motroy/singularity-amrfinder:latest

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

Singularity Recipe

Bootstrap: docker
From: ubuntu:16.04

%environment
export PATH="/amrfinderplus/amr/:/amrfinderplus/amr/data/:/usr/bin:$PATH"

%post
apt update && apt install -y git curl wget less locate build-essential openssh-server hmmer ncbi-blast+ libcurl4-openssl-dev
mkdir /amrfinderplus && cd /amrfinderplus
git clone --recursive https://github.com/ncbi/amr.git
cd amr && make
#download and index dbs to ./data/
./amrfinder -u
#test run
./amrfinder -o test_dna.RESULTS -d data/latest/ -n test_dna.fa -O Escherichia
export PATH="/amrfinderplus/amr/:/amrfinderplus/amr/data/:/usr/bin:$PATH"

Collection

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

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