phgenomics-singularity/abricate_k:latest

$ singularity pull shub://phgenomics-singularity/abricate_k:latest

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=0.8.13
  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 libpath-tiny-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_k
• License: None

Metrics

Feedback

Was this page helpful?

Glad to hear it! Please tell us how we can improve.

Sorry to hear that. Please tell us how we can improve.