Amjadhpc/Mosaik:latest
$ singularity pull shub://Amjadhpc/Mosaik:latest
Singularity Recipe
BootStrap: yum
OSVersion : 7
MirrorURL: http://mirror.centos.org/centos-%{OSVERSION}/%{OSVERSION}/os/$basearch/
Include : yum tar
%help
This is singularity 2.6.0 image for Phenix pipeline build for centos 7 system.
%runscript
/usr/bin/MosaikAligner --help
%setup
%files
# jdk-7u15-linux-x64.tar.gz # phenix does not work with jdk 8 hence we have to use old version of 7u
# GenomeAnalysisTK.jar # Again GATK we downloaded old version to work with phenix
# picard.jar # picard .jar as pre requisite
%environment
# VARIABLE=MEATBALLVALUE
# PATH=/usr/local/bin:/usr/jdk1.7.0_15/bin:$PATH
# export PATH
# LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
#export LD_LIBRARY_PATH
# GATK_JAR=/GenomeAnalysisTK.jar
# export GATK_JAR
# JAVA_HOME=/usr/1.7.0_15
# export JAVA_HOME
# JRE_HOME=/usr//1.7.0_15/jre/
# export JRE_HOME
#export CLASSPATH=$(SINGULARITY_ROOTFS)/usr/local/bin/GenomeAnalysisTK.jar
# PICARD_JAR=/picard.jar
# export PICARD_JAR
%labels
AUTHOR Amjad Syed
Email amjadcsu@gmail.com
%post
yum -y install git autoconf gcc make gcc-devel gcc-c++ gcc-c++-devel hostname zlib zlib-devel libstdc++-devel libstdc++ glibc-devel glibc-static
mkdir -p /opt/sourcecode
echo $SINGULARITY_ROOTFS
echo $PWD
ls -l
cd /
cd /root
git clone https://github.com/wanpinglee/MOSAIK.git
cd MOSAIK
cd src
echo "export PLATFORM_FLAGS = -D_FILE_OFFSET_BITS=64" > includes/linux.inc
make
pwd
cd /root/MOSAIK/bin
cp MosaikAligner /usr/bin
cp MosaikBuild /usr/bin
cp MosaikJump /usr/bin
cp MosaikText /usr/bin
ls /usr/bin
# cp /root/MOSAIK/src/bin/MosaikAligner /usr/bin
rm -rf /root/MOSAIK
Collection
- Name: Amjadhpc/Mosaik
- License: GNU General Public License v3.0
View on Datalad
Metrics
key | value |
---|---|
id | /containers/Amjadhpc-Mosaik-latest |
collection name | Amjadhpc/Mosaik |
branch | master |
tag | latest |
commit | deaaef3c85563b1fd80aafe274742ec357c7c536 |
version (container hash) | c2017304002fdfbb1dc728b56dcb8268 |
build date | 2018-11-05T14:28:49.881Z |
size (MB) | 648 |
size (bytes) | 224264223 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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