[med-svn] r1571 - in trunk/packages: . martj martj/trunk martj/trunk/debian martj/trunk/debian/patches
tille at alioth.debian.org
tille at alioth.debian.org
Thu Mar 13 09:13:17 UTC 2008
Author: tille
Date: 2008-03-13 09:13:16 +0000 (Thu, 13 Mar 2008)
New Revision: 1571
Added:
trunk/packages/martj/
trunk/packages/martj/trunk/
trunk/packages/martj/trunk/README
trunk/packages/martj/trunk/debian/
trunk/packages/martj/trunk/debian/README.Debian
trunk/packages/martj/trunk/debian/changelog
trunk/packages/martj/trunk/debian/compat
trunk/packages/martj/trunk/debian/control
trunk/packages/martj/trunk/debian/copyright
trunk/packages/martj/trunk/debian/manpages
trunk/packages/martj/trunk/debian/martj-doc.docs
trunk/packages/martj/trunk/debian/martj.dirs
trunk/packages/martj/trunk/debian/martj.docs
trunk/packages/martj/trunk/debian/martj.examples
trunk/packages/martj/trunk/debian/martshell.1
trunk/packages/martj/trunk/debian/menu
trunk/packages/martj/trunk/debian/patches/
trunk/packages/martj/trunk/debian/patches/xyz.diff
trunk/packages/martj/trunk/debian/rules
Log:
Moved Steffen M?\195?\182llers work which was stalled to svn to keep track of previous work.
Added: trunk/packages/martj/trunk/README
===================================================================
--- trunk/packages/martj/trunk/README (rev 0)
+++ trunk/packages/martj/trunk/README 2008-03-13 09:13:16 UTC (rev 1571)
@@ -0,0 +1,3 @@
+Work on this project was started by Steffen Möller but has stalled.
+Feel free to take it over.
+
Added: trunk/packages/martj/trunk/debian/README.Debian
===================================================================
--- trunk/packages/martj/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/martj/trunk/debian/README.Debian 2008-03-13 09:13:16 UTC (rev 1571)
@@ -0,0 +1,18 @@
+martj for Debian
+----------------
+
+The Oracle Jar file is not distributed with the Debian package.
+
+The p6spy debian package is not yet available, hence the file distributed with it.
+Check out http://sourceforge.net/project/showfiles.php?group_id=49288 if interested.
+
+The ecp1 jar is on http://www.ewin.org/~bret/java/connectionPool/index.html,
+again, not Debian package yet.
+
+I could not get rid of jdom (did not build) or jdbc.
+
+The EnsJ jars should become a Debian package themselves, too.
+
+Steffen
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de>, Fri, 7 Jan 2005 23:58:01 +0100
Added: trunk/packages/martj/trunk/debian/changelog
===================================================================
--- trunk/packages/martj/trunk/debian/changelog (rev 0)
+++ trunk/packages/martj/trunk/debian/changelog 2008-03-13 09:13:16 UTC (rev 1571)
@@ -0,0 +1,6 @@
+martj (0.1-1) unstable; urgency=low
+
+ * Initial Release.
+
+ -- Steffen Möller <moeller at pzr.uni-rostock.de> Fri, 7 Jan 2005 23:58:01 +0100
+
Added: trunk/packages/martj/trunk/debian/compat
===================================================================
--- trunk/packages/martj/trunk/debian/compat (rev 0)
+++ trunk/packages/martj/trunk/debian/compat 2008-03-13 09:13:16 UTC (rev 1571)
@@ -0,0 +1 @@
+4
Added: trunk/packages/martj/trunk/debian/control
===================================================================
--- trunk/packages/martj/trunk/debian/control (rev 0)
+++ trunk/packages/martj/trunk/debian/control 2008-03-13 09:13:16 UTC (rev 1571)
@@ -0,0 +1,27 @@
+Source: martj
+Section: science
+Priority: optional
+Maintainer: Steffen Moeller <moeller at pzr.uni-rostock.de>
+Build-Depends: debhelper (>= 4.0.0), ant, junit, libreadline-java, jython, libgetopt-java, liblog4j1.2-java, libmysql-java, libant1.6-java, libxalan-java, libjdom-java
+Standards-Version: 3.6.1.1
+
+Package: martj
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}, libreadline-java, jython, libgetopt-java, liblog4j1.2-java, libmysql-java, libant1.6-java, libxalan-java, libjdom-java
+Description: distributed data integration system with powerful query capabilities
+ BioMart is a simple, distributed data integration system with powerful
+ query capabilities.
+ .
+ It has been designed to provide researchers with an easy and interactive
+ access to both the wealth of data available on the Internet and for
+ in house data integration. BioMart is a successor to the generic
+ query system originally developed for the Ensembl genome database
+ (EnsMart). Building on its success, BioMart, has now been applied to
+ other biological databases.
+ .
+ Homepage: http://www.ebi.ac.uk/biomart/
+
+Package: martj-doc
+Architecture: all
+Description: Documentation for martj
+ Javadoc API to MartJ.
Added: trunk/packages/martj/trunk/debian/copyright
===================================================================
--- trunk/packages/martj/trunk/debian/copyright (rev 0)
+++ trunk/packages/martj/trunk/debian/copyright 2008-03-13 09:13:16 UTC (rev 1571)
@@ -0,0 +1,28 @@
+This package was debianized by Steffen Moeller <moeller at pzr.uni-rostock.de> on
+Fri, 7 Jan 2005 23:58:01 +0100.
+
+It was downloaded from http://www.ebi.ac.uk/biomart/MartJ.html
+
+Copyright:
+
+Upstream Author: Arek Kasprzyk <arek at ebi.ac.uk>
+
+License:
+
+ This package is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser 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
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public
+ License along with this package; if not, write to the Free Software
+ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+
+On Debian systems, the complete text of the GNU Lesser General
+Public License can be found in `/usr/share/common-licenses/LGPL'.
+
Added: trunk/packages/martj/trunk/debian/manpages
===================================================================
--- trunk/packages/martj/trunk/debian/manpages (rev 0)
+++ trunk/packages/martj/trunk/debian/manpages 2008-03-13 09:13:16 UTC (rev 1571)
@@ -0,0 +1,3 @@
+debian/martshell.1
+marteditor.1
+martexplorer.1
Added: trunk/packages/martj/trunk/debian/martj-doc.docs
===================================================================
--- trunk/packages/martj/trunk/debian/martj-doc.docs (rev 0)
+++ trunk/packages/martj/trunk/debian/martj-doc.docs 2008-03-13 09:13:16 UTC (rev 1571)
@@ -0,0 +1,220 @@
+docs/api/constant-values.html
+docs/api/resources/inherit.gif
+docs/api/org/ensembl/mart/lib/class-use/UpStreamUTRSeqQueryRunner.html
+docs/api/org/ensembl/mart/lib/class-use/UnprocessedFilterHandlerFactory.html
+docs/api/org/ensembl/mart/lib/class-use/URLIDListFilterHandler.html
+docs/api/org/ensembl/mart/lib/class-use/TranscriptFlankSeqQueryRunner.html
+docs/api/org/ensembl/mart/lib/class-use/TranscriptExonSeqQueryRunner.html
+docs/api/org/ensembl/mart/lib/class-use/TranscriptEISeqQueryRunner.html
+docs/api/org/ensembl/mart/lib/class-use/Table.html
+docs/api/org/ensembl/mart/lib/class-use/SubQueryIDListFilterHandler.html
+docs/api/org/ensembl/mart/lib/class-use/SequenceLocation.html
+docs/api/org/ensembl/mart/lib/class-use/Sequence.html
+docs/api/org/ensembl/mart/lib/class-use/QueryRunnerFactory.html
+docs/api/org/ensembl/mart/lib/class-use/QueryAdaptor.html
+docs/api/org/ensembl/mart/lib/class-use/PeptideSeqQueryRunner.html
+docs/api/org/ensembl/mart/lib/class-use/LoggingUtils.html
+docs/api/org/ensembl/mart/lib/class-use/InvalidListException.html
+docs/api/org/ensembl/mart/lib/class-use/InputSourceUtil.html
+docs/api/org/ensembl/mart/lib/class-use/IDListFilter.html
+docs/api/org/ensembl/mart/lib/class-use/GenericHandler.html
+docs/api/org/ensembl/mart/lib/class-use/GeneFlankSeqQueryRunner.html
+docs/api/org/ensembl/mart/lib/class-use/GeneExonSeqQueryRunner.html
+docs/api/org/ensembl/mart/lib/class-use/GeneEISeqQueryRunner.html
+docs/api/org/ensembl/mart/lib/class-use/IDListFilterHandlerBase.html
+docs/api/org/ensembl/mart/lib/class-use/FileIDListFilterHandler.html
+docs/api/org/ensembl/mart/lib/class-use/UnprocessedFilterHandler.html
+docs/api/org/ensembl/mart/lib/class-use/ExpressionFilterHandler.html
+docs/api/org/ensembl/mart/lib/class-use/DownStreamUTRSeqQueryRunner.html
+docs/api/org/ensembl/mart/lib/class-use/DNAAdaptor.html
+docs/api/org/ensembl/mart/lib/class-use/CodingSeqQueryRunner.html
+docs/api/org/ensembl/mart/lib/class-use/CdnaSeqQueryRunner.html
+docs/api/org/ensembl/mart/lib/class-use/BooleanFilter.html
+docs/api/org/ensembl/mart/lib/class-use/BaseSeqQueryRunner.html
+docs/api/org/ensembl/mart/lib/class-use/BaseSeqQueryRunner.SeqWriter.html
+docs/api/org/ensembl/mart/lib/class-use/QueryCompiler.html
+docs/api/org/ensembl/mart/lib/class-use/QueryRunner.html
+docs/api/org/ensembl/mart/lib/class-use/AttributeQueryRunner.html
+docs/api/org/ensembl/mart/lib/class-use/Engine.html
+docs/api/org/ensembl/mart/lib/class-use/BasicFilter.html
+docs/api/org/ensembl/mart/lib/class-use/FormatSpec.html
+docs/api/org/ensembl/mart/lib/class-use/FieldAttribute.html
+docs/api/org/ensembl/mart/lib/class-use/Filter.html
+docs/api/org/ensembl/mart/lib/class-use/SequenceDescription.html
+docs/api/org/ensembl/mart/lib/class-use/Field.html
+docs/api/org/ensembl/mart/lib/class-use/Attribute.html
+docs/api/org/ensembl/mart/lib/class-use/Query.html
+docs/api/org/ensembl/mart/lib/class-use/QueryListener.html
+docs/api/org/ensembl/mart/lib/class-use/InvalidQueryException.html
+docs/api/org/ensembl/mart/lib/class-use/FormatException.html
+docs/api/org/ensembl/mart/lib/class-use/SequenceException.html
+docs/api/org/ensembl/mart/lib/class-use/DetailedDataSource.html
+docs/api/org/ensembl/mart/lib/config
+docs/api/org/ensembl/mart/lib/config/class-use
+docs/api/org/ensembl/mart/lib/config/class-use/URLDSConfigAdaptor.html
+docs/api/org/ensembl/mart/lib/config/class-use/SimpleDSConfigAdaptor.html
+docs/api/org/ensembl/mart/lib/config/class-use/NaiveDatasetConfigGenerator.html
+docs/api/org/ensembl/mart/lib/config/class-use/RegistryLocation.html
+docs/api/org/ensembl/mart/lib/config/class-use/URLLocation.html
+docs/api/org/ensembl/mart/lib/config/class-use/MartRegistryXMLUtils.html
+docs/api/org/ensembl/mart/lib/config/class-use/MartFilterGroupFilter.html
+docs/api/org/ensembl/mart/lib/config/class-use/MartFilterDescriptionFilter.html
+docs/api/org/ensembl/mart/lib/config/class-use/MartElementFilter.html
+docs/api/org/ensembl/mart/lib/config/class-use/MartConfiguration.html
+docs/api/org/ensembl/mart/lib/config/class-use/MartAttributeGroupFilter.html
+docs/api/org/ensembl/mart/lib/config/class-use/DatasetConfigUploader.html
+docs/api/org/ensembl/mart/lib/config/class-use/MartLocationBase.html
+docs/api/org/ensembl/mart/lib/config/class-use/DatabaseLocation.html
+docs/api/org/ensembl/mart/lib/config/class-use/DatasetConfigCache.html
+docs/api/org/ensembl/mart/lib/config/class-use/LeafDSConfigAdaptor.html
+docs/api/org/ensembl/mart/lib/config/class-use/DatabaseDSConfigAdaptor.html
+docs/api/org/ensembl/mart/lib/config/class-use/ClasspathDTDEntityResolver.html
+docs/api/org/ensembl/mart/lib/config/class-use/BaseMartElementFilter.html
+docs/api/org/ensembl/mart/lib/config/class-use/MartRegistry.html
+docs/api/org/ensembl/mart/lib/config/class-use/MultiDSConfigAdaptor.html
+docs/api/org/ensembl/mart/lib/config/class-use/CompositeDSConfigAdaptor.html
+docs/api/org/ensembl/mart/lib/config/class-use/RegistryDSConfigAdaptor.html
+docs/api/org/ensembl/mart/lib/config/class-use/DatabaseDatasetConfigUtils.html
+docs/api/org/ensembl/mart/lib/config/class-use/DatasetConfigXMLUtils.html
+docs/api/org/ensembl/mart/lib/config/class-use/DSFilterGroup.html
+docs/api/org/ensembl/mart/lib/config/class-use/DSAttributeGroup.html
+docs/api/org/ensembl/mart/lib/config/class-use/PushAction.html
+docs/api/org/ensembl/mart/lib/config/class-use/Disable.html
+docs/api/org/ensembl/mart/lib/config/class-use/Enable.html
+docs/api/org/ensembl/mart/lib/config/class-use/MartLocation.html
+docs/api/org/ensembl/mart/lib/config/class-use/DatasetConfigIterator.html
+docs/api/org/ensembl/mart/lib/config/class-use/FilterPage.html
+docs/api/org/ensembl/mart/lib/config/class-use/AttributePage.html
+docs/api/org/ensembl/mart/lib/config/class-use/DefaultFilter.html
+docs/api/org/ensembl/mart/lib/config/class-use/Option.html
+docs/api/org/ensembl/mart/lib/config/class-use/ConfigurationException.html
+docs/api/org/ensembl/mart/lib/config/class-use/AttributeCollection.html
+docs/api/org/ensembl/mart/lib/config/class-use/AttributeGroup.html
+docs/api/org/ensembl/mart/lib/config/class-use/FilterCollection.html
+docs/api/org/ensembl/mart/lib/config/class-use/FilterGroup.html
+docs/api/org/ensembl/mart/lib/config/class-use/QueryFilterSettings.html
+docs/api/org/ensembl/mart/lib/config/class-use/FilterDescription.html
+docs/api/org/ensembl/mart/lib/config/class-use/AttributeDescription.html
+docs/api/org/ensembl/mart/lib/config/class-use/DSConfigAdaptor.html
+docs/api/org/ensembl/mart/lib/config/class-use/BaseNamedConfigurationObject.html
+docs/api/org/ensembl/mart/lib/config/class-use/DatasetConfig.html
+docs/api/org/ensembl/mart/lib/config/class-use/BaseConfigurationObject.html
+docs/api/org/ensembl/mart/lib/config/package-use.html
+docs/api/org/ensembl/mart/lib/config/package-frame.html
+docs/api/org/ensembl/mart/lib/config/package-summary.html
+docs/api/org/ensembl/mart/lib/config/package-tree.html
+docs/api/org/ensembl/mart/lib/config/DSConfigAdaptor.html
+docs/api/org/ensembl/mart/lib/config/MartLocation.html
+docs/api/org/ensembl/mart/lib/config/MultiDSConfigAdaptor.html
+docs/api/org/ensembl/mart/lib/config/AttributeCollection.html
+docs/api/org/ensembl/mart/lib/config/AttributeDescription.html
+docs/api/org/ensembl/mart/lib/config/AttributeGroup.html
+docs/api/org/ensembl/mart/lib/config/AttributePage.html
+docs/api/org/ensembl/mart/lib/config/BaseConfigurationObject.html
+docs/api/org/ensembl/mart/lib/config/BaseMartElementFilter.html
+docs/api/org/ensembl/mart/lib/config/BaseNamedConfigurationObject.html
+docs/api/org/ensembl/mart/lib/config/ClasspathDTDEntityResolver.html
+docs/api/org/ensembl/mart/lib/config/CompositeDSConfigAdaptor.html
+docs/api/org/ensembl/mart/lib/config/DatabaseDatasetConfigUtils.html
+docs/api/org/ensembl/mart/lib/config/DatabaseDSConfigAdaptor.html
+docs/api/org/ensembl/mart/lib/config/DatabaseLocation.html
+docs/api/org/ensembl/mart/lib/config/DatasetConfig.html
+docs/api/org/ensembl/mart/lib/config/DatasetConfigCache.html
+docs/api/org/ensembl/mart/lib/config/DatasetConfigIterator.html
+docs/api/org/ensembl/mart/lib/config/DatasetConfigUploader.html
+docs/api/org/ensembl/mart/lib/config/DatasetConfigXMLUtils.html
+docs/api/org/ensembl/mart/lib/config/DefaultFilter.html
+docs/api/org/ensembl/mart/lib/config/Disable.html
+docs/api/org/ensembl/mart/lib/config/DSAttributeGroup.html
+docs/api/org/ensembl/mart/lib/config/DSFilterGroup.html
+docs/api/org/ensembl/mart/lib/config/Enable.html
+docs/api/org/ensembl/mart/lib/config/FilterCollection.html
+docs/api/org/ensembl/mart/lib/config/FilterDescription.html
+docs/api/org/ensembl/mart/lib/config/FilterGroup.html
+docs/api/org/ensembl/mart/lib/config/FilterPage.html
+docs/api/org/ensembl/mart/lib/config/LeafDSConfigAdaptor.html
+docs/api/org/ensembl/mart/lib/config/MartAttributeGroupFilter.html
+docs/api/org/ensembl/mart/lib/config/MartConfiguration.html
+docs/api/org/ensembl/mart/lib/config/MartElementFilter.html
+docs/api/org/ensembl/mart/lib/config/MartFilterDescriptionFilter.html
+docs/api/org/ensembl/mart/lib/config/MartFilterGroupFilter.html
+docs/api/org/ensembl/mart/lib/config/MartLocationBase.html
+docs/api/org/ensembl/mart/lib/config/MartRegistry.html
+docs/api/org/ensembl/mart/lib/config/MartRegistryXMLUtils.html
+docs/api/org/ensembl/mart/lib/config/NaiveDatasetConfigGenerator.html
+docs/api/org/ensembl/mart/lib/config/Option.html
+docs/api/org/ensembl/mart/lib/config/PushAction.html
+docs/api/org/ensembl/mart/lib/config/QueryFilterSettings.html
+docs/api/org/ensembl/mart/lib/config/RegistryDSConfigAdaptor.html
+docs/api/org/ensembl/mart/lib/config/RegistryLocation.html
+docs/api/org/ensembl/mart/lib/config/SimpleDSConfigAdaptor.html
+docs/api/org/ensembl/mart/lib/config/URLDSConfigAdaptor.html
+docs/api/org/ensembl/mart/lib/config/URLLocation.html
+docs/api/org/ensembl/mart/lib/config/ConfigurationException.html
+docs/api/org/ensembl/mart/lib/package-use.html
+docs/api/org/ensembl/mart/lib/package-frame.html
+docs/api/org/ensembl/mart/lib/package-summary.html
+docs/api/org/ensembl/mart/lib/package-tree.html
+docs/api/org/ensembl/mart/lib/Attribute.html
+docs/api/org/ensembl/mart/lib/Field.html
+docs/api/org/ensembl/mart/lib/Filter.html
+docs/api/org/ensembl/mart/lib/QueryListener.html
+docs/api/org/ensembl/mart/lib/QueryRunner.html
+docs/api/org/ensembl/mart/lib/UnprocessedFilterHandler.html
+docs/api/org/ensembl/mart/lib/AttributeQueryRunner.html
+docs/api/org/ensembl/mart/lib/BaseSeqQueryRunner.html
+docs/api/org/ensembl/mart/lib/BaseSeqQueryRunner.SeqWriter.html
+docs/api/org/ensembl/mart/lib/BasicFilter.html
+docs/api/org/ensembl/mart/lib/BooleanFilter.html
+docs/api/org/ensembl/mart/lib/CdnaSeqQueryRunner.html
+docs/api/org/ensembl/mart/lib/CodingSeqQueryRunner.html
+docs/api/org/ensembl/mart/lib/DetailedDataSource.html
+docs/api/org/ensembl/mart/lib/DNAAdaptor.html
+docs/api/org/ensembl/mart/lib/DownStreamUTRSeqQueryRunner.html
+docs/api/org/ensembl/mart/lib/Engine.html
+docs/api/org/ensembl/mart/lib/ExpressionFilterHandler.html
+docs/api/org/ensembl/mart/lib/FieldAttribute.html
+docs/api/org/ensembl/mart/lib/FileIDListFilterHandler.html
+docs/api/org/ensembl/mart/lib/FormatSpec.html
+docs/api/org/ensembl/mart/lib/GeneEISeqQueryRunner.html
+docs/api/org/ensembl/mart/lib/GeneExonSeqQueryRunner.html
+docs/api/org/ensembl/mart/lib/GeneFlankSeqQueryRunner.html
+docs/api/org/ensembl/mart/lib/GenericHandler.html
+docs/api/org/ensembl/mart/lib/IDListFilter.html
+docs/api/org/ensembl/mart/lib/IDListFilterHandlerBase.html
+docs/api/org/ensembl/mart/lib/InputSourceUtil.html
+docs/api/org/ensembl/mart/lib/LoggingUtils.html
+docs/api/org/ensembl/mart/lib/PeptideSeqQueryRunner.html
+docs/api/org/ensembl/mart/lib/Query.html
+docs/api/org/ensembl/mart/lib/QueryAdaptor.html
+docs/api/org/ensembl/mart/lib/QueryCompiler.html
+docs/api/org/ensembl/mart/lib/QueryRunnerFactory.html
+docs/api/org/ensembl/mart/lib/Sequence.html
+docs/api/org/ensembl/mart/lib/SequenceDescription.html
+docs/api/org/ensembl/mart/lib/SequenceLocation.html
+docs/api/org/ensembl/mart/lib/SubQueryIDListFilterHandler.html
+docs/api/org/ensembl/mart/lib/Table.html
+docs/api/org/ensembl/mart/lib/TranscriptEISeqQueryRunner.html
+docs/api/org/ensembl/mart/lib/TranscriptExonSeqQueryRunner.html
+docs/api/org/ensembl/mart/lib/TranscriptFlankSeqQueryRunner.html
+docs/api/org/ensembl/mart/lib/UnprocessedFilterHandlerFactory.html
+docs/api/org/ensembl/mart/lib/UpStreamUTRSeqQueryRunner.html
+docs/api/org/ensembl/mart/lib/URLIDListFilterHandler.html
+docs/api/org/ensembl/mart/lib/FormatException.html
+docs/api/org/ensembl/mart/lib/InvalidListException.html
+docs/api/org/ensembl/mart/lib/InvalidQueryException.html
+docs/api/org/ensembl/mart/lib/SequenceException.html
+docs/api/overview-tree.html
+docs/api/index-all.html
+docs/api/deprecated-list.html
+docs/api/allclasses-frame.html
+docs/api/allclasses-noframe.html
+docs/api/index.html
+docs/api/packages.html
+docs/api/overview-summary.html
+docs/api/overview-frame.html
+docs/api/serialized-form.html
+docs/api/package-list
+docs/api/help-doc.html
+docs/api/stylesheet.css
+docs/developer.txt
Added: trunk/packages/martj/trunk/debian/martj.dirs
===================================================================
--- trunk/packages/martj/trunk/debian/martj.dirs (rev 0)
+++ trunk/packages/martj/trunk/debian/martj.dirs 2008-03-13 09:13:16 UTC (rev 1571)
@@ -0,0 +1,4 @@
+usr/bin
+usr/share/martj
+usr/share/java
+usr/share/doc/martj/examples
Added: trunk/packages/martj/trunk/debian/martj.docs
===================================================================
--- trunk/packages/martj/trunk/debian/martj.docs (rev 0)
+++ trunk/packages/martj/trunk/debian/martj.docs 2008-03-13 09:13:16 UTC (rev 1571)
@@ -0,0 +1 @@
+docs/developer.txt
Added: trunk/packages/martj/trunk/debian/martj.examples
===================================================================
--- trunk/packages/martj/trunk/debian/martj.examples (rev 0)
+++ trunk/packages/martj/trunk/debian/martj.examples 2008-03-13 09:13:16 UTC (rev 1571)
@@ -0,0 +1,9 @@
+data/examples
+data/examples/XML
+data/examples/XML/exampleMartRegistryComposite.xml
+data/examples/XML/exampleMartRegistryDB.xml
+data/examples/XML/exampleMartRegistryRegistry.xml
+data/examples/XML/exampleMartRegistryURL.xml
+data/examples/exampleDotMartShellURL
+data/examples/exampleInitScriptURL
+data/examples/exampleLoggingConfig.properties
Added: trunk/packages/martj/trunk/debian/martshell.1
===================================================================
--- trunk/packages/martj/trunk/debian/martshell.1 (rev 0)
+++ trunk/packages/martj/trunk/debian/martshell.1 2008-03-13 09:13:16 UTC (rev 1571)
@@ -0,0 +1,45 @@
+.\" Hey, EMACS: -*- nroff -*-
+.TH MARTJ 1 "January 7, 2005"
+.\" Please adjust this date whenever revising the manpage.
+.\"
+.\" Some roff macros, for reference:
+.\" .nh disable hyphenation
+.\" .hy enable hyphenation
+.\" .ad l left justify
+.\" .ad b justify to both left and right margins
+.\" .nf disable filling
+.\" .fi enable filling
+.\" .br insert line break
+.\" .sp <n> insert n+1 empty lines
+.\" for manpage-specific macros, see man(7)
+.SH NAME
+martshell \- Interactive shell to interact with biological sequence databases
+marteditor \- GUI
+martexplorer \- GUI
+.SH SYNOPSIS
+.B martshell
+.br
+.B marteditor
+.br
+.B martexplorer
+.SH DESCRIPTION
+Start BioMartBioMart is a simple, distributed data integration system
+with powerful query capabilities.
+.BR
+It has been designed to provide researchers with an easy and interactive
+access to both the wealth of data available on the Internet and for
+in house data integration. BioMart is a successor to the generic
+query system originally developed for the Ensembl genome database
+(EnsMart). Building on its success, BioMart, has now been applied to
+other biological databases. BioMart is an open source project and all
+software is free without any restrictions.
+.br
+.SH SEE ALSO
+.BR online documentation
+.BR http://www.ebi.ac.uk/biomart
+.br
+.SH AUTHOR
+martj was written by the EnsEMBL group aroud Arek Kasprzyk <arek at ebi.ac.uk>
+.PP
+This manual page was written by Steffen Moeller <moeller at pzr.uni-rostock.de>,
+for the Debian project (but may be used by others).
Added: trunk/packages/martj/trunk/debian/menu
===================================================================
--- trunk/packages/martj/trunk/debian/menu (rev 0)
+++ trunk/packages/martj/trunk/debian/menu 2008-03-13 09:13:16 UTC (rev 1571)
@@ -0,0 +1,2 @@
+?package(martj):needs="X11|text|vc|wm" section="Apps/see-menu-manual"\
+ title="martj" command="/usr/bin/martj"
Added: trunk/packages/martj/trunk/debian/patches/xyz.diff
===================================================================
--- trunk/packages/martj/trunk/debian/patches/xyz.diff (rev 0)
+++ trunk/packages/martj/trunk/debian/patches/xyz.diff 2008-03-13 09:13:16 UTC (rev 1571)
@@ -0,0 +1,140 @@
+--- martj-0.1.orig/bin/marteditor.sh
++++ martj-0.1/bin/marteditor.sh
+@@ -10,18 +10,27 @@
+ # prompt> bin/martgui.sh
+ TMP_ROOT=`dirname $0`/..
+
+-TMP_ROOT=`dirname $0`/..
+-
+-TMP_CLASSPATH=${TMP_ROOT}
++TMP_CLASSPATH=.
+ TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/build/classes
+ TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/lib/mysql-connector-java-3.0.7-stable-bin.jar
+-TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/lib/log4j-1.2.6.jar
++TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/lib/mysql.jar
++TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/lib/log4j-1.2.jar
+ TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/lib/jython.jar
+ TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/lib/ensj-util.jar
+ TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/lib/jdom.jar
+ TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/lib/martj.jar
+ TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/lib/ojdbc14.jar
+ TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/lib/ecp1_0beta.jar
++
++TMP_CLASSPATH=${TMP_CLASSPATH}:/usr/share/martj/jdom.jar
++JAR_DIR=/usr/share/java
++for i in /mysql log4j-1.2 jython ensj-util martj ojdbc14 ecp1_0beta; do
++ TMP_CLASSPATH=${TMP_CLASSPATH}:$JAR_DIR/$i.jar
++done
++for i in junit nodeps trax; do
++ TMP_CLASSPATH=${TMP_CLASSPATH}:/usr/share/ant1.6/lib/ant-$i.jar
++done
++
+ TMP_CLASSPATH=${TMP_CLASSPATH}:${CLASSPATH}
+
+ TMP_JYTHON_LIB=${TMP_ROOT}/lib
+--- martj-0.1.orig/bin/martexplorer.sh
++++ martj-0.1/bin/martexplorer.sh
+@@ -23,6 +23,16 @@
+ TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/lib/p6spy.jar
+ TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/lib/ojdbc14.jar
+ TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/lib/ecp1_0beta.jar
++
++TMP_CLASSPATH=${TMP_CLASSPATH}:/usr/share/martj/jdom.jar
++JAR_DIR=/usr/share/java
++for i in /mysql log4j-1.2 jython ensj-util martj ojdbc14 ecp1_0beta; do
++ TMP_CLASSPATH=${TMP_CLASSPATH}:$JAR_DIR/$i.jar
++done
++for i in junit nodeps trax; do
++ TMP_CLASSPATH=${TMP_CLASSPATH}:/usr/share/ant1.6/lib/ant-$i.jar
++done
++
+ TMP_CLASSPATH=${TMP_CLASSPATH}:${CLASSPATH}
+
+ TMP_JYTHON_LIB=${TMP_ROOT}/lib
+--- martj-0.1.orig/bin/martshell.sh
++++ martj-0.1/bin/martshell.sh
+@@ -22,7 +22,9 @@
+ TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/build/classes
+ TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/lib/martj.jar
+ TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/lib/mysql-connector-java-3.0.7-stable-bin.jar
++TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/lib/mysql.jar
+ TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/lib/java-getopt-1.0.9.jar
++TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/lib/gnu-getopt.jar
+ TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/lib/jdom.jar
+ TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/lib/libreadline-java.jar
+ TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/lib/ensj-util.jar
+@@ -30,27 +32,18 @@
+ TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/lib/jdbc2_0-stdext.jar
+ TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/lib/p6spy.jar
+ TMP_CLASSPATH=${TMP_CLASSPATH}:${TMP_ROOT}/lib/ojdbc14.jar
+-TMP_CLASSPATH=${TMP_CLASSPATH}:${CLASSPATH}
+
+-TMP_LD_LIBPATH=${LD_LIBRARY_PATH}
++TMP_CLASSPATH=${TMP_CLASSPATH}:/usr/share/martj/jdom.jar
++JAR_DIR=/usr/share/java
++for i in mysql log4j-1.2 jython ensj-util martj ojdbc14 ecp1_0beta libreadline-java; do
++ TMP_CLASSPATH=${TMP_CLASSPATH}:$JAR_DIR/$i.jar
++done
++for i in junit nodeps trax; do
++ TMP_CLASSPATH=${TMP_CLASSPATH}:/usr/share/ant1.6/lib/ant-$i.jar
++done
++
++TMP_CLASSPATH=${TMP_CLASSPATH}:${CLASSPATH}
+
+-PLATFORM=`uname -ms`
+-case "$PLATFORM" in
+-[Ll]inux*)
+- TMP_LD_LIBPATH="${TMP_LD_LIBPATH}:${TMP_ROOT}/lib/linux"
+- ;;
+-*alpha*)
+- TMP_LD_LIBPATH="${TMP_LD_LIBPATH}:${TMP_ROOT}/lib/alpha"
+- ;;
+-# arp
+-*Darwin*Power*Mac*)
+- TMP_LD_LIBPATH="${TMP_:D_LIBPATH}:${TMP_ROOT}/lib/macosx/"
+- ;;
+-# arp
+-*)
+- echo "warning, this platform is not known to be supported, using linux libraries\n"
+- TMP_LD_LIBPATH="${TMP_LD_LIBPATH}:${TMP_ROOT}/lib/linux"
+- ;;
+-esac
++echo "Classpath: $TMP_CLASSPATH"
+
+-LD_LIBRARY_PATH=$TMP_LD_LIBPATH java -ea -classpath ${TMP_CLASSPATH} org.ensembl.mart.shell.MartShell $@
++LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/jni java -ea -classpath ${TMP_CLASSPATH} org.ensembl.mart.shell.MartShell $@
+--- martj-0.1.orig/build.xml
++++ martj-0.1/build.xml
+@@ -74,18 +74,24 @@
+ <include name="ecp1_0beta.jar" />
+ <include name="ensj.jar" />
+ <include name="ensj-util.jar" />
+- <include name="java-getopt-1.0.9.jar" />
++ <include name="gnu-getopt.jar" /> <!-- Debian -->
+ <include name="jdbc2_0-stdext.jar" />
+ <include name="jdom.jar" />
+- <include name="junit.jar" />
+- <include name="jython.jar" />
+- <include name="libreadline-java.jar" />
+- <include name="log4j-1.2.6.jar" />
+- <include name="mysql-connector-java-3.0.7-stable-bin.jar" />
+- <include name="optional.jar" />
++ <include name="junit.jar" /> <!-- Debian -->
++ <include name="jython.jar" /> <!-- Debian -->
++ <include name="libreadline-java.jar" /> <!-- Debian -->
++ <include name="log4j-1.2.jar" /> <!-- Debian -->
++ <include name="ojdbc14.jar" />
++ <include name="mysql.jar" />
++ <!--
++ <include name="optional.jar" />
++ -->
++ <include name="ant-junit.jar" />
++ <include name="ant-nodeps.jar" />
++ <include name="ant-trax.jar" />
++
+ <include name="xalan.jar" />
+ <include name="p6spy.jar" />
+- <include name="ojdbc14.jar" />
+ </fileset>
+
+ <!-- patternsets to use in various zip and tar filesets during the dist-* targets -->
Added: trunk/packages/martj/trunk/debian/rules
===================================================================
--- trunk/packages/martj/trunk/debian/rules (rev 0)
+++ trunk/packages/martj/trunk/debian/rules 2008-03-13 09:13:16 UTC (rev 1571)
@@ -0,0 +1,123 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+#
+# This file was originally written by Joey Hess and Craig Small.
+# As a special exception, when this file is copied by dh-make into a
+# dh-make output file, you may use that output file without restriction.
+# This special exception was added by Craig Small in version 0.37 of dh-make.
+#
+# Modified to make a template file for a multi-binary package with separated
+# build-arch and build-indep targets by Bill Allombert 2001
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+# This has to be exported to make some magic below work.
+export DH_OPTIONS
+
+DEBIANJARS= /usr/share/java/junit.jar \
+ /usr/share/java/gnu-getopt.jar /usr/share/java/jython.jar \
+ /usr/share/java/libreadline-java.jar \
+ /usr/share/java/log4j-1.2.jar /usr/share/java/mysql.jar \
+ /usr/share/ant1.6/lib/ant-nodeps.jar /usr/share/ant1.6/lib/ant-junit.jar \
+ /usr/share/java/xalan.jar \
+ /usr/share/ant1.6/lib/ant-trax.jar
+
+links:
+ ( cd lib ; ln -sf $(DEBIANJARS) . )
+ ln -sf martshell.1 marteditor.1
+ ln -sf martshell.1 martexplorer.1
+
+#Architecture
+build: build-indep
+
+build-arch: build-arch-stamp
+build-arch-stamp:
+
+ # Add here commands to compile the arch part of the package.
+ #ant
+ touch build-arch-stamp
+
+build-indep: build-indep-stamp
+build-indep-stamp: links
+
+ # Add here commands to compile the indep part of the package.
+ ant api
+ ant jar
+ touch build-indep-stamp
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-arch-stamp build-indep-stamp #CONFIGURE-STAMP#
+
+ # Add here commands to clean up after the build process.
+ -ant clean
+ find lib -type l | xargs -r rm
+
+ dh_clean martexplorer.1 marteditor.1
+
+install: install-indep
+install-arch:
+ dh_testdir
+ dh_testroot
+ dh_clean -k -s
+ dh_installdirs -s
+
+ # Add here commands to install the indep part of the package into
+ # debian/<package>-doc.
+ #INSTALLDOC#
+
+ dh_install -s
+
+install-indep:
+ dh_testdir
+ dh_testroot
+ dh_clean -k -i
+ dh_installdirs -i
+
+ # Add here commands to install the arch part of the package into
+ # debian/tmp.
+ #$(MAKE) install DESTDIR=$(CURDIR)/debian/martj
+ cp `find lib -name '*.jar' -a \! -type l | grep -v jdom` $(CURDIR)/debian/martj/usr/share/java
+ cp lib/jdom.jar $(CURDIR)/debian/martj/usr/share/martj
+ cp ./build/martj.jar $(CURDIR)/debian/martj/usr/share/java
+ cp bin/martshell.sh $(CURDIR)/debian/martj/usr/bin/martshell
+ cp bin/marteditor.sh $(CURDIR)/debian/martj/usr/bin/marteditor
+ cp bin/martexplorer.sh $(CURDIR)/debian/martj/usr/bin/martexplorer
+
+ cp -r data $(CURDIR)/debian/martj/usr/share/martj
+
+ dh_install -i
+# Must not depend on anything. This is to be called by
+# binary-arch/binary-indep
+# in another 'make' thread.
+binary-common:
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs
+ dh_installexamples
+ dh_installmenu
+ dh_installman
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+ dh_makeshlibs
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+# Build architecture independant packages using the common target.
+binary-indep: build-indep install-indep
+ $(MAKE) -f debian/rules DH_OPTIONS=-i binary-common
+
+# Build architecture dependant packages using the common target.
+#binary-arch: build-arch install-arch
+# #$(MAKE) -f debian/rules DH_OPTIONS=-a binary-common
+
+binary: binary-indep
+.PHONY: build clean binary-indep binary-arch binary install install-indep install-arch configure
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