[med-svn] r4207 - in trunk/packages/alien-hunter/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Wed Oct 14 09:54:05 UTC 2009
Author: tille
Date: 2009-10-14 09:54:04 +0000 (Wed, 14 Oct 2009)
New Revision: 4207
Added:
trunk/packages/alien-hunter/trunk/debian/README.source
trunk/packages/alien-hunter/trunk/debian/copyright
trunk/packages/alien-hunter/trunk/debian/docs
trunk/packages/alien-hunter/trunk/debian/examples
trunk/packages/alien-hunter/trunk/debian/install
trunk/packages/alien-hunter/trunk/debian/patches/
trunk/packages/alien-hunter/trunk/debian/patches/10_fix_classpath.patch
trunk/packages/alien-hunter/trunk/debian/patches/series
Modified:
trunk/packages/alien-hunter/trunk/debian/changelog
trunk/packages/alien-hunter/trunk/debian/control
trunk/packages/alien-hunter/trunk/debian/get-orig-source
trunk/packages/alien-hunter/trunk/debian/rules
Log:
More packaging stuff but not yet a working package
Added: trunk/packages/alien-hunter/trunk/debian/README.source
===================================================================
--- trunk/packages/alien-hunter/trunk/debian/README.source (rev 0)
+++ trunk/packages/alien-hunter/trunk/debian/README.source 2009-10-14 09:54:04 UTC (rev 4207)
@@ -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 <tille at debian.org> Wed, 16 Apr 2008 19:45:31 +0200
Modified: trunk/packages/alien-hunter/trunk/debian/changelog
===================================================================
--- trunk/packages/alien-hunter/trunk/debian/changelog 2009-10-14 07:59:44 UTC (rev 4206)
+++ trunk/packages/alien-hunter/trunk/debian/changelog 2009-10-14 09:54:04 UTC (rev 4207)
@@ -2,4 +2,4 @@
* Raised from priority extra to optional according to policy
- -- Andreas Tille <tille at debian.org> Wed, 16 Apr 2008 19:45:31 +0200
+ -- Andreas Tille <tille at debian.org> Wed, 14 Oct 2009 11:41:51 +0200
Modified: trunk/packages/alien-hunter/trunk/debian/control
===================================================================
--- trunk/packages/alien-hunter/trunk/debian/control 2009-10-14 07:59:44 UTC (rev 4206)
+++ trunk/packages/alien-hunter/trunk/debian/control 2009-10-14 09:54:04 UTC (rev 4207)
@@ -4,7 +4,7 @@
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
+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
@@ -12,19 +12,20 @@
Package: alien-hunter
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Recommends: bioperl
+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 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:
+ 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
Added: trunk/packages/alien-hunter/trunk/debian/copyright
===================================================================
--- trunk/packages/alien-hunter/trunk/debian/copyright (rev 0)
+++ trunk/packages/alien-hunter/trunk/debian/copyright 2009-10-14 09:54:04 UTC (rev 4207)
@@ -0,0 +1,25 @@
+Name : Alien_hunter
+Contact : George Vernikos <gsv at sanger.ac.uk>
+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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+X-Comment: On Debian GNU/Linux you can find these licenses under
+ /usr/share/common-licenses/GPL
+
+Files: debian/*
+Copyright: © 2009 Andreas Tille <tille at debian.org>
+Licence: Same as alien_hunter
Added: trunk/packages/alien-hunter/trunk/debian/docs
===================================================================
--- trunk/packages/alien-hunter/trunk/debian/docs (rev 0)
+++ trunk/packages/alien-hunter/trunk/debian/docs 2009-10-14 09:54:04 UTC (rev 4207)
@@ -0,0 +1 @@
+README
Added: trunk/packages/alien-hunter/trunk/debian/examples
===================================================================
--- trunk/packages/alien-hunter/trunk/debian/examples (rev 0)
+++ trunk/packages/alien-hunter/trunk/debian/examples 2009-10-14 09:54:04 UTC (rev 4207)
@@ -0,0 +1 @@
+demoSeq.dna
Modified: trunk/packages/alien-hunter/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/alien-hunter/trunk/debian/get-orig-source 2009-10-14 07:59:44 UTC (rev 4206)
+++ trunk/packages/alien-hunter/trunk/debian/get-orig-source 2009-10-14 09:54:04 UTC (rev 4207)
@@ -23,3 +23,4 @@
cd ..
GZIP=-9 tar -czf "$PKG"_"$DVERSION".orig.tar.gz ${UNAME}-${DVERSION}
+rm -rf ${UNAME}-${DVERSION}
Added: trunk/packages/alien-hunter/trunk/debian/install
===================================================================
--- trunk/packages/alien-hunter/trunk/debian/install (rev 0)
+++ trunk/packages/alien-hunter/trunk/debian/install 2009-10-14 09:54:04 UTC (rev 4207)
@@ -0,0 +1,4 @@
+*.pm /usr/share/perl5
+PAI_scripts /usr/share/perl5
+*.pl /usr/share/alien_hunter
+*.class /usr/share/alien_hunter
Added: trunk/packages/alien-hunter/trunk/debian/patches/10_fix_classpath.patch
===================================================================
--- trunk/packages/alien-hunter/trunk/debian/patches/10_fix_classpath.patch (rev 0)
+++ trunk/packages/alien-hunter/trunk/debian/patches/10_fix_classpath.patch 2009-10-14 09:54:04 UTC (rev 4207)
@@ -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
Added: trunk/packages/alien-hunter/trunk/debian/patches/series
===================================================================
--- trunk/packages/alien-hunter/trunk/debian/patches/series (rev 0)
+++ trunk/packages/alien-hunter/trunk/debian/patches/series 2009-10-14 09:54:04 UTC (rev 4207)
@@ -0,0 +1 @@
+10_fix_classpath.patch
Modified: trunk/packages/alien-hunter/trunk/debian/rules
===================================================================
--- trunk/packages/alien-hunter/trunk/debian/rules 2009-10-14 07:59:44 UTC (rev 4206)
+++ trunk/packages/alien-hunter/trunk/debian/rules 2009-10-14 09:54:04 UTC (rev 4207)
@@ -3,7 +3,13 @@
# Andreas Tille <tille at debian.org>, GPL
%:
- dh $@
+ dh --with quilt $@
+override_dh_install:
+ CLASSPATH=/usr/share/java/biojava.jar javac -Xlint:deprecation -Xlint:unchecked *.java
+
+override_dh_auto_clean:
+ rm -f *.class
+
get-orig-source:
. debian/get-orig-source
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