gridss.sif  \
                gridss --reference ${FA} -o ${OUTDIR} ${BAM1} ${BAM2}

Fri Aug 16 14:50:29 BST 2024: Not found /usr/bin/time
Fri Aug 16 14:50:29 BST 2024: Using GRIDSS jar /opt/gridss/gridss-2.13.2-gridss-jar-with-dependencies.jar
Fri Aug 16 14:50:29 BST 2024: Using reference genome "${FA}"
Fri Aug 16 14:50:29 BST 2024: Using output VCF ${OUTDIR}
Fri Aug 16 14:50:29 BST 2024: Using assembly bam /.assembly.bam
Fri Aug 16 14:50:29 BST 2024: Using 8 worker threads.
Fri Aug 16 14:50:29 BST 2024: Using no blacklist bed. The encode DAC blacklist is recommended for hg19.
Fri Aug 16 14:50:29 BST 2024: Using JVM maximum heap size of 30g for assembly and variant calling.
Fri Aug 16 14:50:29 BST 2024: Using input file ${BAM1}
Fri Aug 16 14:50:29 BST 2024: Using input file ${BAM2}
Fri Aug 16 14:50:29 BST 2024: Error: unable to find Rscript on $PATH

Running the same command in a conda env instead works without errors (but is annoying we dont like conda env)

Running the following also works

singularity exec -B /computer gridss.sif which Rscript

> /usr/bin/Rscript

singularity exec -B /computer gridss.sif Rscript --version

> R scripting front-end version 4.1.2 (2021-11-01)

Could you produce an updated docker image for gridss? The latest one is 3yrs old, and I suspect it's outdated

Thanks

PapenfussLab / gridss

Docker img doesnt work #669