debian/0000755000000000000000000000000012262520347007171 5ustar debian/source/0000755000000000000000000000000012262520345010467 5ustar debian/source/format0000755000000000000000000000001412262004677011705 0ustar 3.0 (quilt) debian/rules0000755000000000000000000000142512262515771010260 0ustar #!/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_clean: dh_auto_clean rm -f metastudent.1 override_dh_auto_install: dh_auto_install find debian/metastudent -regex ".*/knn_weighted\|.*/CafaWrapper1\.pl\|.*/CafaWrapper2\.pl\|.*/CafaWrapper3\.pl\|.*/CafaWrapper3_new\.pl\|.*/exercise3\.pl\|.*/treehandler\.pl\|.*/validate\.pl" -exec chmod +x {} \; mv *.jar $(CURDIR)/debian/metastudent/usr/share/metastudent/ # lkajan 20140106: # The jars in d/metastudent.jlibs are for use by this package only, and should not end up in /usr/share/java. override_jh_installlibs: exit 0; get-orig-source: mkdir -p ../tarballs uscan --verbose --force-download --destdir=../tarballs debian/README.Debian0000644000000000000000000000050712262004677011237 0ustar metastudent for Debian ====================== metastudent searches through large data files (>100M compressed) in order to predict gene ontology terms. These data files are available from the metastudent-data package or [1], and are released under the GPL-2+. [1] ftp://rostlab.org/metastudent/metastudent-data_[0-9.]+.tar.gz debian/javabuild0000644000000000000000000000020012262004677011050 0ustar gossip.jar metastudentPkg/lib/groupA/GOSSIP/src blastfilep.jar metastudentPkg/lib/groupB/java pp2.jar metastudentPkg/lib/groupB debian/compat0000644000000000000000000000000212262004677010372 0ustar 9 debian/upstream0000644000000000000000000000145312262004677010762 0ustar Name: metastudent Contact: Tobias Hamp 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/ debian/changelog0000644000000000000000000000151312262520243011036 0ustar metastudent (1.0.11-1) unstable; urgency=low * New upstream release. -- Tobias Hamp Fri, 13 Dec 2013 09:21:18 +0200 metastudent (1.0.10-1) unstable; urgency=low * New upstream release. -- Tobias Hamp Sat, 08 Jun 2013 17:41:08 +0200 metastudent (1.0.9-1) unstable; urgency=low * New upstream release. -- Tobias Hamp Wed, 05 Jun 2013 16:41:08 +0200 metastudent (1.0.8-2) unstable; urgency=low * This version depends on data packaged as metastudent-data. -- Laszlo Kajan Wed, 08 May 2013 17:23:51 +0200 metastudent (1.0.8-1) unstable; urgency=low * Initial release (Closes: #705537) [Laszlo Kajan ] * Added BMC Bioinfo paper to d/upstream. -- Tobias Hamp Mon, 15 Apr 2013 12:08:13 +0100 debian/watch0000644000000000000000000000014312262004677010223 0ustar version=3 opts=pasv ftp://rostlab.org/metastudent/metastudent[_-]([0-9.]+)\.tar\.gz debian uupdate debian/control0000644000000000000000000000262112262057402010572 0ustar Source: metastudent Maintainer: Debian Med Packaging Team Uploaders: Tobias Hamp , Laszlo Kajan Section: science Priority: optional Build-Depends-Indep: debhelper (>=9~), python-support, python, javahelper, default-jdk Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/wsvn/debian-med/trunk/packages/metastudent/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/metastudent/trunk/ Homepage: https://rostlab.org/owiki/index.php/Metastudent X-Python-Version: >= 2.6 Package: metastudent Architecture: all Depends: ${misc:Depends}, ${perl:Depends}, python, blast2, default-jre, libgo-perl, libipc-run-perl, libgraphviz-perl, libfile-chdir-perl, metastudent-data, metastudent-data-2 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. debian/copyright0000644000000000000000000000672112262004677011135 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: metastudent Upstream-Contact: Tobias Hamp 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 License: GPL-2+ Files: debian/* Copyright: 2011-2013, Tobias Hamp 2013, Laszlo Kajan License: GPL-2+ Files: * Copyright: 2010-2013, Tobias Hamp 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' debian/metastudent.jlibs0000644000000000000000000000004212262004677012552 0ustar gossip.jar blastfilep.jar pp2.jar