Container Specifications
November 3, 2022 ยท View on GitHub
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" |
| LABEL 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
LABEL 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:$PATH
WORKDIR /data/
Dockerfile example (Multiple lines LABEL):
# Base Image
FROM biocontainers/biocontainers:latest
# Metadata
LABEL base_image="biocontainers:latest" \
version="3" \
software="Comet" \
software.version="2016012" \
about.summary="an open source tandem mass spectrometry sequence database search tool" \
about.home="http://comet-ms.sourceforge.net/" \
about.documentation="http://comet-ms.sourceforge.net/parameters/parameters_2016010/" \
about.license="SPDX:Apache-2.0" \
about.license_file="/usr/share/common-licenses/Apache-2.0" \
about.tags="Proteomics" \
extra.identifiers.biotools=comet
# Maintainer
LABEL maintainer="Felipe da Veiga Leprevost <felipe@leprevost.com.br>"
USER biodocker
RUN ZIP=comet_binaries_2016012.zip && \
wget https://github.com/BioDocker/software-archive/releases/download/Comet/$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/