[med-svn] r11792 - trunk/packages/norsp/trunk/debian

Fri Jul 13 15:55:21 UTC 2012

Author: lkajan-guest
Date: 2012-07-13 15:55:20 +0000 (Fri, 13 Jul 2012)
New Revision: 11792

Added:
   trunk/packages/norsp/trunk/debian/README.source
Modified:
   trunk/packages/norsp/trunk/debian/changelog
   trunk/packages/norsp/trunk/debian/control
   trunk/packages/norsp/trunk/debian/copyright
   trunk/packages/norsp/trunk/debian/rules
   trunk/packages/norsp/trunk/debian/upstream
   trunk/packages/norsp/trunk/debian/watch
Log:
reviewed Debianization

Added: trunk/packages/norsp/trunk/debian/README.source
===================================================================

--- trunk/packages/norsp/trunk/debian/README.source	                        (rev 0)
+++ trunk/packages/norsp/trunk/debian/README.source	2012-07-13 15:55:20 UTC (rev 11792)
@@ -0,0 +1,7 @@
+norsp for Debian
+================
+
+Uncompressed examples
+---------------------
+dh_compress excludes examples that appear on the man page.
+This is in order to allow the example to work as it is pasted on the command like from the man page.

Modified: trunk/packages/norsp/trunk/debian/changelog
===================================================================
--- trunk/packages/norsp/trunk/debian/changelog	2012-07-13 14:55:20 UTC (rev 11791)
+++ trunk/packages/norsp/trunk/debian/changelog	2012-07-13 15:55:20 UTC (rev 11792)
@@ -1,4 +1,4 @@
-norsp (1.0.3-1) UNRELEASED; urgency=low
+norsp (1.0.4-1) UNRELEASED; urgency=low
 
   * Initial release (Closes: #680367) 
 

Modified: trunk/packages/norsp/trunk/debian/control
===================================================================
--- trunk/packages/norsp/trunk/debian/control	2012-07-13 14:55:20 UTC (rev 11791)
+++ trunk/packages/norsp/trunk/debian/control	2012-07-13 15:55:20 UTC (rev 11792)
@@ -3,28 +3,28 @@
 Priority: extra
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Laszlo Kajan <lkajan at rostlab.org>, Eva Reisinger <e.reisinger at gmx.net> 
-DM-Upload-Allowed: yes
-Build-Depends: debhelper (>= 8), autotools-dev
+Build-Depends: debhelper (>= 8)
 Standards-Version: 3.9.3
 Homepage: https://rostlab.org/owiki/index.php/NORSp_-_predictor_of_NOn-Regular_Secondary_Structure
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/norsp/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/norsp/trunk/
+DM-Upload-Allowed: yes
 
 Package: norsp
 Architecture: all
-Depends: ${misc:Depends}
+Depends: ${misc:Depends}, perl
 Recommends: pp-popularity-contest, profphd, profphd-utils, ncoils (>= 2002-3)
-Description: predictor of NOn-Regular Secondary Structure 
- Many structurally flexible regions play important roles in biological
- processes. It has been shown that extended loopy regions are very abundant in
- nature, and that they are evolutionarily conserved. NORSp is a publicly
- available predictor for disordered regions in protein. Specifically, it
- predicts long regions with no regular secondary structure. Upon user
- submission of protein sequence, NORSp will analyse the protein about its
- secondary structure, and presence of transmembrane helices and coiled-coil. It
- will then return e-mail to user about the presence and position of disordered
- regions.NORSp can be useful for biologists in several ways. For example,
+Description: predictor of non-regular secondary structure 
+ NORSp is a publicly available predictor for disordered regions in proteins.
+ Specifically, it predicts long regions with no regular secondary structure.
+ Upon submission of a protein sequence, NORSp analyses the protein about its
+ secondary structure, the presence of transmembrane helices and coiled-coils.
+ It then returns the presence and position of disordered regions.
+ .
+ NORSp can be useful for biologists in several ways. For example,
  crystallographers can check whether their proteins contain NORS regions and
  make the decision about whether to proceed with the experiments since NORS
  proteins may be difficult to crystallise, as demonstrated by the their low
  occurrence in PDB. Biologists interested in protein structure-function
  relationship may also find it interesting to verify whether the
- protein-protein interaction sites coincide with NORS region.
+ protein-protein interaction sites coincide with NORS regions.

Modified: trunk/packages/norsp/trunk/debian/copyright
===================================================================
--- trunk/packages/norsp/trunk/debian/copyright	2012-07-13 14:55:20 UTC (rev 11791)
+++ trunk/packages/norsp/trunk/debian/copyright	2012-07-13 15:55:20 UTC (rev 11792)
@@ -1,12 +1,19 @@
 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: norsp
-Source: http://www.predictprotein.org 
+Upstream-Contact: Guy Yachdav <gyachdav at rostlab.org>
+Source: ftp://rostlab.org/norsp/
 
+Files: debian/*
+Copyright: 2010 Guy Yachdav <gyachdav at rostlab.org>
+           2012 Laszlo Kajan <lkajan at rostlab.org>
+	   2012 Eva Reisinger <e.reisinger at gmx.net>
+License: GPL-3+
+
 Files: *
-Copyright: 2010 ROSTLAB
+Copyright: 2003 Jinfeng Liu <jinfeng.liu at gmail.com>
+           2003 Burkhard Rost
 License: GPL-3+
 
-
 License: GPL-3+
  This package is free software; you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by

Modified: trunk/packages/norsp/trunk/debian/rules
===================================================================
--- trunk/packages/norsp/trunk/debian/rules	2012-07-13 14:55:20 UTC (rev 11791)
+++ trunk/packages/norsp/trunk/debian/rules	2012-07-13 15:55:20 UTC (rev 11792)
@@ -3,6 +3,10 @@
 # Uncomment this to turn on verbose mode.
 #export DH_VERBOSE=1
 
+.PHONY: override_dh_compress
+override_dh_compress:
+	dh_compress -Xexamples/query.fasta -Xexamples/query.hssp -Xexamples/query.prof -Xexamples/query.phdHtm -Xexamples/query.coils
+
 %:
 	dh $@
 

Modified: trunk/packages/norsp/trunk/debian/upstream
===================================================================
--- trunk/packages/norsp/trunk/debian/upstream	2012-07-13 14:55:20 UTC (rev 11791)
+++ trunk/packages/norsp/trunk/debian/upstream	2012-07-13 15:55:20 UTC (rev 11792)
@@ -1,13 +1,13 @@
 Bug-Database: https://rostlab.org/bugzilla3/buglist.cgi?product=norsp
 Bug-Submit: https://rostlab.org/bugzilla3/enter_bug.cgi?product=norsp
 Reference:
- Author: Liu J and Rost B
- Title: NORSp Predictions of long regions without regular secondary structure
+ Author: Jinfeng Liu and Burkhard Rost
+ Title: 'NORSp: Predictions of long regions without regular secondary structure.'
  Journal: Nucleic Acids Res
  Year: 2003
- Volume: 1
- Number: 31
+ Volume: 31
+ Number: 13
+ Pages: 3833-3835
  PMID: 12824431
- Type: article
- URL: http://www.ncbi.nlm.nih.gov/pubmed?term=norsp
- Eprint: http://nar.oxfordjournals.org/content/31/13/3833.long
+ URL: http://nar.oxfordjournals.org/content/31/13/3833.long
+ Eprint: http://nar.oxfordjournals.org/content/31/13/3833.full.pdf

Modified: trunk/packages/norsp/trunk/debian/watch
===================================================================
--- trunk/packages/norsp/trunk/debian/watch	2012-07-13 14:55:20 UTC (rev 11791)
+++ trunk/packages/norsp/trunk/debian/watch	2012-07-13 15:55:20 UTC (rev 11792)
@@ -1,4 +1,3 @@
-# watch control file for uscan
 version=3
-ftp://rostlab.org/norsp/norsp-(.+)\.tar\.gz debian uupdate
+ftp://rostlab.org/norsp/norsp-([0-9.]+)\.tar\.gz debian uupdate
 


