Author: tille Date: 2009-10-14 07:59:44 +0000 (Wed, 14 Oct 2009) New Revision: 4206
Added: trunk/packages/alien-hunter/ trunk/packages/alien-hunter/trunk/ trunk/packages/alien-hunter/trunk/debian/ trunk/packages/alien-hunter/trunk/debian/changelog trunk/packages/alien-hunter/trunk/debian/compat trunk/packages/alien-hunter/trunk/debian/control trunk/packages/alien-hunter/trunk/debian/get-orig-source trunk/packages/alien-hunter/trunk/debian/rules trunk/packages/alien-hunter/trunk/debian/watch Log: Quick shot at Sanger alien_hunter which might be used here in my institute. debian/rules is not working for the moment Added: trunk/packages/alien-hunter/trunk/debian/changelog =================================================================== --- trunk/packages/alien-hunter/trunk/debian/changelog (rev 0) +++ trunk/packages/alien-hunter/trunk/debian/changelog 2009-10-14 07:59:44 UTC (rev 4206) @@ -0,0 +1,5 @@ +alien-hunter (1.7-1) UNRELEASED; urgency=low + + * Raised from priority extra to optional according to policy + + -- Andreas Tille <[email protected]> Wed, 16 Apr 2008 19:45:31 +0200 Added: trunk/packages/alien-hunter/trunk/debian/compat =================================================================== --- trunk/packages/alien-hunter/trunk/debian/compat (rev 0) +++ trunk/packages/alien-hunter/trunk/debian/compat 2009-10-14 07:59:44 UTC (rev 4206) @@ -0,0 +1 @@ +7 Added: trunk/packages/alien-hunter/trunk/debian/control =================================================================== --- trunk/packages/alien-hunter/trunk/debian/control (rev 0) +++ trunk/packages/alien-hunter/trunk/debian/control 2009-10-14 07:59:44 UTC (rev 4206) @@ -0,0 +1,35 @@ +Source: alien-hunter +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Andreas Tille <[email protected]> +Build-Depends: debhelper (>= 7.0), libbiojava-java +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: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Recommends: bioperl +Description: Interpolated Variable Order Motifs for identification of 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 + Added: trunk/packages/alien-hunter/trunk/debian/get-orig-source =================================================================== --- trunk/packages/alien-hunter/trunk/debian/get-orig-source (rev 0) +++ trunk/packages/alien-hunter/trunk/debian/get-orig-source 2009-10-14 07:59:44 UTC (rev 4206) @@ -0,0 +1,25 @@ +#!/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:[email protected]:/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} Added: trunk/packages/alien-hunter/trunk/debian/rules =================================================================== --- trunk/packages/alien-hunter/trunk/debian/rules (rev 0) +++ trunk/packages/alien-hunter/trunk/debian/rules 2009-10-14 07:59:44 UTC (rev 4206) @@ -0,0 +1,9 @@ +#!/usr/bin/make -f +# debian/rules for alien-hunter +# Andreas Tille <[email protected]>, GPL + +%: + dh $@ + +get-orig-source: + . debian/get-orig-source Property changes on: trunk/packages/alien-hunter/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/alien-hunter/trunk/debian/watch =================================================================== --- trunk/packages/alien-hunter/trunk/debian/watch (rev 0) +++ trunk/packages/alien-hunter/trunk/debian/watch 2009-10-14 07:59:44 UTC (rev 4206) @@ -0,0 +1,3 @@ +version=3 +http://www.sanger.ac.uk/Software/analysis/alien_hunter/alien_hunter-([.\d]+)\.tar\.gz + _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
