phgenomics-singularity/meningotype:latest
$ singularity pull shub://phgenomics-singularity/meningotype:latest
Singularity Recipe
Bootstrap: shub
From: phgenomics-singularity/mlst:latest
%help
A Singularity image for MENINGOTYPE v0.8.2-beta
%labels
Maintainer Anders Goncalves da Silva
Build 1.0
MENINGOTYPE version 0.8.2-beta
isPCR version 33
MLST version latest
%environment
export MENINGOTYPE_VERSION=0.8.2-beta
export PATH=/opt/conda/bin:$PATH
export PYTHONUSERBASE=False
%post
export PATH=/opt/conda/bin:$PATH
MENINGOTYPE_VERSION=0.8.2-beta
isPCR_VERSION=33
apt-get --yes update
apt-get --yes install build-essential autoconf automake wget git zlib1g-dev libbz2-dev libncurses5-dev curl unzip
apt-get --yes install software-properties-common
# add python3 support
conda install python==2.7.14
echo "Installing isPCR"
export MACHTYPE='unix'
export OLDHOME=${HOME}
isPCR_VERSION=33
isPCR_DL="http://hgwdev.cse.ucsc.edu/~kent/src/isPcr${isPCR_VERSION}.zip"
isPCR_ZIP=ispcr.zip
wget -O ${isPCR_ZIP} "${isPCR_DL}"
unzip -o ${isPCR_ZIP}
cd isPcrSrc
export HOME=${PWD}
sed -i 's/-Werror//g' inc/common.mk
mkdir -p bin/${MACHTYPE}
mkdir -p lib/${MACHTYPE}
make
mv bin/${MACHTYPE}/*Pcr /usr/local/bin
cd ..
rm -r isPcrSrc ${isPCR_ZIP}
export HOME=${OLDHOME}
echo "Installing MENINGOTYPE"
MENINGOTYPE_GT="git+https://github.com/MDU-PHL/meningotype.git@v${MENINGOTYPE_VERSION}"
pip install ${MENINGOTYPE_GT}
echo "UPDATING MENINGOTYPE DB"
meningotype --updatedb
echo "Sorting some env variables..."
echo "DB updated on $(date "+%Y-%m-%d")" > /etc/dbupdate
chmod 555 /etc/dbupdate
echo 'LANGUAGE="en_US:en"' >> $SINGULARITY_ENVIRONMENT
echo 'LC_ALL="en_US.UTF-8"' >> $SINGULARITY_ENVIRONMENT
echo 'LC_CTYPE="UTF-8"' >> $SINGULARITY_ENVIRONMENT
echo 'LANG="en_US.UTF-8"' >> $SINGULARITY_ENVIRONMENT
echo "Done"
%runscript
echo "Welcome to MENINGOTYPE 0.8.2-beta" >&2
cat /etc/dbupdate >&2
exec meningotype "$@"
%test
export PATH=/opt/conda/bin:$PATH
echo "Testing MENINGOTYPE"
meningotype --all --test
Collection
- Name: phgenomics-singularity/meningotype
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/phgenomics-singularity-meningotype-latest |
collection name | phgenomics-singularity/meningotype |
branch | master |
tag | latest |
commit | 1fcdaecab037a83caf8b1f2e2b5cdef643aa0262 |
version (container hash) | ef2dd84fc7cdf1309229ea88add9f062 |
build date | 2021-02-22T10:44:14.555Z |
size (MB) | 3967 |
size (bytes) | 1474502687 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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