[med-svn] r23628 - trunk/community/edam

[Steffen Möller]

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