This folder collects tools to automated the transformation of Debian package annotation in the a syntax of the ELIXIR registry 'bio.tools' [3].
The tools are tailored to packages curated by the Debian Med project. A key technology in this process is the EDAM ontology [1], This addresses the categorisation of tools and collections of tools that contribute to computational biology in its broadest sense.
The bio.tools entry can retrieve some information directly from the available annotation by e.g. using dpkg-parsechangelog. The EDAM annotation is however external to Debian and considered sufficiently beneficial to the Debian packages to have these annotated along the regular packaging. Since package annotation is immediately amendable via the git repository of Debian Med [4], this shall also invite Debian-external contributors.
The following tools are available
- packages.list.update.sh
- registry-tool.py
- registry-tool-iterator.sh
The packages.list.update.sh script retrieves a list of binry packages (the ones with code executed by the user) from the Debian Med tasks pages and determines the source packages for these (the ones with the source code and especially also the package annotation). A list of packages is created as the file 'packages.list.txt'.
The registry-tool.py script is not meant to be executed directly. It translates all information gathere from a single package source tree into a single json file. The latter is provided in a form that may be directly uploaded to the bio.tools repository.
The registry-tool-iterator.sh reads the packages.list.txt file and checks out the master branch of each such referenced package. The iterator checks the format of each EDAM file and in a second iteration creates the json files mean to export from Debian to the bio.tools repository.
While the upload of packages is at ease for packages that are yet unknown to the bio.tools registry, the information for entries already existing demands a manual act of merging. There is yet no means in the bio.tools repository to support that process (i.e. provenance management).
To the rescue comes a git repository [5] to which the files created by the registry-tool are submitted. The information in bio.tools placed in an independent branch. A third branch merges the two to prepare the submission.
Steffen Möller, Matúš Kalaš, Hervé Ménager St. Malo/Lyngby/Trondheim/Niendorf(2x)/Bucharest 2015-2017
[1] http://edamontology.org/ [2] http://www.yaml.org/ [3] https://bio.tools [4] https://anonscm.debian.org/cgit/debian-med [5] https://github.com/bio-tools-community/json-buffer