--- alien-hunter-1.7.orig/debian/watch +++ alien-hunter-1.7/debian/watch @@ -0,0 +1,3 @@ +version=3 +http://www.sanger.ac.uk/Software/analysis/alien_hunter/alien_hunter-([.\d]+)\.tar\.gz + --- alien-hunter-1.7.orig/debian/copyright +++ alien-hunter-1.7/debian/copyright @@ -0,0 +1,25 @@ +Name : Alien_hunter +Contact : George Vernikos +Source : http://www.sanger.ac.uk/Software/analysis/alien_hunter/ + +Copyright : © 2006-2008 George Vernikos +License: + 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 + /usr/share/common-licenses/GPL + +Files: debian/* +Copyright: © 2009 Andreas Tille +Licence: Same as alien_hunter --- alien-hunter-1.7.orig/debian/manpages +++ alien-hunter-1.7/debian/manpages @@ -0,0 +1 @@ +debian/alien_hunter.1 --- alien-hunter-1.7.orig/debian/changelog +++ alien-hunter-1.7/debian/changelog @@ -0,0 +1,5 @@ +alien-hunter (1.7-1) unstable; urgency=low + + * Initial release (Closes: #550954) + + -- Andreas Tille Wed, 14 Oct 2009 11:41:51 +0200 --- alien-hunter-1.7.orig/debian/README.source +++ alien-hunter-1.7/debian/README.source @@ -0,0 +1,16 @@ +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 --- alien-hunter-1.7.orig/debian/compat +++ alien-hunter-1.7/debian/compat @@ -0,0 +1 @@ +7 --- alien-hunter-1.7.orig/debian/install +++ alien-hunter-1.7/debian/install @@ -0,0 +1,5 @@ +*.pm usr/share/perl5 +PAI_scripts usr/share/perl5 +*.pl usr/share/alien_hunter +*.class usr/share/alien_hunter +alien_hunter usr/bin --- alien-hunter-1.7.orig/debian/get-orig-source +++ alien-hunter-1.7/debian/get-orig-source @@ -0,0 +1,26 @@ +#!/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=-9 tar -czf "$PKG"_"$DVERSION".orig.tar.gz ${UNAME}-${DVERSION} +rm -rf ${UNAME}-${DVERSION} --- alien-hunter-1.7.orig/debian/rules +++ alien-hunter-1.7/debian/rules @@ -0,0 +1,18 @@ +#!/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 --with quilt $@ + +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 --- alien-hunter-1.7.orig/debian/control +++ alien-hunter-1.7/debian/control @@ -0,0 +1,36 @@ +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/ + +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/. + . + 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 + --- alien-hunter-1.7.orig/debian/examples +++ alien-hunter-1.7/debian/examples @@ -0,0 +1 @@ +demoSeq.dna --- alien-hunter-1.7.orig/debian/alien_hunter.1 +++ alien-hunter-1.7/debian/alien_hunter.1 @@ -0,0 +1,73 @@ +.\" 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\. --- alien-hunter-1.7.orig/debian/patches/10_fix_classpath.patch +++ alien-hunter-1.7/debian/patches/10_fix_classpath.patch @@ -0,0 +1,24 @@ +--- 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 --- alien-hunter-1.7.orig/debian/patches/series +++ alien-hunter-1.7/debian/patches/series @@ -0,0 +1,2 @@ +10_fix_classpath.patch +10_location_of_perl.patch --- alien-hunter-1.7.orig/debian/patches/10_location_of_perl.patch +++ alien-hunter-1.7/debian/patches/10_location_of_perl.patch @@ -0,0 +1,7 @@ +--- 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 +