kapsakcj/singularities:lyveset.1.1.4f

$ singularity pull shub://kapsakcj/singularities:lyveset.1.1.4f

Singularity Recipe

Bootstrap: docker
From: ubuntu:xenial

%help
### This is the help for building a singularity image from a recipe (sudo priveleges required).
### To build me into an image, run:
    sudo singularity build my-new-lyveset-image.simg /path/to/lyveset/1.1.4f/Singularity.lyveset.1.1.4f
### If the image already exists, add the --force flag to overwrite
    sudo singularity build --force my-new-lyveset-image.simg /path/to/lyveset/1.1.4f/Singularity.lyveset.1.1.4f

#### Then to run in an interactive shell run:
    singularity shell my-new-lyveset-image.simg
    launch_set.pl [options]

#### To run without interactive shell
    singularity exec my-new-lyveset-image.simg launch_set.pl [options]

%labels
    MAINTAINER Curtis Kapsak
    SINGULARITY-IMAGE-VERSION 1.0.0
    SOFTWARE-VERSION 1.1.4f
    SOFTWARE-WEBSITE https://github.com/lskatz/lyve-SET/
    SOFTWARE-LICENSE https://github.com/lskatz/lyve-SET/blob/master/LICENSE

%environment
    PATH=${PATH}:/edirect:/lyve-SET-1.1.4f:/lyve-SET-1.1.4f/scripts
    export PATH
    export LC_ALL=C

%post
    apt-get update
    apt-get -y install wget \
                       perl \
                       libfile-slurp-perl \
                       openjdk-9-jre \
                       bioperl \
                       zlib1g-dev \
                       libncurses5-dev \
                       libncursesw5-dev \
                       make \
                       build-essential \
                       ncbi-blast+ \
                       libsvn-perl \
                       subversion \
                       libsvn1 \
                       automake1.11 \
                       libpthread-stubs0-dev \
                       cpanminus \
                       git \
                       clang \
                       mpich
    apt-get clean
    apt-get autoclean
    # install edirect
    wget ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/edirect.tar.gz
    tar -xzf edirect.tar.gz
    rm edirect.tar.gz
    cd edirect
    ./setup.sh
    # install smalt
    cd /
    wget --max-redirect 50 --continue 'https://downloads.sourceforge.net/project/smalt/smalt-0.7.6-static.tar.gz' -O smalt-0.7.6-static.tar.gz
    tar -zxf smalt-0.7.6-static.tar.gz
    rm smalt-0.7.6-static.tar.gz
    cd smalt-0.7.6
    ./configure
    make
    make install
    # get lyveset files
    cd /
    wget https://github.com/lskatz/lyve-SET/archive/v1.1.4f.tar.gz
    tar -xzf v1.1.4f.tar.gz
    rm v1.1.4f.tar.gz
    # install perl modules
    cpanm Test::Most Bio::FeatureIO String::Escape File::Slurp URI::Escape
    # install lyveset
    cd lyve-SET-1.1.4f
    make install
    make env
    # make /data directory for mounting volume
    mkdir /data

%runscript
    echo "This runscript shows Lyve-SET help options"
    launch_set.pl
    echo ""
    echo ""
    echo ""
    echo 'Run "singularity help name-of-lyveset-image.simg" for more help on running the image'
    echo ""

Collection

• Name: kapsakcj/singularities
• License: MIT License

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