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 <[email protected]> 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 <[email protected]> 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 <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Andreas Tille <[email protected]> +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 <[email protected]> +Source: http://code.google.com/p/figtree/ + +Files: * +Copyright: © 2005-2011 Andrew Rambaut <[email protected]> +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 <[email protected]> +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 <[email protected]> +# 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 \ _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
