motroy/singularity-c-SSTAR:latest

$ singularity pull shub://motroy/singularity-c-SSTAR:latest

Singularity Recipe

Bootstrap: docker
From: ubuntu:latest

%environment
export PATH="/c-SSTAR/c-SSTAR/:/usr/bin:$PATH"

%post
apt update && apt install -y git curl wget less locate build-essential openssh-server python python-pip ncbi-blast+
mkdir /c-SSTAR && cd /c-SSTAR
pip install biopython
git clone https://github.com/chrisgulvik/c-SSTAR.git
cd /c-SSTAR/c-SSTAR/
sed -i -e 's#/usr/bin/env python#/usr/bin/env python2.7#g' c-SSTAR
wget https://github.com/tomdeman-bio/Sequence-Search-Tool-for-Antimicrobial-Resistance-SSTAR-/blob/master/Latest_AR_database/ResGANNOT_srst2.fasta
export PATH="/c-SSTAR/c-SSTAR/:/usr/bin:$PATH"

Collection

• Name: motroy/singularity-c-SSTAR
• License: MIT License

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