pipeline1.def

Bootstrap: docker
From: centos:7

%runscript

   #"I can put here whatever I want to happen by default when the user runs the container"
   cat << EOF
This container includes the following apps:
STAR version 2.5.2b - https://github.com/alexdobin/STAR
HTSeq version 0.6.1p1 - http://www-huber.embl.de/HTSeq/
To execute a binary inside the container do "singularity exec /path/to/container.img binary-name"
EOF

%post

   echo "Here we are installing software and other dependencies for the container!"

   echo "Installing STAR"
   yum -y install make gcc gcc-c++ zlib-devel
   cd /usr/local/src/
   curl -o STAR-2.5.2b.tar.gz  https://codeload.github.com/alexdobin/STAR/tar.gz/2.5.2b
   tar xf STAR-2.5.2b.tar.gz
   cd /usr/local/src/STAR-2.5.2b/source
   make STAR && make STARlong
   cp /usr/local/src/STAR-2.5.2b/source/{STAR,STARlong} /usr/local/bin

   echo "Installing HTSeq"
   yum -y install epel-release
   yum -y install make gcc gcc-c++ zlib-devel python-devel python-pip numpy
   pip install HTSeq==0.6.1p1

   yum clean all