MathijsSanders/SangerLCMFilteringSingularity:latest

$ singularity pull shub://MathijsSanders/SangerLCMFilteringSingularity:latest

Singularity Recipe

Bootstrap: docker
From: ubuntu:18.04

%labels
Maintainer MathijsSanders
Version v1.1

%post
apt-get -y update
apt-get -y install make openjdk-11-jre git samtools gcc-4.8 g++-4.8 zlib1g-dev
apt-get clean
ln -s /usr/bin/g++-4.8 /usr/bin/g++
ln -s /usr/bin/gcc-4.8 /usr/bin/gcc
cd /tmp/
git clone https://github.com/MathijsSanders/AnnotateBAMStatistics.git
cd AnnotateBAMStatistics
make all
cp /tmp/AnnotateBAMStatistics/dist/Release/GNU-Linux/AnnotateBAMStatistics /usr/bin/
mkdir /code
cp /tmp/AnnotateBAMStatistics/runScript.sh /code/runScriptAnnotate.sh
cd ..
rm -rf /tmp/AnnotateBAMStatistics
git clone https://github.com/MathijsSanders/AdditionalBAMStatistics.git
cd AdditionalBAMStatistics/
mv additionalBamStatistics.jar runScript.sh /code/
mv /code/runScript.sh /code/runScriptAdditional.sh
cd ..
rm -rf /tmp/AdditionalBAMStatistics
git clone https://github.com/MathijsSanders/SangerLCMFiltering.git
cd SangerLCMFiltering
mv *.sh /code/
chmod u+x /code/*.sh
cd ../
rm -rf /tmp/SangerLCMFiltering

#======================================
# Preselect variants
#======================================

%apprun preselect 
exec /bin/bash /code/runScriptPreselect.sh "$@"

#======================================
# ImitateANNOVAR
#======================================

%apprun imitateANNOVAR
exec /bin/bash /code/runScriptImitateANNOVAR.sh "$@"

#======================================
# AnnotateBAMStatistics
#======================================

%apprun annotateBAMStatistics
exec /bin/bash /code/runScriptAnnotate.sh "$@"

#======================================
# AdditionalBAMStatistics
#======================================

%apprun additionalBAMStatistics
exec /bin/bash /code/runScriptAdditional.sh "$@"

#=====================================
# Filtering
#====================================

%apprun filtering
exec /bin/bash /code/runScriptFiltering.sh "$@"

%environment
export LC_ALL=C

Collection

• Name: MathijsSanders/SangerLCMFilteringSingularity
• License: None

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