cokelaer/pacbio4all:v1

$ singularity pull shub://cokelaer/pacbio4all:v1

Singularity Recipe

BootStrap: docker
From: ubuntu:17.04

#DistType "debian"
#MirrorURL: http://us.archive.ubuntu.com/ubuntu/
#OSVersion: xenial-updates

%labels

    AUTHOR thomas.cokelaer@pasteur.fr
    VERSION v1.0

%runscript

   echo "Welcome to Pacbio-dedicated container "
   echo "(maintainer: thomas cokelaer, Institut Pasteur 2017-)"
   echo "Available tools: blasr, bax2bam, pbbam, hmmer, gmap, ..."
   echo "Usage: singularity exec pacbio.img samtools"

%help

    This container contains a bunch of executables related to pacbio analysis.
    You can enter the conatiner as follows:

       singularity shell name.img

    Executables are are stored in /usr/local/bin



%post

    apt-get -y update
    apt-get install -y wget
    apt-get install -y bzip2
    apt-get install -y vim
    apt-get install -y git
    apt-get install -y make gcc python g++ gfortran pkg-config
    apt-get install -y libfreetype6*
    #apt-get install -y libstdc++
    apt-get install -y graphviz

    git clone https://github.com/PacificBiosciences/pitchfork.git
    cd pitchfork
    git reset --hard b7bdf01f12bbd43977f140923b0144d75c863348

    export TMPBUILD=/usr/local/
    make PREFIX=$TMPBUILD samtools
    make PREFIX=$TMPBUILD blasr   # installs boost,zlib,bzip2,htslib
    make PREFIX=$TMPBUILD bax2bam
    # make PREFIX=/tmp/mybuild bam2bax
    make PREFIX=$TMPBUILD pbbam
    make PREFIX=$TMPBUILD bam2fastx
    make PREFIX=$TMPBUILD bamtools
    make PREFIX=$TMPBUILD hmmer
    make PREFIX=$TMPBUILD isoseq-core
    make PREFIX=$TMPBUILD gmap
    make PREFIX=$TMPBUILD falcon
    make PREFIX=$TMPBUILD world  # this should install many more packages
    # sbt and jre cannot be installed

    #
    #cp -r $TMPBUILD/* /usr/local/
    export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
    export PATH=/usr/local/bin:$PATH

    if [ ! -d /data ]; then mkdir /data; fi
    if [ ! -d /scripts ]; then mkdir /scripts; fi
    if [ ! -d /scratch ]; then mkdir /scratch; fi
    if [ ! -d /mounting ]; then mkdir /mounting; fi
    if [ ! -d /pasteur ]; then mkdir /pasteur; fi

    # What can be cleaned ?
    rm -rf staging
    rm -rf workspace
    rm -rf distfile


%environment
    export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
    export PATH=/usr/local/bin:$PATH

Collection

• Name: cokelaer/pacbio4all
• License: None

Metrics

Feedback

Was this page helpful?

Glad to hear it! Please tell us how we can improve.

Sorry to hear that. Please tell us how we can improve.