[med-svn] r7377 - in trunk/community/infrastructure/getData: . debian

Steffen Möller moeller at alioth.debian.org
Wed Aug 3 14:07:46 UTC 2011 

Author: moeller
Date: 2011-08-03 14:07:46 +0000 (Wed, 03 Aug 2011)
New Revision: 7377

Modified:
   trunk/community/infrastructure/getData/README
   trunk/community/infrastructure/getData/debian/changelog
   trunk/community/infrastructure/getData/debian/control
   trunk/community/infrastructure/getData/debian/rules
   trunk/community/infrastructure/getData/getData
Log:
Series of updates preparing for an upload.


Modified: trunk/community/infrastructure/getData/README
===================================================================
--- trunk/community/infrastructure/getData/README	2011-08-03 10:11:12 UTC (rev 7376)
+++ trunk/community/infrastructure/getData/README	2011-08-03 14:07:46 UTC (rev 7377)
@@ -1,12 +1,30 @@
 getData
 =======
 
-While the community is discussing the possibility to prepare large
-Debian packages for the distribution of biological databases, this
-package instead sets out to prepare such distributions automatically -
-not the Debian package, but the provisioning of local updates and first
-installations of the data.
+Computational biology as a science works without data. Well, but one
+cannot prove anything then or just learn from appling the computer to
+some new data, then.  There are many reasons why Debian cares about
+bioinformatics, but alone for a contribution to the education of our
+students at all levels - something we cannot talk enough about, there
+needs to be an easy straight forward way to get access to data. For the
+professionals then around us, we also need those extra features like
+automated updates and whatever else comes to mind to maintain those data
+files in our daily routine.
 
+There are now various approaches to it. Many say that there should be data
+packages available which are tarballs or some other format of that data to
+be installed. This is very reasonable indeed. But alone for the concept
+of releases that comes with our and basically every other Linux distro,
+this concept is doomed. Nobody wants to use old biological databases
+when a new version is available basically at the very same costs.
+
+This package instead sets out to prepare the installation and maintenance
+of databases automatically - directly from the data creator's websites
+and redistributed as a Debian package.  There may still be packages
+with the name of a particular database, like 'uniprot', but those should
+then merely provide the instructions to this new 'getData' tool on how
+to deal with the database for download, indexing and updating.
+
 The download of the databases listed in getData should all
 remain functional. The major challenge is the integration with the
 post-processing of the data. In this respect well performing should
@@ -16,11 +34,23 @@
 that have the EMBOSS tool kit installed, also the respective indexing
 is performed.
 
-Once the package has hit unstable, we shall have the configuration
-files with database-specific tools or database install packages.
-Please help with your direct contributions and/or feedback.
+Once the package has hit unstable, we shall have the configuration files
+with database-specific tools or database install packages.  Please help
+with your direct contributions and/or feedback.
 
+'getData' can be successful only when there is a strong communication
+among ourselves concerning new tools on the horizon that should possibly
+be added. And when there is a new URL for a particular pathway, then
+this should be updated in some community effort.  So, please, should at
+us by saying "reportbug getdata" whenever there is something to report.
+While the development of this tools was indeed seeded by the Debian Med
+community, there is some strong hope that folks at Fedora and OpenSuSE
+would adopt this package from us. We'll see.
 
+Many thanks!!!
+
+Steffen and Charles
+
 Acknowledgements
 ----------------
 

Modified: trunk/community/infrastructure/getData/debian/changelog
===================================================================
--- trunk/community/infrastructure/getData/debian/changelog	2011-08-03 10:11:12 UTC (rev 7376)
+++ trunk/community/infrastructure/getData/debian/changelog	2011-08-03 14:07:46 UTC (rev 7377)
@@ -3,6 +3,7 @@
   [ Steffen Moeller ]
   * Initial release (Closes: #514984)
   * source format 3.0 (quilt)
+  * Suggesting biomaj
 
   [ Charles Plessy ]
   * Renamed getData.pl getData (.pl extensions are unwelcome in /usr/bin)
@@ -14,4 +15,4 @@
     /local/databases/mirrored.
   * Recommends perl-doc as getData --help needs it.
 
- -- Steffen Moeller <moeller at debian.org>  Fri, 05 Nov 2010 14:51:58 +0100
+ -- Steffen Moeller <moeller at debian.org>  Wed, 03 Aug 2011 16:00:22 +0200

Modified: trunk/community/infrastructure/getData/debian/control
===================================================================
--- trunk/community/infrastructure/getData/debian/control	2011-08-03 10:11:12 UTC (rev 7376)
+++ trunk/community/infrastructure/getData/debian/control	2011-08-03 14:07:46 UTC (rev 7377)
@@ -5,7 +5,7 @@
 DM-Upload-Allowed: yes
 Uploaders: Charles Plessy <plessy at debian.org>
 Build-Depends: cdbs, debhelper (>= 7)
-Standards-Version: 3.9.1
+Standards-Version: 3.9.2
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/community/infrastructure/getData/?rev=0&sc=0trunk
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/community/infrastructure/getData
 Homepage: http://debian-med.alioth.debian.org
@@ -14,13 +14,19 @@
 Architecture: all
 Depends: ${shlibs:Depends}, ${misc:Depends}, perl
 Recommends: perl-doc
+Suggests: biomaj
 # perl-doc is needed for getData --help.
 Description: management of external databases
- Many scientific communities share the problem of regularly
- updating external database and keeping internally created
- indices updated. This tool addresses this issue.
+ Many scientific communities share the problem of regularly updating
+ external databases. With every update, also various tasks need to
+ be performed for the update of indices that need to be recreated.
+ This work depends on the tools that are available locally and is
+ not always completely simple.
  .
- Since some activities do depend on the installation
- of additional tools, getdata needs to be aware of 
- packages being installed to the system and hence 
- will be tailored to Debian Linux.
+ This package provides the getData Perl script, which in some not
+ so complicated manner performs the invocation to wget to download
+ data and then knows how to perform the indexing. There is only
+ a hash table to be filled with the commands to be executed. 
+ Maintainers of scientific packages that are strongly coupled to
+ public datasets are invited to add a runtime dependency to this
+ package and add instructions for getData to follow.

Modified: trunk/community/infrastructure/getData/debian/rules
===================================================================
--- trunk/community/infrastructure/getData/debian/rules	2011-08-03 10:11:12 UTC (rev 7376)
+++ trunk/community/infrastructure/getData/debian/rules	2011-08-03 14:07:46 UTC (rev 7377)
@@ -7,3 +7,8 @@
 	$(MAKE) getData.1
 
 install:: getData.1
+
+UPSTREAMVERSION=$(shell dpkg-parsechangelog | grep ^Version|cut -f2 -d\ | cut -f1 -d-)
+get-orig-source:
+	cd .. ; \
+	tar --exclude=debian --exclude-vcs -czvf getdata_$(UPSTREAMVERSION).orig.tar.gz getData

Modified: trunk/community/infrastructure/getData/getData
===================================================================
--- trunk/community/infrastructure/getData/getData	2011-08-03 10:11:12 UTC (rev 7376)
+++ trunk/community/infrastructure/getData/getData	2011-08-03 14:07:46 UTC (rev 7377)
@@ -12,11 +12,11 @@
 =cut
 
 # This script shall help maintaining sets of frequently changing databases
-# of various sorts. It is motivated by demands in bioinformatics and
-# astronomy.
+# of various sorts. It is motivated by demands in computational biology
+# and astronomy.
 
-# Copyright (c) 2008 Steffen Moeller <moeller at debian.org>
-# Copyright (c) 2008 Charles Plessy <plessy at debian.org>
+# Copyright (c) 2008-2011 Steffen Moeller <moeller at debian.org>
+# Copyright (c) 2008-2011 Charles Plessy <plessy at debian.org>
 # 
 # This program is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License

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