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 <[email protected]> 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 <[email protected]> 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) + + _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
