[med-svn] r4206 - in trunk/packages: . alien-hunter alien-hunter/trunk alien-hunter/trunk/debian

[Andreas Tille]

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 <tille at debian.org>  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 <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>
+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:cvsuser at 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}

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 <tille at debian.org>, 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
+