[med-svn] r6014 - in trunk/packages: . patristic patristic/trunk patristic/trunk/debian patristic/trunk/debian/source
Andreas Tille
tille at alioth.debian.org
Thu Feb 17 15:24:18 UTC 2011
Author: tille
Date: 2011-02-17 15:24:17 +0000 (Thu, 17 Feb 2011)
New Revision: 6014
Added:
trunk/packages/patristic/
trunk/packages/patristic/trunk/
trunk/packages/patristic/trunk/debian/
trunk/packages/patristic/trunk/debian/README.source
trunk/packages/patristic/trunk/debian/changelog
trunk/packages/patristic/trunk/debian/compat
trunk/packages/patristic/trunk/debian/control
trunk/packages/patristic/trunk/debian/copyright
trunk/packages/patristic/trunk/debian/get-orig-source
trunk/packages/patristic/trunk/debian/maven.cleanIgnoreRules
trunk/packages/patristic/trunk/debian/maven.ignoreRules
trunk/packages/patristic/trunk/debian/maven.publishedRules
trunk/packages/patristic/trunk/debian/maven.rules
trunk/packages/patristic/trunk/debian/patristic.poms
trunk/packages/patristic/trunk/debian/rules
trunk/packages/patristic/trunk/debian/source/
trunk/packages/patristic/trunk/debian/source/format
trunk/packages/patristic/trunk/debian/watch
Log:
Inject some initial packaging for patristic - just a preparation, build fails
Added: trunk/packages/patristic/trunk/debian/README.source
===================================================================
--- trunk/packages/patristic/trunk/debian/README.source (rev 0)
+++ trunk/packages/patristic/trunk/debian/README.source 2011-02-17 15:24:17 UTC (rev 6014)
@@ -0,0 +1,7 @@
+The source of patristic can be obtained via
+ debian/get-orig-source
+it was repackaged because the tarball was not clean (gpl-3.0.txt in
+root). Once the tarball was repackaged anyway some additional examples
+which were originally in a separate archive were added.
+
+ -- Andreas Tille <tille at debian.org> Mon, 07 Feb 2011 12:02:43 +0100
Added: trunk/packages/patristic/trunk/debian/changelog
===================================================================
--- trunk/packages/patristic/trunk/debian/changelog (rev 0)
+++ trunk/packages/patristic/trunk/debian/changelog 2011-02-17 15:24:17 UTC (rev 6014)
@@ -0,0 +1,5 @@
+patristic (0.0.20100817-1) unstable; urgency=low
+
+ * Initial release (Closes: #????)
+
+ -- Andreas Tille <tille at debian.org> Sun, 13 Feb 2011 12:53:06 +0100
Added: trunk/packages/patristic/trunk/debian/compat
===================================================================
--- trunk/packages/patristic/trunk/debian/compat (rev 0)
+++ trunk/packages/patristic/trunk/debian/compat 2011-02-17 15:24:17 UTC (rev 6014)
@@ -0,0 +1 @@
+7
Added: trunk/packages/patristic/trunk/debian/control
===================================================================
--- trunk/packages/patristic/trunk/debian/control (rev 0)
+++ trunk/packages/patristic/trunk/debian/control 2011-02-17 15:24:17 UTC (rev 6014)
@@ -0,0 +1,23 @@
+Source: patristic
+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 (>= 7.1), cdbs, default-jdk, maven-debian-helper, openjdk-6-jdk
+Standards-Version: 3.9.1
+Homepage: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1352388/
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/patristic/trunk
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/patristic/trunk/?rev=0&sc=0
+
+Package: patristic
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Calculate patristic distances and comparing the components of genetic change
+ Patristic overcomes some logistic barriers to analysing signals in
+ sequences. In additional to calculating patristic distances, it provides
+ plots for any combination of matrices, calculates commonly used
+ statistics, allows data such as isolation dates to be entered and
+ reorders matrices with matching species or gene labels. It will be used
+ to analyse rates of mutation and substitutional saturation and the
+ evolution of viruses.
Added: trunk/packages/patristic/trunk/debian/copyright
===================================================================
--- trunk/packages/patristic/trunk/debian/copyright (rev 0)
+++ trunk/packages/patristic/trunk/debian/copyright 2011-02-17 15:24:17 UTC (rev 6014)
@@ -0,0 +1,34 @@
+Format: http://dep.debian.net/deps/dep5/
+Upstream-Name: FigTree
+Upstream-Contact: Andrew Rambaut <a.rambaut at ed.ac.uk>
+Source: http://code.google.com/p/figtree/
+
+Files: *
+Copyright: © 2005-2011 Andrew Rambaut <a.rambaut at ed.ac.uk>
+License: GPL
+ 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 package; if not, write to the Free
+ Software Foundation, Inc., 51 Franklin St, Fifth Floor,
+ Boston, MA 02110-1301 USA
+ .
+ On Debian systems, the full text of the GNU General Public
+ License version 2 can be found in the file
+ `/usr/share/common-licenses/GPL'.
+
+
+Files: debian/*
+Copyright: © 2011 Andreas Tille <tille at debian.org>
+License: PD
+ The packaging work is in the public domain unless stated otherwise.
Added: trunk/packages/patristic/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/patristic/trunk/debian/get-orig-source (rev 0)
+++ trunk/packages/patristic/trunk/debian/get-orig-source 2011-02-17 15:24:17 UTC (rev 6014)
@@ -0,0 +1,29 @@
+#!/bin/sh
+# The upstream tarball is not clean (gpl-3.0.txt in root).
+# Once the tarball was repackaged anyway some additional examples
+# which were originally in a separate archive were added.
+# Links:
+# Paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1352388/
+# http://mac.softpedia.com/get/Math-Scientific/Patristic.shtml
+
+# upstream has no versioning scheme, use timestamp of last changed file
+version=0.0.20100817
+name=patristic
+
+mkdir -p ../tarballs
+cd ../tarballs
+
+wget ftp://ftp.bioinformatics.org/pub/patristic/Patristic-src.tar.gz
+wget ftp://ftp.bioinformatics.org/pub/patristic/Patristic-example.zip
+
+tar -xzf Patristic-src.tar.gz
+# avoid dirty tarball
+mv gpl-3.0.txt Patristic
+# unpack examples
+mkdir -p Patristic/examples
+cd Patristic/examples
+unzip ../../Patristic-example.zip
+cd ../..
+
+GZIP="--best --no-name" tar -czf "$name"_"$version".orig.tar.gz Patristic
+rm -rf Patristic
Added: trunk/packages/patristic/trunk/debian/maven.cleanIgnoreRules
===================================================================
--- trunk/packages/patristic/trunk/debian/maven.cleanIgnoreRules (rev 0)
+++ trunk/packages/patristic/trunk/debian/maven.cleanIgnoreRules 2011-02-17 15:24:17 UTC (rev 6014)
@@ -0,0 +1,17 @@
+# Maven clean ignore rules - ignore some Maven dependencies and plugins
+# during the clean phase of a Maven build
+# Format of this file is:
+# [group] [artifact] [type] [version] [classifier] [scope]
+# where each element can be either
+# - the exact string, for example org.apache for the group, or 3.1
+# for the version. In this case, the element is simply matched
+# and left as it is
+# - * (the star character, alone). In this case, anything will
+# match and be left as it is. For example, using * on the
+# position of the artifact field will match any artifact id
+# All elements much match before a rule can be applied
+# Example rule: match jar with groupid= junit, artifactid= junit
+# and version starting with 3., this dependency is then removed
+# from the POM before mvn clean is called
+# junit junit jar s/3\\..*/3.x/
+
Added: trunk/packages/patristic/trunk/debian/maven.ignoreRules
===================================================================
--- trunk/packages/patristic/trunk/debian/maven.ignoreRules (rev 0)
+++ trunk/packages/patristic/trunk/debian/maven.ignoreRules 2011-02-17 15:24:17 UTC (rev 6014)
@@ -0,0 +1,16 @@
+# Maven ignore rules - ignore some Maven dependencies and plugins
+# Format of this file is:
+# [group] [artifact] [type] [version] [classifier] [scope]
+# where each element can be either
+# - the exact string, for example org.apache for the group, or 3.1
+# for the version. In this case, the element is simply matched
+# and left as it is
+# - * (the star character, alone). In this case, anything will
+# match and be left as it is. For example, using * on the
+# position of the artifact field will match any artifact id
+# All elements much match before a rule can be applied
+# Example rule: match jar with groupid= junit, artifactid= junit
+# and version starting with 3., this dependency is then removed
+# from the POM
+# junit junit jar s/3\\..*/3.x/
+
Added: trunk/packages/patristic/trunk/debian/maven.publishedRules
===================================================================
--- trunk/packages/patristic/trunk/debian/maven.publishedRules (rev 0)
+++ trunk/packages/patristic/trunk/debian/maven.publishedRules 2011-02-17 15:24:17 UTC (rev 6014)
@@ -0,0 +1,19 @@
+# Maven published rules - additional rules to publish, to help
+# the packaging work of Debian maintainers using mh_make
+# Format of this file is:
+# [group] [artifact] [type] [version] [classifier] [scope]
+# where each element can be either
+# - the exact string, for example org.apache for the group, or 3.1
+# for the version. In this case, the element is simply matched
+# and left as it is
+# - * (the star character, alone). In this case, anything will
+# match and be left as it is. For example, using * on the
+# position of the artifact field will match any artifact id
+# - a regular expression of the form s/match/replace/
+# in this case, elements that match are transformed using
+# the regex rule.
+# All elements much match before a rule can be applied
+# Example rule: match jar with groupid= junit, artifactid= junit
+# and version starting with 3., replacing the version with 3.x
+# junit junit jar s/3\\..*/3.x/
+
Added: trunk/packages/patristic/trunk/debian/maven.rules
===================================================================
--- trunk/packages/patristic/trunk/debian/maven.rules (rev 0)
+++ trunk/packages/patristic/trunk/debian/maven.rules 2011-02-17 15:24:17 UTC (rev 6014)
@@ -0,0 +1,19 @@
+# Maven rules - transform Maven dependencies and plugins
+# Format of this file is:
+# [group] [artifact] [type] [version] [classifier] [scope]
+# where each element can be either
+# - the exact string, for example org.apache for the group, or 3.1
+# for the version. In this case, the element is simply matched
+# and left as it is
+# - * (the star character, alone). In this case, anything will
+# match and be left as it is. For example, using * on the
+# position of the artifact field will match any artifact id
+# - a regular expression of the form s/match/replace/
+# in this case, elements that match are transformed using
+# the regex rule.
+# All elements much match before a rule can be applied
+# Example rule: match jar with groupid= junit, artifactid= junit
+# and version starting with 3., replacing the version with 3.x
+# junit junit jar s/3\\..*/3.x/
+
+junit junit jar s/3\..*/3.x/ * *
Added: trunk/packages/patristic/trunk/debian/patristic.poms
===================================================================
--- trunk/packages/patristic/trunk/debian/patristic.poms (rev 0)
+++ trunk/packages/patristic/trunk/debian/patristic.poms 2011-02-17 15:24:17 UTC (rev 6014)
@@ -0,0 +1,7 @@
+# List of POM files for the package
+# Format of this file is:
+# <path to pom file> [option]
+# where option can be:
+# --ignore: ignore this POM or
+# --no-parent: remove the <parent> tag from the POM
+pom.xml
Added: trunk/packages/patristic/trunk/debian/rules
===================================================================
--- trunk/packages/patristic/trunk/debian/rules (rev 0)
+++ trunk/packages/patristic/trunk/debian/rules 2011-02-17 15:24:17 UTC (rev 6014)
@@ -0,0 +1,13 @@
+#!/usr/bin/make -f
+# debian/rules for patristic
+# Andreas Tille <tille at debian.org>
+# GPL
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/maven.mk
+include /usr/share/cdbs/1/rules/patchsys-quilt.mk
+
+JAVA_HOME := /usr/lib/jvm/default-java
Property changes on: trunk/packages/patristic/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/patristic/trunk/debian/source/format
===================================================================
--- trunk/packages/patristic/trunk/debian/source/format (rev 0)
+++ trunk/packages/patristic/trunk/debian/source/format 2011-02-17 15:24:17 UTC (rev 6014)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/patristic/trunk/debian/watch
===================================================================
--- trunk/packages/patristic/trunk/debian/watch (rev 0)
+++ trunk/packages/patristic/trunk/debian/watch 2011-02-17 15:24:17 UTC (rev 6014)
@@ -0,0 +1,10 @@
+# Obtaining the source tarball of FigTree is a bit tricky because here is no
+# explicite link to a downloadable tarball on the web page and the source is
+# only in SVN
+
+version=3
+http://tree.bio.ed.ac.uk/software/figtree/ \
+ /download\.html\?name=figtree&version=v([\d.]*).id=\d+&num=3 \
+ debian debian/get-orig-source
+
+# /download.html?name=figtree&version=v(.*)&id=82&num=3 \
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