[med-svn] r7305 - trunk/packages/rostlab/disulfinder/trunk/debian

Steffen Möller moeller at alioth.debian.org
Tue Jul 19 08:02:08 UTC 2011 

Author: moeller
Date: 2011-07-19 08:02:07 +0000 (Tue, 19 Jul 2011)
New Revision: 7305

Modified:
   trunk/packages/rostlab/disulfinder/trunk/debian/README.Debian
   trunk/packages/rostlab/disulfinder/trunk/debian/changelog
   trunk/packages/rostlab/disulfinder/trunk/debian/control
   trunk/packages/rostlab/disulfinder/trunk/debian/rules
Log:
Finalising disulfinder


Modified: trunk/packages/rostlab/disulfinder/trunk/debian/README.Debian
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/README.Debian	2011-07-19 07:50:34 UTC (rev 7304)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/README.Debian	2011-07-19 08:02:07 UTC (rev 7305)
@@ -1,22 +1,34 @@
 Disulfinder
 ===========
+
 References
 ----------
-* A. Ceroni, A. Passerini, A. Vullo and P. Frasconi. DISULFIND: a Disulfide Bonding State and Cysteine Connectivity Prediction Server, Nucleic Acids Research, 34(Web Server issue):W177-W181, 2006. 
+* A. Ceroni, A. Passerini, A. Vullo and P. Frasconi. DISULFIND: a
+  Disulfide Bonding State and Cysteine Connectivity Prediction Server,
+  Nucleic Acids Research, 34(Web Server issue):W177-W181, 2006.
 
 For the disulphide connectivity predictor see:
 
-* A. Vullo and P. Frasconi. Disulfide Connectivity Prediction using Recursive Neural Networks and Evolutionary Information, Bioinformatics, 20, 653-659, 2004.
+* A. Vullo and P. Frasconi. Disulfide Connectivity Prediction using
+  Recursive Neural Networks and Evolutionary Information, Bioinformatics,
+  20, 653-659, 2004.
 
 For the cystein bonding state predictor see:
 
-* P. Frasconi, A. Passerini, and A. Vullo. A Two-Stage SVM Architecture for Predicting the Disulfide Bonding State of Cysteines, Proc. IEEE Workshop on Neural Networks for Signal Processing, pp.25-34, 2002.
+* P. Frasconi, A. Passerini, and A. Vullo. A Two-Stage SVM Architecture
+  for Predicting the Disulfide Bonding State of Cysteines, Proc. IEEE
+  Workshop on Neural Networks for Signal Processing, pp.25-34, 2002.
 
-* A.Ceroni, P.Frasconi, A.Passerini and A.Vullo. Predicting the Disulfide Bonding State of Cysteines with Combinations of Kernel Machines, Journal of VLSI Signal Processing, 35, 287-295, 2003. 
+* A.Ceroni, P.Frasconi, A.Passerini and A.Vullo. Predicting the Disulfide
+  Bonding State of Cysteines with Combinations of Kernel Machines, Journal
+  of VLSI Signal Processing, 35, 287-295, 2003.
 
+
 Upstream
 --------
-The upstream package is maintained and made available by the Rost Lab instead of P. Frasconi et al. at this time (2011).
 
+The upstream package is maintained and made available by the Rost Lab
+instead of P. Frasconi et al. at this time (2011).
+
 -- Laszlo Kajan <lkajan at rostlab.org>  Sat, 09 Jul 2011 12:08:06 +0200
 

Modified: trunk/packages/rostlab/disulfinder/trunk/debian/changelog
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/changelog	2011-07-19 07:50:34 UTC (rev 7304)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/changelog	2011-07-19 08:02:07 UTC (rev 7305)
@@ -1,5 +1,5 @@
-disulfinder (1.2.8-1) UNRELEASED; urgency=low
+disulfinder (1.2.8-1) unstable; urgency=low
 
-  * Initial release in Debian Med
+  * Initial release (Closes: #634177).
 
  -- Laszlo Kajan <lkajan at rostlab.org>  Sat, 09 Jul 2011 11:54:46 +0200

Modified: trunk/packages/rostlab/disulfinder/trunk/debian/control
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/control	2011-07-19 07:50:34 UTC (rev 7304)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/control	2011-07-19 08:02:07 UTC (rev 7305)
@@ -18,12 +18,13 @@
  and their disulfide connectivity starting from sequence alone. Disulfide
  bridges play a major role in the stabilization of the folding process for
  several proteins. Prediction of disulfide bridges from sequence alone is
- therefore useful for the study of structural and functional properties of
- specific proteins. In addition, knowledge about the disulfide bonding state of
- cysteines may help the experimental structure determination process and may be
- useful in other genomic annotation tasks.
- 'disulfinder' predicts disulfide patterns in two computational stages: (1) the
- disulfide bonding state of each cysteine is predicted by a BRNN-SVM binary
- classifier; (2) cysteines that are known to participate in the formation of
- bridges are paired by a Recursive Neural Network to obtain a connectivity
- pattern. 
+ therefore useful for the study of structural and functional properties
+ of specific proteins. In addition, knowledge about the disulfide bonding
+ state of cysteines may help the experimental structure determination
+ process and may be useful in other genomic annotation tasks.
+ .
+ 'disulfinder' predicts disulfide patterns in two computational stages:
+ (1) the disulfide bonding state of each cysteine is predicted by a
+ BRNN-SVM binary classifier; (2) cysteines that are known to participate
+ in the formation of bridges are paired by a Recursive Neural Network
+ to obtain a connectivity pattern.

Modified: trunk/packages/rostlab/disulfinder/trunk/debian/rules
===================================================================
--- trunk/packages/rostlab/disulfinder/trunk/debian/rules	2011-07-19 07:50:34 UTC (rev 7304)
+++ trunk/packages/rostlab/disulfinder/trunk/debian/rules	2011-07-19 08:02:07 UTC (rev 7305)
@@ -10,20 +10,8 @@
 #export DH_VERBOSE=1
 
 
-
-
-
-configure: configure-stamp
-configure-stamp:
-	dh_testdir
-	# Add here commands to configure the package.
-
-	touch configure-stamp
-
-
 build: build-stamp
-
-build-stamp: configure-stamp  
+build-stamp:
 	dh_testdir
 
 	# Add here commands to compile the package.
@@ -35,7 +23,7 @@
 clean: 
 	dh_testdir
 	dh_testroot
-	rm -f build-stamp configure-stamp
+	rm -f build-stamp 
 
 	# Add here commands to clean up after the build process.
 	$(MAKE) distclean
@@ -64,23 +52,12 @@
 	dh_installdocs
 	dh_installexamples
 #	dh_install
-#	dh_installmenu
-#	dh_installdebconf	
-#	dh_installlogrotate
-#	dh_installemacsen
-#	dh_installpam
-#	dh_installmime
 #	dh_python
-#	dh_installinit
-#	dh_installcron
-#	dh_installinfo
 	dh_installman
 	dh_link
 	dh_strip
 	dh_compress
 	dh_fixperms
-#	dh_perl
-#	dh_makeshlibs
 	dh_installdeb
 	dh_shlibdeps
 	dh_gencontrol
@@ -89,3 +66,19 @@
 
 binary: binary-indep binary-arch
 .PHONY: build clean binary-indep binary-arch binary install configure
+
+VERSION=`dpkg-parsechangelog  | grep Version | cut -f2 -d\ | cut -f1 -d-`
+get-orig-source:
+	uscan --force-download --verbose --download-current-version
+	cd .. && tar xzvf disulfinder_$(VERSION).orig.tar.gz
+	cd .. ; \
+	if [ ! -r disulfinder-$(VERSION)/disulfind.tgz ]; then \
+		echo "orig.tar.gz can stay as it is." ; \
+	else \
+		disulfinder_$(VERSION).orig.tar.gz ; \
+		rm disulfinder-$(VERSION)/disulfind.tgz  ; \
+		GZIP="--best --no-name" tar czvf disulfinder_$(VERSION).orig.tar.gz disulfinder-$(VERSION) ; \
+	fi 
+	cd .. && rm -r disulfinder-$(VERSION)
+	
+

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