ISU-HPC/braker:latest

$ singularity pull shub://ISU-HPC/braker:latest

Singularity Recipe

Bootstrap: shub
From: ISU-HPC/augustus


%labels
MAINTAINER ynanyam@iastate.edu

%post

#Install GeneMark
cd /
wget http://topaz.gatech.edu/GeneMark/tmp/GMtool_8oebP/gm_et_linux_64.tar.gz
tar xvf gm_et_linux_64.tar.gz
rm gm_et_linux_64.tar.gz
cd gm_et_linux_64
wget http://topaz.gatech.edu/GeneMark/tmp/GMtool_8oebP/gm_key_64.gz
echo 'export PATH=/gm_et_linux_64/gmes_petap:$PATH' >>$SINGULARITY_ENVIRONMENT
#Install perl dependencies
echo 'export LANG=C' >>$SINGULARITY_ENVIRONMENT
cpan App::cpanminus
cpanm YAML File::Spec::Functions Hash::Merge List::Util Logger::Simple \
  Module::Load::Conditional Parallel::ForkManager POSIX Scalar::Util::Numeric File::Which

#Install blast,biotools and bamtools
apt-get install -y ncbi-blast+ bamtools python3-biopython

#Install braker and set required variables
cd /
wget https://github.com/Gaius-Augustus/BRAKER/archive/v2.1.2.tar.gz

tar xvf v2.1.2.tar.gz
rm v2.1.2.tar.gz
echo 'export PATH=/augustus/scripts:/BRAKER-2.1.2/scripts:$PATH' >>$SINGULARITY_ENVIRONMENT
echo 'export AUGUSTUS_SCRIPTS_PATH=/augustus/scripts' >>$SINGULARITY_ENVIRONMENT
echo 'export AUGUSTUS_BIN_PATH=/augustus/bin' >>$SINGULARITY_ENVIRONMENT

Collection

• Name: ISU-HPC/braker
• License: None

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