debian/0000755000000000000000000000000012214377133007171 5ustar debian/watch0000644000000000000000000000014112214301005010177 0ustar version=3 http://www.sanger.ac.uk/Software/analysis/alien_hunter/alien_hunter-([.\d]+)\.tar\.gz debian/copyright0000644000000000000000000000220512214370534011121 0ustar 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/ 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. . On Debian GNU/Linux you can find these licenses under /usr/share/common-licenses/GPL Files: debian/* Copyright: 2009 Andreas Tille License: GPL2 debian/manpages0000644000000000000000000000002612214301005010666 0ustar debian/alien_hunter.1 debian/changelog0000644000000000000000000000134512214371051011037 0ustar 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) -- Andreas Tille Wed, 14 Oct 2009 11:41:51 +0200 debian/README.source0000644000000000000000000000124712214301005011335 0ustar README.source for alien_hunter: ------------------------------- The upstream tarball contained several jar files of other projects like BioJava, Bytecode and some projects from http://commons.apache.org. These jar files were stripped from the soure tarball as well as the CVS directories. Also the java source code of Changepoint{Left,Right}.class was lacking from the tarball. So the precompiled class files were removed and the Java sources obtained from CVS to build the original tarball. This packages uses the quilt patch system. Please read /usr/share/doc/quilt/README.source for more information. -- Andreas Tille Wed, 16 Apr 2008 19:45:31 +0200 debian/source/0000755000000000000000000000000012214301011010447 5ustar debian/source/format0000644000000000000000000000001412214301011011655 0ustar 3.0 (quilt) debian/compat0000644000000000000000000000000212214355525010370 0ustar 9 debian/install0000644000000000000000000000023412214301005010542 0ustar *.pm usr/share/perl5 PAI_scripts usr/share/perl5 *.pl usr/share/alien_hunter *.class usr/share/alien_hunter alien_hunter usr/bin debian/get-orig-source0000644000000000000000000000164012214301005012111 0ustar #!/bin/sh -e # Upstream source contains outdated BioJava code and is lacking java source # files which need to be obtained from CVS set -x UNAME=alien_hunter PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` DVERSION=`dpkg-parsechangelog | awk '/^Version/ { print $2 }' | cut -d- -f1` mkdir -p ../tarballs cd ../tarballs wget -q http://www.sanger.ac.uk/Software/analysis/${UNAME}/${UNAME}-${DVERSION}.tar.gz if [ ! -d alien_hunter -o ! -d alien_hunter/alien_hunter -o ! -f alien_hunter/alien_hunter/ChangepointLeft.java ] ; then cvs -d :pserver:cvsuser@cvs.sanger.ac.uk:/cvsroot/pathsoft co alien_hunter fi tar -xzf ${UNAME}-${DVERSION}.tar.gz cd ${UNAME}-${DVERSION} find . -type d -name CVS -exec rm -rf \{\} \; rm -rf biojava *.class cp -a ../alien_hunter/alien_hunter/Changepoint*.java . cd .. GZIP="--best --no-name" tar -czf "$PKG"_"$DVERSION".orig.tar.gz ${UNAME}-${DVERSION} rm -rf ${UNAME}-${DVERSION} debian/patches/0000755000000000000000000000000012214370713010615 5ustar debian/patches/10_fix_classpath.patch0000644000000000000000000000213712214370644014774 0ustar 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 @@ #$4 -a | -c | -i #$5 -a | -c | -i -USERPATH=`dirname $0` +USERPATH=/usr/share/alien_hunter -CLASSPATH=${CLASSPATH}:$USERPATH/biojava/biojava-1.4_new.jar -CLASSPATH=${CLASSPATH}:$USERPATH/biojava/commons-cli.jar -CLASSPATH=${CLASSPATH}:$USERPATH/biojava/commons-collections-2.1.jar -CLASSPATH=${CLASSPATH}:$USERPATH/biojava/commons-dbcp-1.1.jar -CLASSPATH=${CLASSPATH}:$USERPATH/biojava/commons-pool-1.1.jar -CLASSPATH=${CLASSPATH}:$USERPATH/biojava/bytecode-0.92.jar +#CLASSPATH=${CLASSPATH}:$USERPATH/biojava/biojava-1.4_new.jar +#CLASSPATH=${CLASSPATH}:$USERPATH/biojava/commons-cli.jar +#CLASSPATH=${CLASSPATH}:$USERPATH/biojava/commons-collections-2.1.jar +#CLASSPATH=${CLASSPATH}:$USERPATH/biojava/commons-dbcp-1.1.jar +#CLASSPATH=${CLASSPATH}:$USERPATH/biojava/commons-pool-1.1.jar +#CLASSPATH=${CLASSPATH}:$USERPATH/biojava/bytecode-0.92.jar CLASSPATH=${CLASSPATH}:$USERPATH/ export CLASSPATH debian/patches/series0000644000000000000000000000006112214355117012030 0ustar 10_fix_classpath.patch 10_location_of_perl.patch debian/patches/10_location_of_perl.patch0000644000000000000000000000037712214370713015463 0ustar Author: Andreas Tille Date: Wed, 14 Oct 2009 11:41:51 +0200 Description: Do not point to /usr/local --- alien_hunter-1.7.orig/alien_hunter.pl +++ alien_hunter-1.7/alien_hunter.pl @@ -1,4 +1,3 @@ -#!/usr/local/bin/perl =head1 NAME debian/rules0000755000000000000000000000065012214356472010255 0ustar #!/usr/bin/make -f # debian/rules for alien-hunter # Andreas Tille , GPL version=$(shell dpkg-parsechangelog | awk '/^Version/ { print $2 }' | cut -d- -f1 ) executable=alien_hunter %: dh $@ override_dh_auto_build: CLASSPATH=/usr/share/java/biojava.jar javac -Xlint:deprecation -Xlint:unchecked *.java override_dh_auto_clean: rm -f *.class $(executable).1 get-orig-source: . debian/get-orig-source debian/control0000644000000000000000000000315712214355747010611 0ustar Source: alien-hunter Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille 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 Suggests: bioperl Description: Interpolated Variable Order Motifs to identify horizontally acquired DNA Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). An IVOM approach exploits compositional biases using variable order motif distributions and captures more reliably the local composition of a sequence compared to fixed-order methods. Optionally the predictions can be parsed into a 2-state 2nd order Hidden Markov Model (HMM), in a change-point detection framework, to optimize the localization of the boundaries of the predicted regions. The predictions (embl format) can be automatically loaded into Artemis genome viewer freely available at: http://www.sanger.ac.uk/Software/Artemis/. debian/examples0000644000000000000000000000001412214301005010706 0ustar demoSeq.dna debian/upstream0000644000000000000000000000132112214301005010732 0ustar 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 debian/alien_hunter.10000644000000000000000000000472712214301005011723 0ustar .\" Originally generated by help2man 1.36. .TH ALIEN_HUNTER "1" "October 2009" "alien_hunter 1.7" "User Commands" .SH NAME alien_hunter \- Interpolated Variable Order Motifs for identification of horizontally acquired DNA .SH SYNOPSIS .B alien_hunter \fI\fR \fI\fR [\fIOptions\fR] .SH DESCRIPTION .PP Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). An IVOM approach exploits compositional biases using variable order motif distributions and captures more reliably the local composition of a sequence compared to fixed-order methods. Optionally the predictions can be parsed into a 2-state 2nd order Hidden Markov Model (HMM), in a change-point detection framework, to optimize the localization of the boundaries of the predicted regions. The predictions (embl format) can be automatically loaded into Artemis genome viewer freely available at: http://www.sanger.ac.uk/Software/Artemis/. .PP INPUT: raw genomic sequence PREDICTION: HGT regions based on Interpolated Variable Order Motifs (IVOMs) arguments: .TP raw genomic sequence .TP filename for output data .PP Optional arguments: .TP \-a to load the prediction file into Artemis .TP \-c optimize predicted boundaries with a change\-point detection 2 state 2nd order HMM .PP Output files: .TP predictions (tab file) in embl format .TP .opt optimized (HMM) predictions (tab file) in embl format .TP .plot predictions in Artemis User Plot format to be loaded manually using Graph \-> Add User Plot... .TP .opt.plot optimized (HMM) predictions in Artemis User Plot format to be loaded manually using Graph \-> Add User Plot... .TP .sco the scores over all the sliding windows \- for score distribution check .PP Note: Predictions that overlap with rRNA operon are mentioned in the note qualifier .SH SEE ALSO 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 .SH "AUTHOR" .PP This manual page was written by Andreas Tille for the Debian(TM) system (but may be used by others)\. This man page is released under the same conditions as the software, that is GPL\.