[med-svn] r6699 - in trunk/packages: . mgltools/opengltk/tags raxml raxml/trunk raxml/trunk/debian raxml/trunk/debian/source
Andreas Tille
tille at alioth.debian.org
Thu Apr 28 12:52:05 UTC 2011
Author: tille
Date: 2011-04-28 12:52:03 +0000 (Thu, 28 Apr 2011)
New Revision: 6699
Added:
trunk/packages/mgltools/opengltk/tags/1.5.4.cvs.20100912-2/
trunk/packages/raxml/
trunk/packages/raxml/trunk/
trunk/packages/raxml/trunk/debian/
trunk/packages/raxml/trunk/debian/README.Debian
trunk/packages/raxml/trunk/debian/changelog
trunk/packages/raxml/trunk/debian/compat
trunk/packages/raxml/trunk/debian/control
trunk/packages/raxml/trunk/debian/copyright
trunk/packages/raxml/trunk/debian/dirs
trunk/packages/raxml/trunk/debian/install
trunk/packages/raxml/trunk/debian/rules
trunk/packages/raxml/trunk/debian/source/
trunk/packages/raxml/trunk/debian/source/format
trunk/packages/raxml/trunk/debian/watch
Log:
Inject RAxML packaging (which was hanging around on my HD for a long time :-()
Added: trunk/packages/raxml/trunk/debian/README.Debian
===================================================================
--- trunk/packages/raxml/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/raxml/trunk/debian/README.Debian 2011-04-28 12:52:03 UTC (rev 6699)
@@ -0,0 +1,14 @@
+RAxML for Debian
+----------------
+
+This version of RAxML comes without a documentation. The homepage
+ http://wwwkramer.in.tum.de/exelixis/software.html
+contains several useful hints like
+
+For the most basic RAxML commands see the old v704 manual
+ http://icwww.epfl.ch/%7Estamatak/index-Dateien/countManual7.0.4.php
+
+RAxML step-by-step tutorial
+ http://wwwkramer.in.tum.de/exelixis/hands-On.html
+
+ -- Andreas Tille <tille at debian.org> Thu, 28 Apr 2011 14:29:21 +0200
Added: trunk/packages/raxml/trunk/debian/changelog
===================================================================
--- trunk/packages/raxml/trunk/debian/changelog (rev 0)
+++ trunk/packages/raxml/trunk/debian/changelog 2011-04-28 12:52:03 UTC (rev 6699)
@@ -0,0 +1,5 @@
+raxml (7.2.6-1) unstable; urgency=low
+
+ * Initial release Closes: #xxxxxx
+
+ -- Andreas Tille <tille at debian.org> Thu, 28 Apr 2011 14:29:21 +0200
Added: trunk/packages/raxml/trunk/debian/compat
===================================================================
--- trunk/packages/raxml/trunk/debian/compat (rev 0)
+++ trunk/packages/raxml/trunk/debian/compat 2011-04-28 12:52:03 UTC (rev 6699)
@@ -0,0 +1 @@
+7
Added: trunk/packages/raxml/trunk/debian/control
===================================================================
--- trunk/packages/raxml/trunk/debian/control (rev 0)
+++ trunk/packages/raxml/trunk/debian/control 2011-04-28 12:52:03 UTC (rev 6699)
@@ -0,0 +1,23 @@
+Source: raxml
+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 (>= 8), help2man
+Standards-Version: 3.9.2
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/raxml/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/raxml/trunk/
+Homepage: http://wwwkramer.in.tum.de/exelixis/software.html
+
+Package: raxml
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Randomized Axelerated Maximum Likelihood
+ RAxML is a program for sequential and parallel Maximum Likelihood-based
+ inference of large phylogenetic trees. It has originally been derived
+ from fastDNAml.
+ .
+ There are freely accessible web-servers available for RAxML at
+ http://phylobench.vital-it.ch/raxml-bb/ and
+ http://8ball.sdsc.edu:8889/cipres-web/Bootstrap.do .
Added: trunk/packages/raxml/trunk/debian/copyright
===================================================================
--- trunk/packages/raxml/trunk/debian/copyright (rev 0)
+++ trunk/packages/raxml/trunk/debian/copyright 2011-04-28 12:52:03 UTC (rev 6699)
@@ -0,0 +1,27 @@
+Format: http://dep.debian.net/deps/dep5/
+Name: RAxML
+Maintainer: Alexandros Stamatakis <Alexandros.Stamatakis at epfl.ch>
+Source: http://wwwkramer.in.tum.de/exelixis/software.html
+
+Copyright: © 2000-2011 Alexandros Stamatakis
+License: GPL-2+
+ 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 program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+X-Comment: On Debian systems, the complete text of the GNU General Public
+ License version 2 can be found in `/usr/share/common-licenses/GPL-2'.
+
+
+Files: debian/*
+Copyright: © 2011 Andreas Tille <tille at debian.org>
+License: Same as RAxML
Added: trunk/packages/raxml/trunk/debian/dirs
===================================================================
--- trunk/packages/raxml/trunk/debian/dirs (rev 0)
+++ trunk/packages/raxml/trunk/debian/dirs 2011-04-28 12:52:03 UTC (rev 6699)
@@ -0,0 +1,2 @@
+usr/share/man/man1
+
Added: trunk/packages/raxml/trunk/debian/install
===================================================================
--- trunk/packages/raxml/trunk/debian/install (rev 0)
+++ trunk/packages/raxml/trunk/debian/install 2011-04-28 12:52:03 UTC (rev 6699)
@@ -0,0 +1 @@
+raxmlHPC usr/bin
Added: trunk/packages/raxml/trunk/debian/rules
===================================================================
--- trunk/packages/raxml/trunk/debian/rules (rev 0)
+++ trunk/packages/raxml/trunk/debian/rules 2011-04-28 12:52:03 UTC (rev 6699)
@@ -0,0 +1,25 @@
+#!/usr/bin/make -f
+
+# Copyright (C) Andreas Tille <tille at debian.org>
+# License: GPL
+
+exe=raxmlHPC
+
+%:
+ dh $@
+
+override_dh_auto_clean:
+ $(MAKE) -f Makefile.gcc clean
+
+override_dh_auto_build:
+ $(MAKE) -f Makefile.gcc
+
+override_dh_auto_install:
+ help2man --no-info --help-option="-h" --version-option="-v" \
+ --name="Randomized Axelerated Maximum Likelihood" \
+ $(CURDIR)/$(exe) > $(CURDIR)/debian/`dh_listpackages`/usr/share/man/man1/$(exe).1
+
+get-orig-source:
+ @echo "The watch file fails in reporting non-Alpha versions."
+ @echo "Just go to http://wwwkramer.in.tum.de/exelixis/software.html"
+ @echo "and download the latest non-Alpha version."
Property changes on: trunk/packages/raxml/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/raxml/trunk/debian/source/format
===================================================================
--- trunk/packages/raxml/trunk/debian/source/format (rev 0)
+++ trunk/packages/raxml/trunk/debian/source/format 2011-04-28 12:52:03 UTC (rev 6699)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/raxml/trunk/debian/watch
===================================================================
--- trunk/packages/raxml/trunk/debian/watch (rev 0)
+++ trunk/packages/raxml/trunk/debian/watch 2011-04-28 12:52:03 UTC (rev 6699)
@@ -0,0 +1,6 @@
+version=3
+opts="downloadurlmangle=s/count(\d+)Win.php/countSource$1.php/","dversionmangle=s/\.//g" \
+ http://wwwkramer.in.tum.de/exelixis/software.html .*countSource(\d+)\.php
+
+#opts="downloadurlmangle=s/RAxML v *(\d+)\.(\d+)\.(\d+) source code now available for download/countSource$1$2$3.php/" \
+# http://wwwkramer.in.tum.de/exelixis/software.html .*countSource(\d+)\.php
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