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Short Description
Official BioPerl Docker images
Full Description

Docker files for BioPerl

This repository contains Dockerfiles for reproducible builds of BioPerl.

At this point there are only two Dockerfiles, each in its own subdirectory. One is for a Docker image with all BioPerl dependencies pre-built, the other is for main BioPerl distribution itself. The latter builds on the dependencies image.

At present, the base OS image is Ubuntu 14.04. This may change in the future, in particular if there is user demand, so please post on the issue tracker if you'd like to see other base OS images as well.

bioperl

This is meant to provide a reproducible and complete build of the main BioPerl distribution, including almost all dependencies. It is based on the bioperl-deps image (see below), which itself is currently based on Ubuntu 14.04.

Currently the following tags are available:

  • latest: Built from the current master branch of the bioperl-live repository. This image gets automatically rebuilt upon every update to the bioperl-live master branch that passes the continuous integration test on Travis CI.
  • stable: Built from the latest stable release of BioPerl on CPAN. This build may change from one major revision to the next if the latest stable release on CPAN changes the major revision. This image gets automatically rebuilt whenever a new release-N-N-N tag is posted on the bioperl-live repository.
  • release-1-6-924: Built from the corresponding tag on the bioperl-live repository. This is at this time the latest, and last planned release for the 1.6.x series.

Other BioPerl release-specific tags will be added as and when they are released.

bioperl-deps

This image is meant to provide a well-defined reproducible base image for BioPerl that has pre-installed all dependencies of at least the main distribution.

The benefit of this image is to allow anyone to build a version of BioPerl on top of this image in a reproducible fashion. Since by far the majority of time when installing BioPerl (or building a BioPerl Docker image) is spent installing dependencies, using this image as the base image also significantly cuts down on build (or installation) time (on Docker Hub from >45 to 5-8 minutes).

The image is available on Docker Hub as bioperl/bioperl-deps. At present there is only one tag, latest. The dependencies include all needed for BioPerl 1.6.x, and we anticipate also for 1.7.x. None of the dependencies should be incompatible with versions of BioPerl earlier than the current one, so it should be safe building earlier versions of BioPerl off of this image, too.

Acknowledgements

The initial starting point for this work was the bioperl-1.6.1924 Dockerfile created by @sophielemoine at Genomic Paris Centre.

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