TomHarrop/ont-containers:chopchop_a301f2d

$ singularity pull shub://TomHarrop/ont-containers:chopchop_a301f2d

Singularity Recipe

Bootstrap: docker
From: python:2.7.16-buster

%help

    Python 2.7.16 with chopchop a301f2d
    
%labels

    MAINTAINER "Tom Harrop (twharrop@gmail.com)"
    VERSION "chopchop a301f2d"

%runscript

    exec /usr/local/bin/python /chopchop/chopchop.py "$@"

%post
    # python dependencies
    /usr/local/bin/pip install \
        argparse \
        biopython \
        keras \
        mysqlclient \
        np-utils \
        numpy \
        pandas \
        scikit-learn==0.18.0 \
        scipy

    # ucsc's gff3ToGenePred
    wget \
        -O /usr/local/bin/gff3ToGenePred \
    http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gff3ToGenePred
    chmod 755 /usr/local/bin/gff3ToGenePred

    # chopchop
    git clone \
        https://bitbucket.org/valenlab/chopchop.git
    cd chopchop || exit 1
    git checkout a301f2d

%environment
    export PATH="${PATH}:/chopchop:/chopchop/bowtie:/chopchop/svm_light"

Collection


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Metrics

key value
id /containers/TomHarrop-ont-containers-chopchop_a301f2d
collection name TomHarrop/ont-containers
branch master
tag chopchop_a301f2d
commit 641f5cf731f2e70d44b54ab0e2143e58d5bcab63
version (container hash) 0ef558220834da993437c922a6186d0869f008417e81147ce20890ffea974e30
build date 2019-11-04T01:32:52.545Z
size (MB) 583.1796875
size (bytes) 611508224
SIF Download URL (please use pull with shub://)
Datalad URL View on Datalad
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