Author: lkajan-guest
Date: 2013-04-17 13:19:34 +0000 (Wed, 17 Apr 2013)
New Revision: 13335
Added:
trunk/packages/metastudent/trunk/
trunk/packages/metastudent/trunk/debian/
trunk/packages/metastudent/trunk/debian/README.Debian
trunk/packages/metastudent/trunk/debian/changelog
trunk/packages/metastudent/trunk/debian/compat
trunk/packages/metastudent/trunk/debian/control
trunk/packages/metastudent/trunk/debian/copyright
trunk/packages/metastudent/trunk/debian/javabuild
trunk/packages/metastudent/trunk/debian/libgossip-java.jlibs
trunk/packages/metastudent/trunk/debian/libgroupb-java.jlibs
trunk/packages/metastudent/trunk/debian/rules
trunk/packages/metastudent/trunk/debian/source/
trunk/packages/metastudent/trunk/debian/source/format
trunk/packages/metastudent/trunk/debian/upstream
Log:
copied Debianization from upstream repository to this Alioth repository
Property changes on: trunk/packages/metastudent/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/metastudent/trunk/debian/README.Debian
===================================================================
--- trunk/packages/metastudent/trunk/debian/README.Debian
(rev 0)
+++ trunk/packages/metastudent/trunk/debian/README.Debian 2013-04-17
13:19:34 UTC (rev 13335)
@@ -0,0 +1,5 @@
+metastudent for Debian
+======================
+metastudent requires large databases (~400M compressed) for operation. These
are available from [1], and are released under the GPL-2+. metastudent
automatically downloads these databases from [1], in case they are not yet
present on the host machine.
+
+[1] ftp://rostlab.org/metastudent/metastudent-data_[0-9.]+.tar.gz
Added: trunk/packages/metastudent/trunk/debian/changelog
===================================================================
--- trunk/packages/metastudent/trunk/debian/changelog
(rev 0)
+++ trunk/packages/metastudent/trunk/debian/changelog 2013-04-17 13:19:34 UTC
(rev 13335)
@@ -0,0 +1,13 @@
+metastudent (1.0.7-1) UNRELEASED; urgency=low
+
+ * New upstream release.
+ [Laszlo Kajan <lka...@rostlab.org>]
+ * Added BMC Bioinfo paper to d/upstream.
+
+ -- Tobias Hamp <ha...@rostlab.org> Mon, 15 Apr 2013 12:08:13 +0100
+
+metastudent (1.0.6) unstable; urgency=low
+
+ * Initial release.
+
+ -- Tobias Hamp <ha...@rostlab.org> Fri, 4 Feb 2013 23:26:00 +0200
Added: trunk/packages/metastudent/trunk/debian/compat
===================================================================
--- trunk/packages/metastudent/trunk/debian/compat
(rev 0)
+++ trunk/packages/metastudent/trunk/debian/compat 2013-04-17 13:19:34 UTC
(rev 13335)
@@ -0,0 +1 @@
+8
Property changes on: trunk/packages/metastudent/trunk/debian/compat
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/metastudent/trunk/debian/control
===================================================================
--- trunk/packages/metastudent/trunk/debian/control
(rev 0)
+++ trunk/packages/metastudent/trunk/debian/control 2013-04-17 13:19:34 UTC
(rev 13335)
@@ -0,0 +1,21 @@
+Source: metastudent
+Section: science
+Priority: optional
+Maintainer: Tobias Hamp <ha...@rostlab.org>
+Uploaders: Laszlo Kajan <lka...@debian.org>
+Build-Depends-Indep: debhelper (>=8~), python-support (>= 0.6), python (>=
2.6), javahelper (>=0.25), default-jdk
+XS-Python-Version: >= 2.6
+Standards-Version: 3.9.4
+
+Package: metastudent
+Architecture: all
+Homepage: http://www.rostlab.org
+Depends: ${misc:Depends}, ${perl:Depends}, ${python:Depends}, python (>= 2.6),
blast2, default-jre, libgo-perl, libipc-run-perl, libgraphviz-perl, perl
+Description: predictor of Gene Ontology terms from protein sequence
+ Often, only the sequence of a protein is known, but
+ not its functions. Metastudent will try to predict
+ missing functional annotations through homology searches (BLAST).
+ .
+ All predicted functions correspond to Gene Ontology (GO)
+ terms from the Molecular Function Ontology (MFO) and the Biological Process
+ Ontology (BPO) and are associated with a reliability score.
Added: trunk/packages/metastudent/trunk/debian/copyright
===================================================================
--- trunk/packages/metastudent/trunk/debian/copyright
(rev 0)
+++ trunk/packages/metastudent/trunk/debian/copyright 2013-04-17 13:19:34 UTC
(rev 13335)
@@ -0,0 +1,68 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: metastudent
+Upstream-Contact: Tobias Hamp <ha...@rostlab.org>
+Source: ftp://rostlab.org/metastudent/
+
+Files: metastudentPkg/lib/groupA/GO_Parser/src/ParseGONew.java
+Copyright: 2010, Ariane Böhm
+License: GPL-2+
+
+Files: metastudentPkg/lib/groupA/Validation/src/Validator.java
+Copyright: 2010, Ariane Böhm
+ 2010, Yannick Mahlich
+License: GPL-2+
+
+Files: metastudentPkg/lib/groupB/pp2/prediction/knn/BlastResultList.java
metastudentPkg/lib/groupB/pp2/prediction/knn/DAGNode.java
metastudentPkg/lib/groupB/pp2/prediction/knn/KNNPredictor.java
metastudentPkg/lib/groupB/pp2/prediction/knn/KNNKernel.java
metastudentPkg/lib/groupB/pp2/prediction/knn/PredictionTarget.java
metastudentPkg/lib/groupB/pp2/prediction/knn/BlastHit.java
metastudentPkg/lib/groupB/pp2/prediction/knn/kNearestNeighbor.java
metastudentPkg/lib/groupB/pp2/prediction/knn/GoNode.java
metastudentPkg/lib/groupB/src/pp2/prediction/knn/BlastResultList.java
metastudentPkg/lib/groupB/src/pp2/prediction/knn/DAGNode.java
metastudentPkg/lib/groupB/src/pp2/prediction/knn/KNNPredictor.java
metastudentPkg/lib/groupB/src/pp2/prediction/knn/KNNKernel.java
metastudentPkg/lib/groupB/src/pp2/prediction/knn/PredictionTarget.java
metastudentPkg/lib/groupB/src/pp2/prediction/knn/BlastHit.java
metastudentPkg/lib/groupB/src/pp2/prediction/knn/kNearestNeighbor.java
metastudentPkg/lib/groupB/src/pp2/prediction/knn/GoNode.java
+Copyright: 2010, Thomas Hopf
+License: GPL-2+
+
+Files: metastudentPkg/lib/groupB/pp2/prediction/knn/DetermineDistribution.java
metastudentPkg/lib/groupB/pp2/tools/RMethods.java
metastudentPkg/lib/groupB/src/pp2/prediction/knn/DetermineDistribution.java
+Copyright: 2010, Stefanie Kaufmann
+License: GPL-2+
+
+Files: metastudentPkg/lib/groupB/pp2/go/Relations.java
metastudentPkg/lib/groupB/pp2/go/DAG.java
metastudentPkg/lib/groupB/src/pp2/go/Relations.java
metastudentPkg/lib/groupB/src/pp2/go/DAG.java
+Copyright: 2010, Mark Heron
+License: GPL-2+
+
+Files: metastudentPkg/lib/groupC/treehandler.pl
metastudentPkg/lib/groupC/treehandler_new.pl
+Copyright: 2010, Peter Hoenigschmid
+License: GPL-2+
+
+Files: metastudentPkg/lib/groupC/Report.*
+Copyright: 2010, Dominik Achten
+ 2010, Michael Kiening
+ 2010, Maximilian Hecht
+ 2010, Peter Hönigschmid
+ 2010, Florian Auer
+ 2010, Manfred Roos
+License: GPL-2+
+
+Files: metastudent metastudentdata
+Copyright: 2012-2013 Tobias Hamp <ha...@rostlab.org>
+License: GPL-2+
+
+Files: debian/*
+Copyright: 2011-2013, Tobias Hamp <ha...@rostlab.org>
+ 2013, Laszlo Kajan <lka...@debian.org>
+License: GPL-2+
+
+Files: *
+Copyright: 2010-2013, Tobias Hamp <ha...@rostlab.org>
+License: GPL-2+
+
+License: GPL-2+
+ This package 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 package 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 package; if not, see .
+ .
+ On Debian systems, the complete text of the GNU General Public
+ License version 2 can be found in `/usr/share/common-licenses/GPL-2'
Added: trunk/packages/metastudent/trunk/debian/javabuild
===================================================================
--- trunk/packages/metastudent/trunk/debian/javabuild
(rev 0)
+++ trunk/packages/metastudent/trunk/debian/javabuild 2013-04-17 13:19:34 UTC
(rev 13335)
@@ -0,0 +1,3 @@
+metastudentPkg/lib/groupA/GOSSIP/gossip.jar
metastudentPkg/lib/groupA/GOSSIP/src
+metastudentPkg/lib/groupB/java/blastfilep.jar metastudentPkg/lib/groupB/java
+metastudentPkg/lib/groupB/pp2.jar metastudentPkg/lib/groupB
Added: trunk/packages/metastudent/trunk/debian/libgossip-java.jlibs
===================================================================
--- trunk/packages/metastudent/trunk/debian/libgossip-java.jlibs
(rev 0)
+++ trunk/packages/metastudent/trunk/debian/libgossip-java.jlibs
2013-04-17 13:19:34 UTC (rev 13335)
@@ -0,0 +1 @@
+metastudentPkg/lib/groupA/GOSSIP/gossip.jar
Added: trunk/packages/metastudent/trunk/debian/libgroupb-java.jlibs
===================================================================
--- trunk/packages/metastudent/trunk/debian/libgroupb-java.jlibs
(rev 0)
+++ trunk/packages/metastudent/trunk/debian/libgroupb-java.jlibs
2013-04-17 13:19:34 UTC (rev 13335)
@@ -0,0 +1,2 @@
+metastudentPkg/lib/groupB/java/blastfilep.jar
+metastudentPkg/lib/groupB/pp2.jar
Added: trunk/packages/metastudent/trunk/debian/rules
===================================================================
--- trunk/packages/metastudent/trunk/debian/rules
(rev 0)
+++ trunk/packages/metastudent/trunk/debian/rules 2013-04-17 13:19:34 UTC
(rev 13335)
@@ -0,0 +1,14 @@
+#!/usr/bin/make -f
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+JAVA_HOME=/usr/lib/jvm/default-java
+
+%:
+ dh $@ --with javahelper
+
+override_dh_auto_install:
+ dh_auto_install
+ find . -regex
".*/knn_weighted\|.*/CafaWrapper1\.pl\|.*/CafaWrapper2\.pl\|.*/CafaWrapper3\.pl\|.*/CafaWrapper3_new\.pl\|.*/exercise3\.pl\|.*/treehandler\.pl\|.*/validate\.pl"
-exec chmod +x {} \;
+
+# chmod +x tmp/usr/s
Property changes on: trunk/packages/metastudent/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/metastudent/trunk/debian/source/format
===================================================================
--- trunk/packages/metastudent/trunk/debian/source/format
(rev 0)
+++ trunk/packages/metastudent/trunk/debian/source/format 2013-04-17
13:19:34 UTC (rev 13335)
@@ -0,0 +1 @@
+3.0 (quilt)
Property changes on: trunk/packages/metastudent/trunk/debian/source/format
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/metastudent/trunk/debian/upstream
===================================================================
--- trunk/packages/metastudent/trunk/debian/upstream
(rev 0)
+++ trunk/packages/metastudent/trunk/debian/upstream 2013-04-17 13:19:34 UTC
(rev 13335)
@@ -0,0 +1,14 @@
+Name: metastudent
+Contact: Tobias Hamp <ha...@rostlab.org>
+Homepage: https://rostlab.org/owiki/index.php/Metastudent
+Reference:
+ - Author: Tobias Hamp and Rebecca Kassner and Stefan Seemayer and Esmeralda
Vicedo and Christian Schaefer and Dominik Achten and Florian Auer and Ariane
Boehm and Tatjana Braun and Maximilian Hecht and Mark Heron and Peter
Hönigschmid and Thomas A. Hopf and Stefanie Kaufmann and Michael Kiening and
Denis Krompass and Cedric Landerer and Yannick Mahlich and Manfred Roos and
Burkhard Rost
+ Title: 'Homology-based inference sets the bar high for protein function
prediction.'
+ Journal: BMC Bioinformatics
+ Year: 2013
+ Volume: 14
+ Number: 'Suppl 3'
+ Pages: S7
+ DOI: 10.1186/1471-2105-14-S3-S7
+ PMID: 23514582
+ URL: http://www.biomedcentral.com/1471-2105/14/S3/S7/
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