diff -Nru alien-hunter-1.7/debian/changelog alien-hunter-1.7/debian/changelog --- alien-hunter-1.7/debian/changelog 2013-10-21 17:27:19.000000000 +0000 +++ alien-hunter-1.7/debian/changelog 2013-09-12 16:56:09.000000000 +0000 @@ -1,3 +1,22 @@ +alien-hunter (1.7-2) unstable; urgency=low + + [ Charles Plessy ] + * Documented information in ‘debian/upstream’. + * Removed mention of the bibliographic reference in ‘debian/control’. + * Updated homepage (debian/control). + + [ Andreas Tille ] + * debian/upstream: Removed duplicated information, reordering + * debian/copyright: DEP5 + * debian/source/format: 3.0 (quilt) + * debian/control: + - cme fix dpkg-control + - debhelper 9 + - anonscm in Vcs fields + - drop quilt from Build-Depends + + -- Andreas Tille Thu, 12 Sep 2013 17:16:21 +0200 + alien-hunter (1.7-1) unstable; urgency=low * Initial release (Closes: #550954) diff -Nru alien-hunter-1.7/debian/compat alien-hunter-1.7/debian/compat --- alien-hunter-1.7/debian/compat 2013-10-21 17:27:19.000000000 +0000 +++ alien-hunter-1.7/debian/compat 2013-09-12 15:18:45.000000000 +0000 @@ -1 +1 @@ -7 +9 diff -Nru alien-hunter-1.7/debian/control alien-hunter-1.7/debian/control --- alien-hunter-1.7/debian/control 2013-10-21 17:27:19.000000000 +0000 +++ alien-hunter-1.7/debian/control 2013-09-12 15:21:11.000000000 +0000 @@ -1,19 +1,26 @@ Source: alien-hunter -Section: science -Priority: optional Maintainer: Debian Med Packaging Team -DM-Upload-Allowed: yes Uploaders: Andreas Tille -Build-Depends: debhelper (>= 7.1), libbiojava-java, default-jdk, quilt -Standards-Version: 3.8.3 -Homepage: http://www.sanger.ac.uk/Software/analysis/alien_hunter/ -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/alien-hunter/trunk/?rev=0&sc=0 -Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/alien-hunter/trunk/ +Section: science +Priority: optional +Build-Depends: debhelper (>= 9), + libbiojava-java, + default-jdk +Standards-Version: 3.9.4 +Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/alien-hunter/trunk/ +Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/alien-hunter/trunk/ +Homepage: http://www.sanger.ac.uk/resources/software/alien_hunter.html Package: alien-hunter Architecture: all -Depends: ${shlibs:Depends}, ${misc:Depends}, libbytecode-java, libbiojava-java, - libcommons-cli-java, libcommons-collections-java, libcommons-dbcp-java, libcommons-pool-java +Depends: ${shlibs:Depends}, + ${misc:Depends}, + libbytecode-java, + libbiojava-java, + libcommons-cli-java, + libcommons-collections-java, + libcommons-dbcp-java, + libcommons-pool-java Suggests: bioperl Description: Interpolated Variable Order Motifs to identify horizontally acquired DNA Alien_hunter is an application for the prediction of putative @@ -27,10 +34,3 @@ predicted regions. The predictions (embl format) can be automatically loaded into Artemis genome viewer freely available at: http://www.sanger.ac.uk/Software/Artemis/. - . - The manuscript describing the alien_hunter algorithm is available - from Bioinformatics: Interpolated variable order motifs for - identification of horizontally acquired DNA: revisiting the - Salmonella pathogenicity islands. Vernikos GS, Parkhill J - Bioinformatics. 2006;. PMID: 16837528 - diff -Nru alien-hunter-1.7/debian/copyright alien-hunter-1.7/debian/copyright --- alien-hunter-1.7/debian/copyright 2013-10-21 17:27:19.000000000 +0000 +++ alien-hunter-1.7/debian/copyright 2013-09-12 16:52:44.000000000 +0000 @@ -1,25 +1,30 @@ -Name : Alien_hunter -Contact : George Vernikos -Source : http://www.sanger.ac.uk/Software/analysis/alien_hunter/ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: Alien_hunter +Upstream-Contact: George Vernikos +Source: http://www.sanger.ac.uk/Software/analysis/alien_hunter/ -Copyright : © 2006-2008 George Vernikos -License: +Files: * +Copyright: 2006-2008 George Vernikos +License: GPL2 + +License: GPL2 This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. - + . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. - + . You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA. -X-Comment: On Debian GNU/Linux you can find these licenses under + . + On Debian GNU/Linux you can find these licenses under /usr/share/common-licenses/GPL Files: debian/* -Copyright: © 2009 Andreas Tille -Licence: Same as alien_hunter +Copyright: 2009 Andreas Tille +License: GPL2 diff -Nru alien-hunter-1.7/debian/get-orig-source alien-hunter-1.7/debian/get-orig-source --- alien-hunter-1.7/debian/get-orig-source 2013-10-21 17:27:19.000000000 +0000 +++ alien-hunter-1.7/debian/get-orig-source 2013-09-12 08:57:41.000000000 +0000 @@ -22,5 +22,5 @@ cp -a ../alien_hunter/alien_hunter/Changepoint*.java . cd .. -GZIP=-9 tar -czf "$PKG"_"$DVERSION".orig.tar.gz ${UNAME}-${DVERSION} +GZIP="--best --no-name" tar -czf "$PKG"_"$DVERSION".orig.tar.gz ${UNAME}-${DVERSION} rm -rf ${UNAME}-${DVERSION} diff -Nru alien-hunter-1.7/debian/patches/10_fix_classpath.patch alien-hunter-1.7/debian/patches/10_fix_classpath.patch --- alien-hunter-1.7/debian/patches/10_fix_classpath.patch 2013-10-21 17:27:19.000000000 +0000 +++ alien-hunter-1.7/debian/patches/10_fix_classpath.patch 2013-09-12 16:53:56.000000000 +0000 @@ -1,3 +1,7 @@ +Author: Andreas Tille +Date: Wed, 14 Oct 2009 11:41:51 +0200 +Description: Set CLASSPATH properly + --- alien_hunter-1.7.orig/alien_hunter +++ alien_hunter-1.7/alien_hunter @@ -27,14 +27,14 @@ diff -Nru alien-hunter-1.7/debian/patches/10_location_of_perl.patch alien-hunter-1.7/debian/patches/10_location_of_perl.patch --- alien-hunter-1.7/debian/patches/10_location_of_perl.patch 2013-10-21 17:27:19.000000000 +0000 +++ alien-hunter-1.7/debian/patches/10_location_of_perl.patch 2013-09-12 16:54:35.000000000 +0000 @@ -1,3 +1,7 @@ +Author: Andreas Tille +Date: Wed, 14 Oct 2009 11:41:51 +0200 +Description: Do not point to /usr/local + --- alien_hunter-1.7.orig/alien_hunter.pl +++ alien_hunter-1.7/alien_hunter.pl @@ -1,4 +1,3 @@ diff -Nru alien-hunter-1.7/debian/rules alien-hunter-1.7/debian/rules --- alien-hunter-1.7/debian/rules 2013-10-21 17:27:19.000000000 +0000 +++ alien-hunter-1.7/debian/rules 2013-09-12 15:26:50.000000000 +0000 @@ -6,7 +6,7 @@ executable=alien_hunter %: - dh --with quilt $@ + dh $@ override_dh_auto_build: CLASSPATH=/usr/share/java/biojava.jar javac -Xlint:deprecation -Xlint:unchecked *.java diff -Nru alien-hunter-1.7/debian/source/format alien-hunter-1.7/debian/source/format --- alien-hunter-1.7/debian/source/format 1970-01-01 00:00:00.000000000 +0000 +++ alien-hunter-1.7/debian/source/format 2013-10-21 17:27:19.872564740 +0000 @@ -0,0 +1 @@ +3.0 (quilt) diff -Nru alien-hunter-1.7/debian/upstream alien-hunter-1.7/debian/upstream --- alien-hunter-1.7/debian/upstream 1970-01-01 00:00:00.000000000 +0000 +++ alien-hunter-1.7/debian/upstream 2013-09-12 08:57:41.000000000 +0000 @@ -0,0 +1,17 @@ +Contact: George Vernikos +Homepage: http://www.sanger.ac.uk/resources/software/alien_hunter.html +Name: Alien_hunter +Reference: + author: Vernikos, Georgios S. and Parkhill, Julian + title: > + Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands + journal: Bioinformatics + volume: 22 + number: 18 + pages: 2196-2203 + doi: 10.1093/bioinformatics/btl369 + year: 2006 + PMID: 16837528 + URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/18/2196 + eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/22/18/2196.pdf +Watch: http://www.sanger.ac.uk/Software/analysis/alien_hunter/alien_hunter-([.\d]+)\.tar\.gz