Author: alteholz Date: 2013-05-01 20:09:53 +0000 (Wed, 01 May 2013) New Revision: 13468
Added: trunk/packages/proalign/trunk/debian/manifest.txt trunk/packages/proalign/trunk/debian/proalign.install trunk/packages/proalign/trunk/debian/rules trunk/packages/proalign/trunk/debian/scripts/ trunk/packages/proalign/trunk/debian/scripts/proalign trunk/packages/proalign/trunk/debian/source/ trunk/packages/proalign/trunk/debian/source/format Modified: trunk/packages/proalign/trunk/debian/ trunk/packages/proalign/trunk/debian/changelog trunk/packages/proalign/trunk/debian/control trunk/packages/proalign/trunk/debian/watch Log: proalign almost ready, just needs a manpage and some tests Property changes on: trunk/packages/proalign/trunk/debian ___________________________________________________________________ Added: mergeWithUpstream + 1 Modified: trunk/packages/proalign/trunk/debian/changelog =================================================================== --- trunk/packages/proalign/trunk/debian/changelog 2013-05-01 13:31:42 UTC (rev 13467) +++ trunk/packages/proalign/trunk/debian/changelog 2013-05-01 20:09:53 UTC (rev 13468) @@ -1,5 +1,5 @@ -proalign (0.603-1) unstable; urgency=low +proalign (0.603-1) UNRELEASED; urgency=low * Initial release (Closes: #378290) - -- Andreas Tille <ti...@debian.org> Thu, 24 May 2012 14:30:13 +0200 + -- Thorsten Alteholz <deb...@alteholz.de> Tue, 01 May 2013 18:00:00 +0200 Modified: trunk/packages/proalign/trunk/debian/control =================================================================== --- trunk/packages/proalign/trunk/debian/control 2013-05-01 13:31:42 UTC (rev 13467) +++ trunk/packages/proalign/trunk/debian/control 2013-05-01 20:09:53 UTC (rev 13468) @@ -3,9 +3,10 @@ Priority: optional Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> DM-Upload-Allowed: yes -Uploaders: Andreas Tille <ti...@debian.org> +Uploaders: Andreas Tille <ti...@debian.org>, + Thorsten Alteholz <deb...@alteholz.de> Build-Depends: debhelper (>= 9) -Standards-Version: 3.9.3 +Standards-Version: 3.9.4 Homepage: http://ueg.ulb.ac.be/ProAlign/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/proalign/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/proalign/trunk/ @@ -18,11 +19,11 @@ models (HMM). It includes a graphical interface (GUI) allowing to (i) perform alignments of nucleotide or amino-acid sequences, (ii) view the quality of solutions, (iii) filter the unreliable alignment regions and - (iv) export alignments to other softwares. + (iv) export alignments to other software. . ProAlign uses a progressive method, such that multiple alignment is created stepwise by performing pairwise alignments in the nodes of a guide tree. Sequences are described with vectors of character probabilities, and each pairwise alignment reconstructs the ancestral (parent) sequence by computing the probabilities of different - characters according to an evolutionary model. \ No newline at end of file + characters according to an evolutionary model. Added: trunk/packages/proalign/trunk/debian/manifest.txt =================================================================== --- trunk/packages/proalign/trunk/debian/manifest.txt (rev 0) +++ trunk/packages/proalign/trunk/debian/manifest.txt 2013-05-01 20:09:53 UTC (rev 13468) @@ -0,0 +1,3 @@ +Manifest-version: 1.0 +Main-Class: proalign.ProAlign + Added: trunk/packages/proalign/trunk/debian/proalign.install =================================================================== --- trunk/packages/proalign/trunk/debian/proalign.install (rev 0) +++ trunk/packages/proalign/trunk/debian/proalign.install 2013-05-01 20:09:53 UTC (rev 13468) @@ -0,0 +1,3 @@ +debian/scripts/proalign usr/bin +build/ProAlign.jar usr/share/proalign + Added: trunk/packages/proalign/trunk/debian/rules =================================================================== --- trunk/packages/proalign/trunk/debian/rules (rev 0) +++ trunk/packages/proalign/trunk/debian/rules 2013-05-01 20:09:53 UTC (rev 13468) @@ -0,0 +1,23 @@ +#!/usr/bin/make -f + +# DH_VERBOSE := 1 + +%: + dh $@ + +override_dh_auto_build: + mkdir -p build + javac -d ./build *.java + find + (cd build; jar cmvf ../debian/manifest.txt ProAlign.jar *) + #(cd build; jar cmvf ../debian/manifest.txt ProAlign.jar proalign/ProAlign.class proalign/OutFile.class) + +override_dh_auto_install: + find + dh_auto_install + #dh_installchangelogs README + +get-orig-source: + mkdir -p ../tarballs + uscan --verbose --force-download --destdir=../tarballs + Property changes on: trunk/packages/proalign/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/proalign/trunk/debian/scripts/proalign =================================================================== --- trunk/packages/proalign/trunk/debian/scripts/proalign (rev 0) +++ trunk/packages/proalign/trunk/debian/scripts/proalign 2013-05-01 20:09:53 UTC (rev 13468) @@ -0,0 +1,19 @@ +#!/bin/sh + +if [ -z $JAVA_HOME ]; then + java=java +else + java=$JAVA_HOME/bin/java +fi + +if [ -x /usr/share/proalign ]; then + if [ -r /usr/share/proalign/ProAlign.jar ]; then + #cd /usr/share/proalign && $java -jar ProAlign.jar + $java -jar /usr/share/proalign/ProAlign.jar + else + echo "Could not find /usr/share/proalign/ProAlign.jar" + fi +else + echo "Could not find /usr/share/proalign directory." +fi + Added: trunk/packages/proalign/trunk/debian/source/format =================================================================== --- trunk/packages/proalign/trunk/debian/source/format (rev 0) +++ trunk/packages/proalign/trunk/debian/source/format 2013-05-01 20:09:53 UTC (rev 13468) @@ -0,0 +1 @@ +3.0 (quilt) Modified: trunk/packages/proalign/trunk/debian/watch =================================================================== --- trunk/packages/proalign/trunk/debian/watch 2013-05-01 13:31:42 UTC (rev 13467) +++ trunk/packages/proalign/trunk/debian/watch 2013-05-01 20:09:53 UTC (rev 13468) @@ -1,4 +1,4 @@ version=3 -opts=dversionmangle=s/\.// \ +opts=uversionmangle=s/0/0\./ \ http://ueg.ulb.ac.be/ProAlign/download/src/proalign_(.+)\.tgz _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit