Skip to content
Permalink
Branch: master
Find file Copy path
Find file Copy path
Fetching contributors…
Cannot retrieve contributors at this time
102 lines (74 sloc) 4.74 KB

Container Specifications

Each container should provide a well-defined metadata header that allows the final users to test, deploy and get support around the container. We explain here the containers metadata, their meaning and use in BioContainers:

Field Description Optional Example
LABEL base_image The original image where the software has been built Mandatory base_image=" biodckr/biodocker"
LABEL version Version of the tool's Dockerfile Mandatory version="2"
LABEL software.version Version of the software or tool Mandatory software.version="2015020"
LABEL software Name of the software or tool Mandatory software="Comet"
LABEL about.summary A short description of the software or tool. Mandatory about.summary="Peptide" identification
LABEL about.home The original software website. Mandatory about.home="http://comet-ms.sourceforge.net/"
LABEL about.documentation URL(s) containing information about software Optional about.documentation="http://comet-ms.sourceforge.net/"
LABEL about.license SPDX license specification. If not in the SPDX list, specify URL in license_file> Mandatory about.license="SPDX:Apache-2.0"
LABEL about.license_file License path location in the container or url (according to license requirements) Optional
LABEL about.tags Tags about the software that enable to find and classify the software tool. Optional about.tags="proteomics, mass spectrometry, biocontainers"
MAINTAINER The developer in charge of the container/software Mandatory MAINTAINER Yasset Perez-Riverol yperez@ebi.ac.uk
LABEL extra.identifiers Extra identifiers are external identifiers in other resources that will allow to pull metadata, an external information from other resources (e.g biotools). In order to be compatible with Docker specification the domain (database) of the identifiers should be specified in the name of the label. Optional extra.identifiers.biotools=abyss

Dockerfile example (Single lines LABEL):

# Base Image
FROM biocontainers/biocontainers:latest

# Metadata
LABEL base_image="biocontainers:latest"
LABEL version="3"
LABEL software="Comet"
LABEL software.version="2016012"
LABEL about.summary="an open source tandem mass spectrometry sequence database search tool"
LABEL about.home="http://comet-ms.sourceforge.net/"
LABEL about.documentation="http://comet-ms.sourceforge.net/parameters/parameters_2016010/"
LABEL about.license="SPDX:Apache-2.0"
LABEL about.license_file="/usr/share/common-licenses/Apache-2.0"
LABEL about.tags="Proteomics"
LABEL extra.identifiers.biotools=comet

# Maintainer
MAINTAINER Felipe da Veiga Leprevost <felipe@leprevost.com.br>

USER biodocker

RUN ZIP=comet_binaries_2016012.zip && \
  wget https://github.com/BioDocker/software-archive/releases/download/Comet/$ZIP -O /tmp/$ZIP && \
  unzip /tmp/$ZIP -d /home/biodocker/bin/Comet/ && \
  chmod -R 755 /home/biodocker/bin/Comet/* && \
  rm /tmp/$ZIP

RUN mv /home/biodocker/bin/Comet/comet_binaries_2016012/comet.2016012.linux.exe /home/biodocker/bin/Comet/comet

ENV PATH /home/biodocker/bin/Comet:$PATH

WORKDIR /data/

Dockerfile example (Multiple lines LABEL):

# Base Image
FROM biocontainers/biocontainers:latest

# Metadata
LABEL base_image="biocontainers:latest" \
      version="3"   \
      software="Comet" \
      software.version="2016012" \
      about.summary="an open source tandem mass spectrometry sequence database search tool" \
      about.home="http://comet-ms.sourceforge.net/" \
      about.documentation="http://comet-ms.sourceforge.net/parameters/parameters_2016010/" \
      about.license="SPDX:Apache-2.0" \
      about.license_file="/usr/share/common-licenses/Apache-2.0" \
      about.tags="Proteomics" \
      extra.identifiers.biotools=comet

# Maintainer
MAINTAINER Felipe da Veiga Leprevost <felipe@leprevost.com.br>

USER biodocker

RUN ZIP=comet_binaries_2016012.zip && \
  wget https://github.com/BioDocker/software-archive/releases/download/Comet/$ZIP -O /tmp/$ZIP && \
  unzip /tmp/$ZIP -d /home/biodocker/bin/Comet/ && \
  chmod -R 755 /home/biodocker/bin/Comet/* && \
  rm /tmp/$ZIP

RUN mv /home/biodocker/bin/Comet/comet_binaries_2016012/comet.2016012.linux.exe /home/biodocker/bin/Comet/comet

ENV PATH /home/biodocker/bin/Comet:$PATH

WORKDIR /data/
You can’t perform that action at this time.