motroy/singularity-crispr-detect2:latest

$ singularity pull shub://motroy/singularity-crispr-detect2:latest

Singularity Recipe

Bootstrap: docker
From: ubuntu:16.04

%environment
export PATH="/ViennaRNA/ViennaRNA-2.4.13/:/cd-hit/cd-hit-v4.8.1-2019-0228/:/cd-hit/cd-hit-v4.8.1-2019-0228/cd-hit-auxtools/:/crispr-detect2/CRISPRDetect_2.2/:/reform/:$PATH"

%post
apt update && apt install -y git curl wget less locate build-essential openssh-server zlib1g-dev perl ncbi-blast+ emboss clustalw libparallel-forkmanager-perl python3 python3-numpy python3-scipy python3-pip
pip3 install biopython
mkdir /ViennaRNA && cd /ViennaRNA
wget https://github.com/ViennaRNA/ViennaRNA/releases/download/v2.4.13/ViennaRNA-2.4.13.tar.gz
tar -zxvf ViennaRNA-2.4.13.tar.gz
cd ViennaRNA-2.4.13
./configure
make && make install
export PATH="/ViennaRNA/ViennaRNA-2.4.13/:$PATH"
mkdir /cd-hit && cd /cd-hit
wget https://github.com/weizhongli/cdhit/releases/download/V4.8.1/cd-hit-v4.8.1-2019-0228.tar.gz
tar xvf cd-hit-v4.8.1-2019-0228.tar.gz
cd cd-hit-v4.8.1-2019-0228 && make
cd cd-hit-auxtools && make
export PATH="/cd-hit/cd-hit-v4.8.1-2019-0228/:/cd-hit/cd-hit-v4.8.1-2019-0228/cd-hit-auxtools/:$PATH"
mkdir /crispr-detect2 && cd /crispr-detect2
git clone --recursive https://github.com/ambarishbiswas/CRISPRDetect_2.2.git
cd CRISPRDetect_2.2 && perl CRISPRDetect.pl -h
cd /
git clone https://github.com/gencorefacility/reform.git
export PATH="/crispr-detect2/CRISPRDetect_2.2/:/reform/:$PATH"

Collection

• Name: motroy/singularity-crispr-detect2
• License: MIT License

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