ISUGIFsingularity/utilities:1.0.1

$ singularity pull shub://ISUGIFsingularity/utilities:1.0.1

Singularity Recipe

Bootstrap:shub
From:ResearchIT/spack-singularity:openmpi

%labels
MAINTAINER severin@iastate.edu
APPLICATION utililities

%help
This container contains all the necessary programs to create genome modules.
See https://github.com/ISUGIFsingularity/genomeModules.git for more inforation 

%environment
source /etc/profile.d/modules.sh
SPACK_ROOT=/opt/spack
export SPACK_ROOT
export PATH=$SPACK_ROOT/bin:$PATH
source /etc/profile.d/modules.sh
source $SPACK_ROOT/share/spack/setup-env.sh
export PATH=$SPACK_ROOT/isugif/utilities/utilities/:$PATH
module load python
module load perl
module load perl-bio-perl
module load py-biopython

%post
export SPACK_ROOT=/opt/spack
export SPACK_ROOT
export PATH=$SPACK_ROOT/bin:$PATH

yum -y install bc paste
yum clean all

export FORCE_UNSAFE_CONFIGURE=1 

source $SPACK_ROOT/share/spack/setup-env.sh
spack install python
spack install perl
spack install perl-bio-perl
spack install py-biopython

export PATH=$SPACK_ROOT/isugif/utilities/utilities:$SPACK_ROOT/isugif/utilities/wrappers:$PATH
#for d in /opt/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/*/bin; do export PATH="$PATH:$d"; done

cd $SPACK_ROOT
rm -rf isugif
mkdir isugif
cd isugif
git clone https://github.com/ISUGIFsingularity/utilities.git
ls utilities/utilities/

%runscript
ls $SPACK_ROOT/isugif/utilities/utilities/

Collection

• Name: ISUGIFsingularity/utilities
• License: None

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