darachm/slapchop:v0.3.0-alpha

$ singularity pull shub://darachm/slapchop:v0.3.0-alpha

Singularity Recipe

Bootstrap: docker
From: ubuntu:16.04

%labels
MAINTAINER darachm

%help

    This container just has 'slapchop.py' and dependencies in it.
    The 'runscript' is just running that script in python3.
    
    For options, do:

        singularity run this-container-name -h

    To run it, do something like:

        singularity exec shub://darachm/slapchop:latest \
            exec python3 /slapchop.py \
            data/raw.fastq output-basename \
            --processes 3 \
            -o "Sample:  input   > (?P<sample>[ATCG]{5})(?P<fixed1>GTCCACGAGGTC){e<=1}(?P<rest>TCT.*){e<=1}" \
            -o "Strain:  rest    > (?P<tag>TCT){e<=1}(?P<strain>[ATCG]{10,26})CGTACGCTGCAGGTCGAC" \
            -o "UMITail: rest    > (?P<fixed2>CGTACGCTGCAGGTC)(?<UMItail>GAC[ATCG]G[ATCG]A[ATCG]G[ATCG]G[ATCG]G[ATCG]GAT){s<=2}" \
            -o "UMI:     UMItail > (GAC(?P<umi1>[ATCG])G(?<umi2>[ATCG])A(?<umi3>[ATCG])G(?<umi4>[ATCG])G(?<umi5>[ATCG])G(?<umi6>[ATCG])G){e<=2}" \
            --output-seq "sample+spacer+strain" \
            --output-id "input.id+'_umi='+umi1.seq+umi2.seq+umi3.seq+ \
                umi4.seq+umi5.seq+umi6.seq+'_sample='+sample.seq" \
            --filter "sample_length == 5 and rest_start >= 16" \
            --verbose --verbose

%runscript

    exec /usr/bin/python3 /slapchop.py "$@"

%files

    slapchop.py

%post

    apt-get -y update
    apt-get -y install apt-utils
    apt-get -y install python3 python3-biopython python3-pip

    pip3 install regex==2019.02.18

%test

    /usr/bin/python3 /slapchop.py -h

Collection

• Name: darachm/slapchop
• License: BSD 2-Clause “Simplified” License

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