motroy/singularity-gottcha:latest

$ singularity pull shub://motroy/singularity-gottcha:latest

Singularity Recipe

Bootstrap: docker
From: ubuntu:16.04

%environment
export PATH="/Software/GOTTCHA/:/Software/GOTTCHA/bin:/Software/bwa/:$PATH"


%post
mkdir /Software && cd /Software
apt update && apt install -y git curl wget less locate unzip build-essential zlib1g-dev
git clone https://github.com/lh3/bwa.git
cd bwa; make
cd /Software
git clone https://github.com/LANL-Bioinformatics/GOTTCHA.git
cd GOTTCHA
sed -i -e 's/if\ (\ hash\ bwa\ 2/if\ (\ hash\ \/Software\/bwa\/bwa\ 2/g' INSTALL.sh
sed -i -e 's/BWA_VER=`bwa/BWA_VER=`\/Software\/bwa\/bwa/g' INSTALL.sh
./INSTALL.sh

Collection

• Name: motroy/singularity-gottcha
• License: MIT License

Metrics

Feedback

Was this page helpful?

Glad to hear it! Please tell us how we can improve.

Sorry to hear that. Please tell us how we can improve.