Author: moeller Date: 2017-01-17 22:53:02 +0000 (Tue, 17 Jan 2017) New Revision: 23628
Added: trunk/community/edam/README.md Removed: trunk/community/edam/README.txt Log: Update of README, transformation to markdown Copied: trunk/community/edam/README.md (from rev 23627, trunk/community/edam/README.txt) =================================================================== --- trunk/community/edam/README.md (rev 0) +++ trunk/community/edam/README.md 2017-01-17 22:53:02 UTC (rev 23628) @@ -0,0 +1,61 @@ += Export of Debian annotation to the bio.tools repository = + +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. + +== Tools == + +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. + +== Data flow == + +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 Moeller, Matus Kalas +St. Malo/Bergen/Rostock/Lyngby/Trondheim/Luebeck/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 Deleted: trunk/community/edam/README.txt =================================================================== --- trunk/community/edam/README.txt 2017-01-17 22:52:03 UTC (rev 23627) +++ trunk/community/edam/README.txt 2017-01-17 22:53:02 UTC (rev 23628) @@ -1,12 +0,0 @@ -This tool is used to automatically generate and update the -ELIXIR registry [3] debian med collection of resources, using -the debian packages metadata. This registry uses EDAM [1], -which addresses the categorisation of tools and collections -of tools that contribute to computational biology in its -broadest sense. For a translation, some bits are meant to be -read by traditional means as with dpkg-parsechangelog. For the -EDAM annotation we had chosen a format compatible with YAML [2]. - -[1] http://edamontology.org/ -[2] http://www.yaml.org/ -[3] https://elixir-registry.cbs.dtu.dk _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
