phgenomics-singularity/abricate:v0.8_db20180717
$ singularity pull shub://phgenomics-singularity/abricate:v0.8_db20180717
Singularity Recipe
Bootstrap: docker
From: ubuntu:trusty-20170817
%help
A Singularity image for ABRICATE v0.8
%labels
Maintainer Anders Goncalves da Silva
Build 1.0
ABRICATE version 0.8
BLAST version 2.7.1+
%environment
ABRICATE_VERSION=0.8
export ABRICATE_VERSION
%post
# set versions of software to install
ABRICATE_VERSION=0.8
BLAST_VERSION=2.7.1
sudo locale-gen en_US.utf8
sudo update-locale
sudo apt-get --yes update
sudo apt-get --yes install make wget unzip gzip emboss git bioperl libjson-perl libtext-csv-perl libfile-slurp-perl liblwp-protocol-https-perl libwww-perl liblist-moreutils-perl
echo "Installing BLAST"
BLAST_DL="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${BLAST_VERSION}/ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz"
BLAST_TAR=blast.tar.gz
wget -O ${BLAST_TAR} "${BLAST_DL}"
tar xzf ${BLAST_TAR}
BLAST_DIR="ncbi-blast-${BLAST_VERSION}+"
sudo cp -R ${BLAST_DIR}/bin/* /usr/local/bin
rm -r ${BLAST_DIR} ${BLAST_TAR}
echo "Installing eDirect"
perl -MNet::FTP -e \
'$ftp = new Net::FTP("ftp.ncbi.nlm.nih.gov", Passive => 1);
$ftp->login; $ftp->binary;
$ftp->get("/entrez/entrezdirect/edirect.tar.gz");'
gunzip -c edirect.tar.gz | tar xf -
rm edirect.tar.gz
# export PATH=${PATH}:$HOME/edirect >& /dev/null || setenv PATH "${PATH}:$HOME/edirect"
./edirect/setup.sh
sudo cp edirect/e* /usr/local/bin
rm -rf edirect*
echo "Installing ABRICATE"
ABRICATE_GH="https://github.com/tseemann/abricate/archive/v${ABRICATE_VERSION}.tar.gz"
ABRICATE_TAR=abricate.tar.gz
wget -O ${ABRICATE_TAR} "${ABRICATE_GH}"
tar zxf ${ABRICATE_TAR}
ABRICATE_DIR="abricate-${ABRICATE_VERSION}"
sudo cp ${ABRICATE_DIR}/bin/* /usr/local/bin
sudo mkdir -p /usr/local/db
sudo cp -R ${ABRICATE_DIR}/db/* /usr/local/db
rm -r ${ABRICATE_DIR} ${ABRICATE_TAR}
echo "UPDATING DATABASES"
sudo abricate-get_db --db resfinder --force
sudo abricate-get_db --db ncbi --force
sudo abricate-get_db --db vfdb --force
sudo abricate-get_db --db ecoh --force
sudo abricate-get_db --db plasmidfinder --force
sudo abricate-get_db --db argannot --force
sudo abricate-get_db --db card --force
echo "Sorting some env variables..."
echo "All DBs updated on $(date "+%Y-%m-%d")" > /etc/dbupdate
sudo chmod 555 /etc/dbupdate
sudo echo 'LANGUAGE="en_US:en"' >> $SINGULARITY_ENVIRONMENT
sudo echo 'LC_ALL="en_US.UTF-8"' >> $SINGULARITY_ENVIRONMENT
sudo echo 'LC_CTYPE="UTF-8"' >> $SINGULARITY_ENVIRONMENT
sudo echo 'LANG="en_US.UTF-8"' >> $SINGULARITY_ENVIRONMENT
echo "Done"
%runscript
echo "Welcome to ABRICATE ${ABRICATE_VERSION}" >&2
cat /etc/dbupdate >&2
exec abricate "$@"
%test
echo "Testing ABRICATE"
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 ${GENOME}
abricate /tmp/test.gbk.gz > /tmp/res 2> /dev/null
cat /tmp/res
res=$(grep penA_1 /tmp/res)
rm /tmp/test.gbk.gz /tmp/res
Collection
- Name: phgenomics-singularity/abricate
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/phgenomics-singularity-abricate-v0.8_db20180717 |
collection name | phgenomics-singularity/abricate |
branch | master |
tag | v0.8_db20180717 |
commit | 92d2dd1eaef4d02d9d6c0914560572fd1908f383 |
version (container hash) | 0d8adb700f5296d086e3d68b98666ebb |
build date | 2019-08-22T09:58:39.892Z |
size (MB) | 1772 |
size (bytes) | 561897503 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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