TomHarrop/singularity-containers:freebayes_1.2.0

$ singularity pull shub://TomHarrop/singularity-containers:freebayes_1.2.0

Singularity Recipe

Bootstrap: shub
From: TomHarrop/singularity-containers:vcflib_1.0.0-rc2

%help
    Container for freebayes 1.2.0 with modified freebayes-parallel 
    that can be run from outside the scripts directory

%labels
    VERSION "freebayes 1.2.0"

%post
    # packages
    apt update
    apt install -y \
        libtabixpp-dev \
        parallel \
        python

    # download freebayes
    git clone \
        https://github.com/ekg/freebayes.git
    cd freebayes || exit 1
    git checkout tags/v1.2.0
    git submodule update --init --recursive
    make

    # fix the scripts
    sed \
        's/..\/vcflib\/scripts\/vcffirstheader/vcffirstheader/g' \
        scripts/freebayes-parallel \
        | sed \
        's/..\/vcflib\/bin\/vcfstreamsort/vcfstreamsort/g' \
        > scripts/freebayes-parallel.new
    rm scripts/freebayes-parallel
    mv scripts/freebayes-parallel.new scripts/freebayes-parallel
    chmod 755 scripts/freebayes-parallel

%environment
    export PATH="${PATH}:/freebayes/bin:/freebayes/scripts"

%runscript
    exec /freebayes/bin/freebayes "$@"

Collection


View on Datalad

Metrics

key value
id /containers/TomHarrop-singularity-containers-freebayes_1.2.0
collection name TomHarrop/singularity-containers
branch master
tag freebayes_1.2.0
commit d25a489081072b131c2937d6c92ba7d15509d16d
version (container hash) 1af8f2a0f6ab59af998b5853124476f3
build date 2019-12-16T22:21:26.412Z
size (MB) 1071
size (bytes) 412246047
SIF Download URL (please use pull with shub://)
Datalad URL View on Datalad
Singularity Recipe Singularity Recipe on Datalad
We cannot guarantee that all containers will still exist on GitHub.