picard_3.0.0.def 1.05 KB
BootStrap: docker
From: centos:8

%help
This is a singularity container packing picard tools v3.0.0 and java 17.
Author : yannis.duffourd@u-bourgogne.fr

This singularity recipe is open source and free. Please redistribute it as well.
No warranty is provided.

%setup
mkdir ${SINGULARITY_ROOTFS}/data

%files

%post
sed -i 's/mirrorlist/#mirrorlist/g' /etc/yum.repos.d/CentOS-*
sed -i 's|#baseurl=http://mirror.centos.org|baseurl=http://vault.centos.org|g' /etc/yum.repos.d/CentOS-*

yum update -y
yum install -y epel-release wget

# install java
yum install -y java-17-openjdk java-17-openjdk-devel

# install picard
mkdir /opt/picard_3.0.0
wget -O /opt/picard_3.0.0/picard.jar https://github.com/broadinstitute/picard/releases/download/3.0.0/picard.jar 

# cleanup

%labels
Maintainer Yannis Duffourd
Updater Yannis Duffourd <yannis.duffourd@u-bourgogne.fr>
ContainerVersion v1.0
PicardTools 3.0.0 (Broad institute)

%environment
    export JAVA_HOME=$(dirname $(dirname $(readlink $(readlink $(which java)))))
    export PATH=$PATH:$JAVA_HOME/bin

%runscript
echo "OK"