phgenomics-singularity/mlst:latest
$ singularity pull shub://phgenomics-singularity/mlst:latest
Singularity Recipe
Bootstrap: docker
From: continuumio/miniconda3:4.5.11
%help
A Singularity image for MLST 2.16.1
%labels
Maintainer Anders Goncalves da Silva
Build 1.0
MLST_version 2.16.1
%environment
MLST_VERSION=2.16.1
export MLST_VERSION
export PATH=/opt/conda/bin:$PATH
export PYTHONUSERBASE=False
export MLST_DB=/opt/mlst/db/blast/mlst.fa
export MLST_PUBMLST=/opt/mlst/db/pubmlst
%files
mlst_db.tar.gz mlst_db.tar.gz
mlst_db_update.log mlst_db_update.log
%post
export PATH=/opt/conda/bin:$PATH
mkdir -p /opt/mlst/db
mv mlst_db.tar.gz mlst_db_update.log /opt/mlst/db
cd /opt/mlst/db
tar xzvf mlst_db.tar.gz
rm mlst_db.tar.gz
echo "All DBs updated on $(date "+%Y-%m-%d")" > /etc/dbupdate
conda config --add channels conda-forge
conda config --add channels defaults
conda config --add channels r
conda config --add channels bioconda
conda config --add channels anaconda
conda install -c bioconda mlst==2.16.1-0
echo "Sorting some env variables..."
chmod 555 /etc/dbupdate
echo 'LC_ALL=C.UTF-8' >> $SINGULARITY_ENVIRONMENT
echo 'LANG=C.UTF-8' >> $SINGULARITY_ENVIRONMENT
echo "Done"
%runscript
echo "Welcome to MLST ${MLST_VERSION}" >&2
cat /etc/dbupdate >&2
exec mlst --blastdb $MLST_DB --datadir $MLST_PUBMLST "$@"
%test
export PATH=/opt/conda/bin:$PATH
export MLST_DB=/opt/mlst/db/blast/mlst.fa
export MLST_PUBMLST=/opt/mlst/db/pubmlst
echo "Testing MLST"
echo "Test Genome is a Neisseria meningitidis ST74!"
GENOME="ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/008/805/GCF_000008805.1_ASM880v1/GCF_000008805.1_ASM880v1_genomic.gbff.gz"
wget -O /tmp/test.gbk.gz ${GENOME}
mlst --blastdb $MLST_DB --datadir $MLST_PUBMLST /tmp/test.gbk.gz > /tmp/res 2> /dev/null
cat /tmp/res
res=$(grep neisseria /tmp/res)
if [ -n "${res}" ];
then
echo "MLST installed successfully!";
else
echo "Something went wrong!";
fi;
rm /tmp/test.gbk.gz /tmp/res
Collection
- Name: phgenomics-singularity/mlst
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/phgenomics-singularity-mlst-latest |
collection name | phgenomics-singularity/mlst |
branch | master |
tag | latest |
commit | 704ac7acc374b772a2e0fb67b5c5b559ccd58f1a |
version (container hash) | f23d310635e5e92e6893bd2b8e541cb9 |
build date | 2020-02-17T23:59:57.055Z |
size (MB) | 3298 |
size (bytes) | 1258065951 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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