phgenomics-singularity/sistr:latest
$ singularity pull shub://phgenomics-singularity/sistr:latest
Singularity Recipe
Bootstrap: docker
From: continuumio/miniconda3:4.5.4
%help
A Singularity image for SISTR
%labels
Maintainer Anders Goncalves da Silva
Build 1.0
SISTR VERSION 1.0.2
%environment
VERSION=1.0.2
export VERSION
PATH=/opt/conda/bin:$PATH
export PATH
%files
requirements.txt
%post
# set versions of software to install
VERSION=1.0.2
export PATH=/opt/conda/bin:$PATH
conda config --add channels conda-forge
conda config --add channels defaults
conda config --add channels r
conda config --add channels bioconda
conda install --yes --file requirements.txt
echo "Sorting some env variables..."
echo "SISTR installed on $(date "+%Y-%m-%d")" > /etc/dbupdate
chmod 555 /etc/dbupdate
echo "Done"
%runscript
echo "Welcome to SISTR $VERSION" >&2
cat /etc/dbupdate >&2
exec sistr "$@"
%test
echo "Testing SISTR"
export PATH=/opt/conda/bin:$PATH
cd /tmp
GENOME=ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/006/945/GCF_000006945.2_ASM694v2/GCF_000006945.2_ASM694v2_genomic.fna.gz
OUT=asm.fna.gz
wget -O $OUT $GENOME
gzip -d $OUT
sistr asm.fna | grep "Typhimurium"
rm asm.fna
echo "Success"
Collection
- Name: phgenomics-singularity/sistr
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/phgenomics-singularity-sistr-latest |
collection name | phgenomics-singularity/sistr |
branch | master |
tag | latest |
commit | eca66fff52b6019d0c0927539a49c3fec7fc176c |
version (container hash) | ba171af1deaa6bf6d31bae264abc7d4d |
build date | 2018-07-03T09:02:32.754Z |
size (MB) | 3358 |
size (bytes) | 1384103967 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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