Bioconda gridss recipe doesn't contain gridsstools

[alexiswl]

After trying to run gridss_extract_overlapping_fragments.sh through the container quay.io/biocontainers/gridss:2.10.2--0,
I found that the gridsstools binary wasn't present.

I was able to get a workaround by downloading the binary 'on the fly' and adding it to the PATH variable.

gridss_tools_path="$(mktemp -d)"
gridss_version="2.10.2"

wget -qO- "https://github.com/PapenfussLab/gridss/releases/download/v${gridss_version}/gridss-${gridss_version}.tar.gz" | \
  tar xz -C "${gridss_tools_path}" --get "gridsstools"

# Add tmp path to path
export PATH="$PATH:$gridss_tools_path"

# Then run the extract fragments command
/usr/local/share/gridss-${gridss_version}-0/gridss_extract_overlapping_fragments.sh ...args

This then led me to the following error:

tmp.Y5OiAo/gridsstools: error while loading shared libraries: libz.so.1: cannot open shared object file: No such file or directory

I updated the script to contain the LD_LIBRARY_PATH to include /usr/local/lib and I was able to continue.

Is there anyway to add this to the meta.yaml file for gridss?

Alexis.

[alexiswl]

Running it with the standard Dockerhub version and updating the entrypoint to the extract fragments command also gives the following error:

$ docker \
    run \
    -i \
    --mount=type=bind,source=/efs/cwl/tmp-outdir/ngey1lng,target=/lcFIRW \
    --mount=type=bind,source=/efs/cwl/tmpdir/mvmv7dpy,target=/tmp \
    --mount=type=bind,source=/efs/cwl/tmp-outdir/rwet5wk5/SBJ_seqcii_020/SBJ_seqcii_020.bam,target=/var/lib/cwl/stg13fa2124-c9c6-42c6-8015-f354f3fbc624/SBJ_seqcii_020.bam,readonly \
    --mount=type=bind,source=/efs/cwl/tmp-outdir/rwet5wk5/SBJ_seqcii_020/SBJ_seqcii_020.bam.bai,target=/var/lib/cwl/stg13fa2124-c9c6-42c6-8015-f354f3fbc624/SBJ_seqcii_020.bam.bai,readonly \
    --mount=type=bind,source=/efs/cwl/tmp-outdir/rwet5wk5/SBJ_seqcii_020/SBJ_seqcii_020.sv.vcf.gz,target=/var/lib/cwl/stgc95bb9ca-04e8-4d54-9b70-24577a6dfac2/SBJ_seqcii_020.sv.vcf.gz,readonly \
    --mount=type=bind,source=/efs/cwl/tmp-outdir/rwet5wk5/SBJ_seqcii_020/SBJ_seqcii_020.sv.vcf.gz.tbi,target=/var/lib/cwl/stgc95bb9ca-04e8-4d54-9b70-24577a6dfac2/SBJ_seqcii_020.sv.vcf.gz.tbi,readonly \
    --mount=type=bind,source=/home/ec2-user/gridsstools,target=/usr/local/share/gridss-2.10.2-0/gridsstools \
    --workdir=/lcFIRW \
    --read-only=true \
    --user=1000:1000 \
    --rm \
    --env=TMPDIR=/tmp \
    --env=HOME=/lcFIRW \
    --entrypoint=gridss_extract_overlapping_fragments.sh \
    gridss/gridss:2.10.2 \
    --output \
    seqcii_N020.slice.bam \
    --targetvcf \
    /var/lib/cwl/stgc95bb9ca-04e8-4d54-9b70-24577a6dfac2/SBJ_seqcii_020.sv.vcf.gz \
    --workingdir \
    seqcii_N020.workingdir \
    /var/lib/cwl/stg13fa2124-c9c6-42c6-8015-f354f3fbc624/SBJ_seqcii_020.bam
    
    
Sat Feb  6 04:24:46 UTC 2021: Using input file "/var/lib/cwl/stg13fa2124-c9c6-42c6-8015-f354f3fbc624/SBJ_seqcii_020.bam"
Sat Feb  6 04:24:46 UTC 2021: Using SVs in /var/lib/cwl/stgc95bb9ca-04e8-4d54-9b70-24577a6dfac2/SBJ_seqcii_020.sv.vcf.gz as regions of interest
Sat Feb  6 04:24:46 UTC 2021: Using GRIDSS jar /opt/gridss/gridss-2.10.2-gridss-jar-with-dependencies.jar
Sat Feb  6 04:24:46 UTC 2021: Using output file seqcii_N020.slice.bam
Sat Feb  6 04:24:46 UTC 2021: Using 1 worker threads.
Sat Feb  6 04:24:46 UTC 2021: Found /opt/gridss/gridsstools
Sat Feb  6 04:24:46 UTC 2021: Found /usr/bin/samtools
Sat Feb  6 04:24:46 UTC 2021: samtools version: 1.7
Sat Feb  6 04:24:46 UTC 2021: samtools 1.10 or later is required
"exit $EX_CONFIG" command completed with exit code 78.

[d-cameron]

Bioconda and Docker packaging should be good now.