[med-svn] r4401 - in trunk/mcl/trunk: . debian debian/patches

Philipp Benner philipp at alioth.debian.org
Tue Nov 24 20:14:45 UTC 2009


Author: philipp
Date: 2009-11-24 20:14:45 +0000 (Tue, 24 Nov 2009)
New Revision: 4401

Added:
   trunk/mcl/trunk/debian/
   trunk/mcl/trunk/debian/README.Debian
   trunk/mcl/trunk/debian/README.source
   trunk/mcl/trunk/debian/changelog
   trunk/mcl/trunk/debian/compat
   trunk/mcl/trunk/debian/control
   trunk/mcl/trunk/debian/copyright
   trunk/mcl/trunk/debian/docs
   trunk/mcl/trunk/debian/mcl-doc.doc-base.clmdist
   trunk/mcl/trunk/debian/mcl-doc.doc-base.clmformat
   trunk/mcl/trunk/debian/mcl-doc.doc-base.mcl
   trunk/mcl/trunk/debian/mcl-doc.doc-base.mclfaq
   trunk/mcl/trunk/debian/mcl-doc.doc-base.mclpipeline
   trunk/mcl/trunk/debian/mcl-doc.doc-base.mcx
   trunk/mcl/trunk/debian/mcl-doc.doc-base.mcxassemble
   trunk/mcl/trunk/debian/mcl-doc.doc-base.mcxio
   trunk/mcl/trunk/debian/mcl-doc.doc-base.mcxload
   trunk/mcl/trunk/debian/mcl-doc.doc-base.mcxsubs
   trunk/mcl/trunk/debian/mcl-doc.install
   trunk/mcl/trunk/debian/patches/
   trunk/mcl/trunk/debian/patches/01-manpage-errors.patch
   trunk/mcl/trunk/debian/patches/02-wrong-interpreter-path.patch
   trunk/mcl/trunk/debian/patches/series
   trunk/mcl/trunk/debian/rules
   trunk/mcl/trunk/debian/watch
Log:
[svn-inject] Applying Debian modifications to trunk


Property changes on: trunk/mcl/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
   + 1

Added: trunk/mcl/trunk/debian/README.Debian
===================================================================
--- trunk/mcl/trunk/debian/README.Debian	                        (rev 0)
+++ trunk/mcl/trunk/debian/README.Debian	2009-11-24 20:14:45 UTC (rev 4401)
@@ -0,0 +1,8 @@
+mcl for Debian
+--------------------------------------------------------------------------------
+
+Install mcl-doc for documentation about how to use mcl. It provides a general
+introduction, input format specifications and more specific documentations as
+well as some examples.
+
+ -- Philipp Benner <pbenner at uni-osnabrueck.de>, Mon, 14 Jan 2008 18:38:36 +0100

Added: trunk/mcl/trunk/debian/README.source
===================================================================
--- trunk/mcl/trunk/debian/README.source	                        (rev 0)
+++ trunk/mcl/trunk/debian/README.source	2009-11-24 20:14:45 UTC (rev 4401)
@@ -0,0 +1,7 @@
+01-manpage-errors.patch:
+  remove spaces in the program name (which is not allowed in manuals)
+
+02-wrong-interpreter-path.patch:
+  fix perl interpreter paths
+
+ -- Philipp Benner <philipp at debian.org>, Thu,  1 Oct 2009 13:38:53 +0000

Added: trunk/mcl/trunk/debian/changelog
===================================================================
--- trunk/mcl/trunk/debian/changelog	                        (rev 0)
+++ trunk/mcl/trunk/debian/changelog	2009-11-24 20:14:45 UTC (rev 4401)
@@ -0,0 +1,306 @@
+mcl (1:09-261-1) unstable; urgency=low
+
+  * New upstream release
+
+ -- Philipp Benner <philipp at debian.org>  Wed, 30 Sep 2009 10:54:28 +0000
+
+mcl (1:09-182-1) unstable; urgency=low
+
+  * New upstream release
+  * New maintainer e-mail address
+  * Removed DMUA
+
+ -- Philipp Benner <philipp at debian.org>  Fri, 24 Jul 2009 08:15:19 +0000
+
+mcl (1:09-149-1) unstable; urgency=low
+
+  * New upstream release.
+  * Standards version 3.8.2.
+
+ -- Philipp Benner <pbenner at uni-osnabrueck.de>  Sat, 27 Jun 2009 20:33:54 +0000
+
+mcl (1:08-312-1) unstable; urgency=low
+
+  * New upstream release.
+  * Added debian/patches/manpages-whatis-fix.patch.
+  * Added debian/patches/perl-interpreter-path.patch
+  * Build-depends on zoem and tidy to regenerate manuals.
+
+ -- Philipp Benner <pbenner at uni-osnabrueck.de>  Sun, 25 Jan 2009 12:29:28 +0000
+
+mcl (1:06-058-2) unstable; urgency=low
+
+  * New maintainer e-mail address.
+  * debian/control: Added DM-Upload-Allowed: yes.
+  * debian/mcl-doc.doc-base.mcxio: fixed typo.
+  * Changed the doc-base section according to the new policy.
+
+ -- Philipp Benner <pbenner at uni-osnabrueck.de>  Mon, 31 Mar 2008 11:04:53 +0200
+
+mcl (1:06-058-1) unstable; urgency=low
+
+  * Adopting package (Closes: #452405).
+  * Standards version 3.7.2.
+  * Added Vcs-Browser and Vcs-Svn field to debian/control.
+  * Machine interpretable copyright file.
+  * Improved config.{guess,sub} handling.
+  * New upstream release.
+
+ -- Philipp Benner <mail at philipp-benner.de>  Mon, 26 Nov 2007 14:37:21 +0100
+
+mcl (1:06-021-2) unstable; urgency=low
+
+  * Orphaning this package (per Bug #452405).  Set maintainer to Debian
+    QA Group.
+  * Move Homepage to control field.
+
+ -- Joost van Baal <joostvb at debian.org>  Sat, 24 Nov 2007 00:35:03 +0100
+
+mcl (1:06-021-1) unstable; urgency=low
+
+  * New stable upstream release: Analysis and cache modes have been improved.
+    This mcl binary in this release displays a citation reference on STDERR.
+    Of course we honor upstream's wishes here, and do not suppress this
+    helpful reminder.  See the comments in debian/rules for hints on how to
+    operate if you disagree.
+  * debian/control: found out how to add Homepage pseudo-field (finally!)
+  * debian/control: we no longer ship plain text manpages in mcl-doc, adjust
+    description.
+
+ -- Joost van Baal <joostvb at debian.org>  Tue, 07 Feb 2006 21:05:31 +0100
+
+mcl (1:05-321-1) unstable; urgency=low
+
+  * New stable upstream release.  (Missed 05-272, 05-300, 05-314.)
+    Some rephrased snippets from the announcement messages:
+    + mcl-05-321:
+     This mainly adds 'transformation' functionality, which complements the
+     label-value streaming stuff.  It means you can apply quite complex
+     transformations on values, albeit only context-insensive transformations.
+    + mcl-05-314:
+     MCL can now read in label input in a simple line based format where
+     each lines contains two labels and an optional value separated by
+     whitespace.  Output clusters are returned as lines of tab-separated
+     labels.  The BLAST parser can stream this format directly to mcl
+     creating a very concise and easy to manage sequence clustering
+     pipeline.  The mcl(1) manual now has a 'getting started' section
+     with some examples.  New utility mcxload(1) with many custom options for
+     reading in label data and transforming the associated numerical values,
+     storing mappings in tab files and saving a graph in native mcl input
+     format.
+    + mcl-05-300:
+     Important for mcxassemble users: Changed mcxassemble to pick the maximum
+     between repeated entries by default.  Other noteworthy changes: mcxdump
+     can now also be used to restrict tab files, and: Fixed mcxsubs bug,
+     introduced in last release, where selections never materialize unless one
+     mysteriously specifies --rand-merge.  No changes in mcl, only stuff done
+     to the graph manipulation programs.
+    + mcl-05-272:
+     Major changes in clmimac, a noticeable change in mclblastline, a minor
+     addition to mcxdeblast, improved dump functionality in mcl.  If you just
+     use mcl there is little need for upgrading.
+    mcl-05-272 adds some extra stuff to doc/mcl/examples/ .
+    As always, read changelog for details.
+  * debian/mcl-doc.doc-base.mcxload: added
+  * debian/{compat,control,rules}: move from debhelper compatibility level 3
+    to 4 (add ${misc:Depends} to Depends)
+  * debian/copyright: new snailmail address of FSF.
+  * debian/watch: make sure it doesn't match the symlink mcl-latest.tar.gz.
+  * debian/rules, debian/mcl-doc.install: no longer install upstream TODO file:
+    it's not useful for users.
+  * debian/control: fix versioned conflicts syntax
+  * debian/rules: make proper use of comments: don't clobber build output.
+  * debian/control: Standards Version bumped from 3.6.1.0 to 3.6.2.0 (no
+    changes needed).
+
+ -- Joost van Baal <joostvb at debian.org>  Wed, 23 Nov 2005 16:36:39 +0100
+
+mcl (1:05-118-1) unstable; urgency=low
+
+  * New stable upstream release: a lot faster on large graphs because a
+    clunky input routine was fixed.
+  * debian/rules: Make sure config.{guess,sub} are up to date.  (Upstream
+    _does_ ship these.)
+  * debian/mcl-doc.doc-base.mcl, debian/mcl-doc.doc-base.mclfaq: We are no
+    longer shipping documentation in txt format.
+
+ -- Joost van Baal <joostvb at debian.org>  Wed, 25 May 2005 08:09:54 +0200
+
+mcl (1:05-096-1) unstable; urgency=low
+
+  * New upstream development release.  (Missed mcl-04-314, mcl-05-090.)
+    The only difference between mcl 05-096 and the official 05-090 release is
+    the addition of a clmorder(1) manpage.  Here's a rephrased snippet from
+    the 05-090 announcement message:
+     Nothing changed in the core clustering algorithm. But:
+     - Better support for diagnostics: mcl can now dump iterand submatrices.
+     - Helper applications for analyzing cluster structure added: clxdo,
+       clxcoarse (primitive hierarchical clustering, undocumented shell
+       scripts, installed in /usr/share/doc/mcl/scripts) and clmorder.
+     - Improvement of sibling applications: large mcxsubs rewrite - cleaner
+       specification language and new modes and options. Also, rewrite of
+       the IO library (umpteenth).
+    Read changelog for details.
+  * Install upstream TODO file.
+  * Removed maintainer scripts: not needed for this package.
+  * mcl-doc.doc-base.clmdist: fixed typo.
+
+ -- Joost van Baal <joostvb at debian.org>  Wed, 06 Apr 2005 09:50:10 +0200
+
+mcl (1:04-250-2) unstable; urgency=medium
+
+  * control: Fixed embarrasing typo in description (closes: #285424).
+    This is the reason urgency=medium rather than high: it'd be very
+    nice if this package made it to sarge, so that not too many people
+    get exposed to this ugly typo: s/computer sciense/computer science/.
+  * mcl 04-314 is out, but might not get packaged: it has no shocking
+    improvements, and a new upstream is likely to get published soon.
+
+ -- Joost van Baal <joostvb at debian.org>  Sun, 16 Jan 2005 16:27:12 +0100
+
+mcl (1:04-250-1) unstable; urgency=low
+
+  * New upstream release.  (Missed mcl-04-230.)
+  * watch: added, so that
+    http://qa.debian.org/developer.php?gpg_key=969457F0 looks even
+    more spiffy.
+
+ -- Joost van Baal <joostvb at debian.org>  Wed, 08 Sep 2004 15:04:32 +0200
+
+mcl (1:04-189-1) unstable; urgency=low
+
+  * New upstream release. (Missed mcl-04-174, 04-185, 04-187.)
+    However, beware!  mcl-04-103 might be considered non-free by some.
+    LICENSE in this release is more clear, and free.  debian/copyright
+    updated accoringly.
+    Furthermore, zoem >= 04-173 is needed for parsing cmlformat(1)'s
+    zoem output.  Such a zoem release is not yet packaged for Debian.
+  * control: added Enhances: blast2, ncbi-tools-bin, bioperl.
+
+ -- Joost van Baal <joostvb at debian.org>  Thu, 08 Jul 2004 12:13:30 +0200
+
+mcl (1:04-103-1) unstable; urgency=low
+
+  * New upstream development release.  (Upstream has published six other
+    development releases since 03-277.)
+  * Splitted in mcl and mcl-doc binary packages.
+  * No longer installs HTML documentation in plain text too.
+  * Some manpages no longer register via doc-base; just the "major" ones
+    do now.
+  * Debian Policy compliance: bumped from Standards Version 3.5.9 to
+    Standards-Version: 3.6.1.0: debian/rules now honors DEB_BUILD_OPTIONS.
+
+ -- Joost van Baal <joostvb at debian.org>  Tue, 13 Apr 2004 07:59:47 +0200
+
+mcl (1:03-277-1) unstable; urgency=low
+
+  * New upstream release.  This is the same as
+    http://micans.org/mcl/src/mcl-03-276.tar.gz, the version number is
+    the only thing which differs.
+  * doc-base.clmmate: added.  Upstream ships a clmmate manpage now: our
+    package is lintian clean again.
+
+ -- Joost van Baal <joostvb at debian.org>  Sun, 05 Oct 2003 12:27:53 +0200
+
+mcl (1:03-276-1) unstable; urgency=low
+
+  * New upstream _development_ release (missed formal releases 03-154,
+    03-178, 03-185, 03-245).
+  * copyright: added note on citations when using the software in writing
+    scientific papers.
+  * rules: build and install BLAST parsing scripts.  Do not build tribe
+    stuff.  See README for details.
+  * doc-base.*: new docs: clmformat, mclblastline, mclpipeline, mcxassemble,
+    mcxdeblast, mcxio.  removed docs: clmconf, mcxformat.
+
+ -- Joost van Baal <joostvb at debian.org>  Fri, 03 Oct 2003 11:48:46 +0200
+
+mcl (1:03-010-2) unstable; urgency=low
+
+  * Removed bogus mcximac doc-base file: mcximac does not exist.  Tnx
+    Laurent Bonnaud. (closes: #193058)
+
+ -- Joost van Baal <joostvb at debian.org>  Thu, 15 May 2003 10:58:17 +0200
+
+mcl (1:03-010-1) unstable; urgency=low
+
+  * New upstream release.
+  * Registered new docs using doc-base: clmimac, clmresidue, mcxmap.  mcl
+    and mclfaq now get installed in plain text format too.
+  * debian/control: Standards 3.5.2 -> 3.5.9 (no changes needed).
+
+ -- Joost van Baal <joostvb at debian.org>  Sat, 10 May 2003 10:29:04 +0200
+
+mcl (1:02-277-1) unstable; urgency=low
+
+  * New upstream release.
+
+ -- Joost van Baal <joostvb at debian.org>  Fri, 25 Oct 2002 11:31:34 +0200
+
+mcl (1:02-172-1) unstable; urgency=low
+
+  * New upstream release.
+  * debian/rules: no longer uses touch-hack to work around timeskew
+    problems: upstreams uses AM_MAINTAINER_MODE now.
+
+ -- Joost van Baal <joostvb at debian.org>  Mon, 24 Jun 2002 14:44:11 +0200
+
+mcl (1:02-116-1) unstable; urgency=low
+
+  * New upstream release.
+
+ -- Joost van Baal <joostvb at debian.org>  Sat, 27 Apr 2002 22:59:49 +0200
+
+mcl (1:02-113-cvs-1) unstable; urgency=low
+
+  * build from current cvs, pre-release
+  * debian/rules: set configure flags based on check equality of
+    DEB_BUILD_GNU_TYPE and DEB_HOST_GNU_TYPE, cf current autotools-dev ideas.
+  * debian/control, debian/copyright: MCL found a new home on the www.
+  * debian/copyright: added note on contrib/tribe/ copyright holder.
+  * doc-base.*: added doc-base.mclfaq and doc-base.mcximac
+
+ -- Joost van Baal <joostvb at debian.org>  Tue, 23 Apr 2002 23:30:37 +0200
+
+mcl (1:02-035-1) unstable; urgency=low
+
+  * First release for the Debian archive (closes: #132283).
+  * copyright: new download location, refer to /usr/share/common-licenses/GPL .
+  * rules: applied some of Henrique de Moraes Holschuh's autotools-dev voodoo,
+    got rid of some NOP dh_ calls.
+  * docs: no longer installs NEWS; this file is not yet maintained upstream.
+
+ -- Joost van Baal <joostvb at debian.org>  Wed,  6 Feb 2002 10:20:17 +0100
+
+mcl (1:02-034-1) unstable; urgency=low
+
+  * New upstream release.
+
+ -- Joost van Baal <joostvb at debian.org>  Mon,  4 Feb 2002 08:33:36 +0100
+
+mcl (1:02-030-1) unstable; urgency=low
+
+  * Snapshot build from CVS.
+  * Use epoch in version numbering, since upstream made order-breaking
+    version numbering policy change.
+  * Use docbase for all .ps and .html manpages.
+
+ -- Joost van Baal <joostvb at debian.org>  Wed, 30 Jan 2002 22:46:28 +0100
+
+mcl (20020116-1) unstable; urgency=low
+
+  * Snapshot build from CVS.
+
+ -- Joost van Baal <joostvb at debian.org>  Wed, 16 Jan 2002 21:08:22 +0100
+
+mcl (20011211-1) unstable; urgency=low
+
+  * New upstream release.  Now registers documentation using doc-base.
+
+ -- Joost van Baal <joostvb at debian.org>  Tue, 11 Dec 2001 20:19:42 +0100
+
+mcl (20011012-1) unstable; urgency=low
+
+  * Initial Release.
+
+ -- Joost van Baal <joostvb at debian.org>  Fri, 12 Oct 2001 22:43:08 +0200

Added: trunk/mcl/trunk/debian/compat
===================================================================
--- trunk/mcl/trunk/debian/compat	                        (rev 0)
+++ trunk/mcl/trunk/debian/compat	2009-11-24 20:14:45 UTC (rev 4401)
@@ -0,0 +1 @@
+5

Added: trunk/mcl/trunk/debian/control
===================================================================
--- trunk/mcl/trunk/debian/control	                        (rev 0)
+++ trunk/mcl/trunk/debian/control	2009-11-24 20:14:45 UTC (rev 4401)
@@ -0,0 +1,36 @@
+Source: mcl
+Section: math
+Priority: optional
+Maintainer: Philipp Benner <philipp at debian.org>
+Build-Depends: debhelper (>= 5), autotools-dev, quilt, zoem, tidy
+Standards-Version: 3.8.3
+Vcs-Browser: http://svn.debian.org/wsvn/pkg-escience/mcl/
+Vcs-Svn: svn://svn.debian.org/pkg-escience/mcl/
+Homepage: http://micans.org/mcl/
+
+Package: mcl
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: mcl-doc
+Enhances: blast2, ncbi-tools-bin, bioperl-run
+Description: the Markov Cluster algorithm
+ The MCL package is an implementation of the MCL algorithm, and offers
+ utilities for manipulating sparse matrices (the essential data
+ structure in the MCL algorithm) and conducting cluster experiments.
+ .
+ MCL is currently being used in sciences like biology (protein family
+ detection, genomics), computer science (node clustering in
+ Peer-to-Peer networks), and linguistics (text analysis).
+
+Package: mcl-doc
+Architecture: all
+Depends: ${misc:Depends}
+Section: doc
+Suggests: mcl
+Conflicts: mcl (<< 04-095-1)
+Description: documentation for mcl
+ The MCL package is an implementation of the Markov Cluster algorithm,
+ for manipulating sparse matricess and conducting cluster experiments.
+ .
+ This is documention for mcl: the MCL FAQ, some examples as well as manpages
+ in HTML and PostScript format.

Added: trunk/mcl/trunk/debian/copyright
===================================================================
--- trunk/mcl/trunk/debian/copyright	                        (rev 0)
+++ trunk/mcl/trunk/debian/copyright	2009-11-24 20:14:45 UTC (rev 4401)
@@ -0,0 +1,64 @@
+This package was downloaded from http://micans.org/mcl/src/
+
+Files: *
+Copyright: © 1999-2007 Stijn van Dongen <stijn at micans.org>
+License: GPL-2
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of version 2 of the GNU General Public License as published
+ by the Free Software Foundation. It should be shipped with MCL in the top
+ level directory as the file COPYING.
+ .
+ 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.
+ .
+ If you use MCL software in your scientific research, please cite it
+ appropriately as you would cite a journal or a book. This includes papers
+ published in regular or electronic journals, usage of MCL as a back-end to a
+ database that is accessible via a web interface, or inclusion of MCL in a
+ larger framework of software that is distributed for other people for
+ scientific use.  Include one of the following citations:
+ .
+ Stijn van Dongen, Graph Clustering by Flow Simulation.
+ PhD thesis, University of Utrecht, May 2000.
+ ( http://www.library.uu.nl/digiarchief/dip/diss/1895620/inhoud.htm )
+ .
+ Stijn van Dongen. A cluster algorithm for graphs.  Technical Report
+ INS-R0010, National Research Institute for Mathematics and Computer
+ Science in the Netherlands, Amsterdam, May 2000.
+ ( http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z )
+ .
+ and proper attributions to mcl's home http://micans.org/mcl/
+ and its author, Stijn van Dongen.
+ The publications listed above can be retrieved from the preceding URL.
+ .
+ If you are using some wrapper around mcl such as the blast module or the
+ tribe module, you are asked to act likewise.
+ .
+ For biological applications, it is appropriate to cite, additionally,
+ the reference article for the first application of mcl to biological data:
+ .
+ Enright A.J., Van Dongen S., Ouzounis C.A.
+ An efficient algorithm for large-scale detection of protein families,
+ Nucleic Acids Research 30(7):1575-1584 (2002).
+
+Files: src/alien/oxygen/src/mcxdeblast
+Copyright: © 2002-2005 Stijn van Dongen,
+           © 2004 Jason Stajich
+License: GPL-2
+
+Files: src/contrib/tribe/*
+Copyright: © 2002 EMBL-EBI Anton Enright
+License: GPL-2
+
+Files: debian/*
+Copyright: © 2001-2007 Joost van Baal <joostvb at debian.org>,
+           © 2007-2009 Philipp Benner <philipp at debian.org>
+License: GPL-2+
+ The Debian packaging information is under the GPL, version 2 or later.
+
+On Debian GNU/Linux systems, the complete text of the GNU General
+Public License can be found in `/usr/share/common-licenses/GPL' and the
+complete text of the GNU Lesser General Public License can be found in
+`/usr/share/common-licenses/LGPL'.

Added: trunk/mcl/trunk/debian/docs
===================================================================
--- trunk/mcl/trunk/debian/docs	                        (rev 0)
+++ trunk/mcl/trunk/debian/docs	2009-11-24 20:14:45 UTC (rev 4401)
@@ -0,0 +1,3 @@
+AUTHORS
+README
+THANKS

Added: trunk/mcl/trunk/debian/mcl-doc.doc-base.clmdist
===================================================================
--- trunk/mcl/trunk/debian/mcl-doc.doc-base.clmdist	                        (rev 0)
+++ trunk/mcl/trunk/debian/mcl-doc.doc-base.clmdist	2009-11-24 20:14:45 UTC (rev 4401)
@@ -0,0 +1,13 @@
+Document: clmdist
+Title: clmdist - compute the split/join distance between two partitions
+ (clusterings)
+Author: Stijn van Dongen
+Abstract: A document describing the clmdist command line tool.
+Section: Science/Mathematics
+
+Format: PostScript
+Files: /usr/share/doc/mcl/clmdist.ps.gz
+
+Format: HTML
+Index: /usr/share/doc/mcl/clmdist.html
+Files: /usr/share/doc/mcl/clmdist.html

Added: trunk/mcl/trunk/debian/mcl-doc.doc-base.clmformat
===================================================================
--- trunk/mcl/trunk/debian/mcl-doc.doc-base.clmformat	                        (rev 0)
+++ trunk/mcl/trunk/debian/mcl-doc.doc-base.clmformat	2009-11-24 20:14:45 UTC (rev 4401)
@@ -0,0 +1,12 @@
+Document: clmformat
+Title: clmformat - display cluster results in readable form
+Author: Stijn van Dongen
+Abstract: A document describing the clmformat command line tool.
+Section: Science/Mathematics
+
+Format: PostScript
+Files: /usr/share/doc/mcl/clmformat.ps.gz
+
+Format: HTML
+Index: /usr/share/doc/mcl/clmformat.html
+Files: /usr/share/doc/mcl/clmformat.html

Added: trunk/mcl/trunk/debian/mcl-doc.doc-base.mcl
===================================================================
--- trunk/mcl/trunk/debian/mcl-doc.doc-base.mcl	                        (rev 0)
+++ trunk/mcl/trunk/debian/mcl-doc.doc-base.mcl	2009-11-24 20:14:45 UTC (rev 4401)
@@ -0,0 +1,12 @@
+Document: mcl
+Title: MCL - the Amsterdam implementation of the Markov Cluster Algorithm
+Author: Stijn van Dongen
+Abstract: Description of the mcl command line tool and the MCL algorithm.
+Section: Science/Mathematics
+
+Format: PostScript
+Files: /usr/share/doc/mcl/mcl.ps.gz
+
+Format: HTML
+Index: /usr/share/doc/mcl/mcl.html
+Files: /usr/share/doc/mcl/mcl.html

Added: trunk/mcl/trunk/debian/mcl-doc.doc-base.mclfaq
===================================================================
--- trunk/mcl/trunk/debian/mcl-doc.doc-base.mclfaq	                        (rev 0)
+++ trunk/mcl/trunk/debian/mcl-doc.doc-base.mclfaq	2009-11-24 20:14:45 UTC (rev 4401)
@@ -0,0 +1,14 @@
+Document: mclfaq
+Title: mclfaq - MCL and mcl quick faqs, facts, and terminology
+Author: Stijn van Dongen
+Abstract: A FAQ answering questions related to both the generic MCL algorithm
+ and the MCL process on which the algorithm is based, as well as those related
+ to the implementation.
+Section: Science/Mathematics
+
+Format: PostScript
+Files: /usr/share/doc/mcl/mclfaq.ps.gz
+
+Format: HTML
+Index: /usr/share/doc/mcl/mclfaq.html
+Files: /usr/share/doc/mcl/mclfaq.html

Added: trunk/mcl/trunk/debian/mcl-doc.doc-base.mclpipeline
===================================================================
--- trunk/mcl/trunk/debian/mcl-doc.doc-base.mclpipeline	                        (rev 0)
+++ trunk/mcl/trunk/debian/mcl-doc.doc-base.mclpipeline	2009-11-24 20:14:45 UTC (rev 4401)
@@ -0,0 +1,13 @@
+Document: mclpipeline
+Title: mclpipeline - a generic pipeline for generating and scrutinizing mcl 
+         clusterings
+Author: Stijn van Dongen
+Abstract: A document describing the mclpipeline command line tool.
+Section: Science/Mathematics
+
+Format: PostScript
+Files: /usr/share/doc/mcl/mclpipeline.ps.gz
+
+Format: HTML
+Index: /usr/share/doc/mcl/mclpipeline.html
+Files: /usr/share/doc/mcl/mclpipeline.html

Added: trunk/mcl/trunk/debian/mcl-doc.doc-base.mcx
===================================================================
--- trunk/mcl/trunk/debian/mcl-doc.doc-base.mcx	                        (rev 0)
+++ trunk/mcl/trunk/debian/mcl-doc.doc-base.mcx	2009-11-24 20:14:45 UTC (rev 4401)
@@ -0,0 +1,12 @@
+Document: mcx
+Title: mcx - a stack language interpreter for interaction with the mcl libraries
+Author: Stijn van Dongen
+Abstract: A document describing the mcx command line and interactive tool.
+Section: Science/Mathematics
+
+Format: PostScript
+Files: /usr/share/doc/mcl/mcx.ps.gz
+
+Format: HTML
+Index: /usr/share/doc/mcl/mcx.html
+Files: /usr/share/doc/mcl/mcx.html

Added: trunk/mcl/trunk/debian/mcl-doc.doc-base.mcxassemble
===================================================================
--- trunk/mcl/trunk/debian/mcl-doc.doc-base.mcxassemble	                        (rev 0)
+++ trunk/mcl/trunk/debian/mcl-doc.doc-base.mcxassemble	2009-11-24 20:14:45 UTC (rev 4401)
@@ -0,0 +1,12 @@
+Document: mcxassemble
+Title: mcxassemble - transform raw cooccurrence data to mcl matrix format
+Author: Stijn van Dongen
+Abstract: A document describing the mcxassemble command line tool.
+Section: Science/Mathematics
+
+Format: PostScript
+Files: /usr/share/doc/mcl/mcxassemble.ps.gz
+
+Format: HTML
+Index: /usr/share/doc/mcl/mcxassemble.html
+Files: /usr/share/doc/mcl/mcxassemble.html

Added: trunk/mcl/trunk/debian/mcl-doc.doc-base.mcxio
===================================================================
--- trunk/mcl/trunk/debian/mcl-doc.doc-base.mcxio	                        (rev 0)
+++ trunk/mcl/trunk/debian/mcl-doc.doc-base.mcxio	2009-11-24 20:14:45 UTC (rev 4401)
@@ -0,0 +1,13 @@
+Document: mcxio
+Title: mcxio - format spec for matrix input and output in mcl family
+Author: Stijn van Dongen
+Abstract: A document describing the generic matrix format used in the mcl
+ libraries. It also describes the raw intermediate format used by mcxassemble.
+Section: Science/Mathematics
+
+Format: PostScript
+Files: /usr/share/doc/mcl/mcxio.ps.gz
+
+Format: HTML
+Index: /usr/share/doc/mcl/mcxio.html
+Files: /usr/share/doc/mcl/mcxio.html

Added: trunk/mcl/trunk/debian/mcl-doc.doc-base.mcxload
===================================================================
--- trunk/mcl/trunk/debian/mcl-doc.doc-base.mcxload	                        (rev 0)
+++ trunk/mcl/trunk/debian/mcl-doc.doc-base.mcxload	2009-11-24 20:14:45 UTC (rev 4401)
@@ -0,0 +1,12 @@
+Document: mcxload
+Title: mcxload - load matrices and tab files from label format
+Author: Stijn van Dongen
+Abstract: A document describing the mcxload command line tool.
+Section: Science/Mathematics
+
+Format: PostScript
+Files: /usr/share/doc/mcl/mcxload.ps.gz
+
+Format: HTML
+Index: /usr/share/doc/mcl/mcxload.html
+Files: /usr/share/doc/mcl/mcxload.html

Added: trunk/mcl/trunk/debian/mcl-doc.doc-base.mcxsubs
===================================================================
--- trunk/mcl/trunk/debian/mcl-doc.doc-base.mcxsubs	                        (rev 0)
+++ trunk/mcl/trunk/debian/mcl-doc.doc-base.mcxsubs	2009-11-24 20:14:45 UTC (rev 4401)
@@ -0,0 +1,13 @@
+Document: mcxsubs
+Title: mcxsubs - extract submatrices (subgraphs) of a matrix (graph) 
+ corresponding with index sets and sets of clusters
+Author: Stijn van Dongen
+Abstract: A document describing the mcxsubs command line tool.
+Section: Science/Mathematics
+
+Format: PostScript
+Files: /usr/share/doc/mcl/mcxsubs.ps.gz
+
+Format: HTML
+Index: /usr/share/doc/mcl/mcxsubs.html
+Files: /usr/share/doc/mcl/mcxsubs.html

Added: trunk/mcl/trunk/debian/mcl-doc.install
===================================================================
--- trunk/mcl/trunk/debian/mcl-doc.install	                        (rev 0)
+++ trunk/mcl/trunk/debian/mcl-doc.install	2009-11-24 20:14:45 UTC (rev 4401)
@@ -0,0 +1,9 @@
+usr/share/doc/mcl/AUTHORS
+usr/share/doc/mcl/README
+usr/share/doc/mcl/THANKS
+usr/share/doc/mcl/*.html
+usr/share/doc/mcl/*.ps
+usr/share/doc/mcl/minimcl
+usr/share/doc/mcl/examples
+usr/share/man/man5
+usr/share/man/man7

Added: trunk/mcl/trunk/debian/patches/01-manpage-errors.patch
===================================================================
--- trunk/mcl/trunk/debian/patches/01-manpage-errors.patch	                        (rev 0)
+++ trunk/mcl/trunk/debian/patches/01-manpage-errors.patch	2009-11-24 20:14:45 UTC (rev 4401)
@@ -0,0 +1,273 @@
+Index: mcl-09-261/doc/clmclose.1
+===================================================================
+--- mcl-09-261.orig/doc/clmclose.1	2009-06-28 14:18:27.000000000 +0000
++++ mcl-09-261/doc/clmclose.1	2009-06-28 14:19:28.000000000 +0000
+@@ -1,5 +1,5 @@
+ .\" Copyright (c) 2009 Stijn van Dongen
+-.TH "clm close" 1 "18 Sep 2009" "clm close 1\&.008, 09-261" "USER COMMANDS "
++.TH "clmclose" 1 "18 Sep 2009" "clm close 1\&.008, 09-261" "USER COMMANDS "
+ .po 2m
+ .de ZI
+ .\" Zoem Indent/Itemize macro I.
+@@ -28,7 +28,7 @@
+ .el .in 8m
+ ..
+ .SH NAME
+-clm close \- Fetch connected components from graphs or subgraphs
++clmclose \- Fetch connected components from graphs or subgraphs
+ 
+ clmclose is not in actual fact a program\&. This manual
+ page documents the behaviour and options of the clm program when
+Index: mcl-09-261/doc/clmdist.1
+===================================================================
+--- mcl-09-261.orig/doc/clmdist.1	2009-06-28 14:18:40.000000000 +0000
++++ mcl-09-261/doc/clmdist.1	2009-06-28 14:19:45.000000000 +0000
+@@ -1,5 +1,5 @@
+ .\" Copyright (c) 2009 Stijn van Dongen
+-.TH "clm dist" 1 "18 Sep 2009" "clm dist 1\&.008, 09-261" "USER COMMANDS "
++.TH "clmdist" 1 "18 Sep 2009" "clm dist 1\&.008, 09-261" "USER COMMANDS "
+ .po 2m
+ .de ZI
+ .\" Zoem Indent/Itemize macro I.
+@@ -28,7 +28,7 @@
+ .el .in 8m
+ ..
+ .SH NAME
+-clm dist \- compute the distance between two or more partitions (clusterings)\&.
++clmdist \- compute the distance between two or more partitions (clusterings)\&.
+ 
+ The distance that is computed can be any of
+ \fIsplit/join distance\fP, \fIvariance of information\fP,
+Index: mcl-09-261/doc/clmformat.1
+===================================================================
+--- mcl-09-261.orig/doc/clmformat.1	2009-06-28 14:18:48.000000000 +0000
++++ mcl-09-261/doc/clmformat.1	2009-06-28 14:19:22.000000000 +0000
+@@ -28,7 +28,7 @@
+ .el .in 8m
+ ..
+ .SH NAME
+-clm format \- display cluster results in readable form
++clmformat \- display cluster results in readable form
+ 
+ (optionally with labels and/or cohesion and stickiness measures
+ attached)\&.
+Index: mcl-09-261/doc/clmimac.1
+===================================================================
+--- mcl-09-261.orig/doc/clmimac.1	2009-06-28 14:19:53.000000000 +0000
++++ mcl-09-261/doc/clmimac.1	2009-06-28 14:19:59.000000000 +0000
+@@ -1,5 +1,5 @@
+ .\" Copyright (c) 2009 Stijn van Dongen
+-.TH "clm imac" 1 "18 Sep 2009" "clm imac 1\&.008, 09-261" "USER COMMANDS "
++.TH "clmimac" 1 "18 Sep 2009" "clm imac 1\&.008, 09-261" "USER COMMANDS "
+ .po 2m
+ .de ZI
+ .\" Zoem Indent/Itemize macro I.
+@@ -28,7 +28,7 @@
+ .el .in 8m
+ ..
+ .SH NAME
+-clm imac \- Interpret Matrices (c\&.q\&. MCL iterands output by \fBmcl\fP) As Clusterings\&.
++clmimac \- Interpret Matrices (c\&.q\&. MCL iterands output by \fBmcl\fP) As Clusterings\&.
+ 
+ clmimac is not in actual fact a program\&. This manual
+ page documents the behaviour and options of the clm program when
+Index: mcl-09-261/doc/clminfo.1
+===================================================================
+--- mcl-09-261.orig/doc/clminfo.1	2009-06-28 14:20:06.000000000 +0000
++++ mcl-09-261/doc/clminfo.1	2009-06-28 14:20:11.000000000 +0000
+@@ -1,5 +1,5 @@
+ .\" Copyright (c) 2009 Stijn van Dongen
+-.TH "clm info" 1 "18 Sep 2009" "clm info 1\&.008, 09-261" "USER COMMANDS "
++.TH "clminfo" 1 "18 Sep 2009" "clm info 1\&.008, 09-261" "USER COMMANDS "
+ .po 2m
+ .de ZI
+ .\" Zoem Indent/Itemize macro I.
+@@ -28,7 +28,7 @@
+ .el .in 8m
+ ..
+ .SH NAME
+-clm info \- Compute performance measures for graphs and clusterings\&.
++clminfo \- Compute performance measures for graphs and clusterings\&.
+ 
+ clminfo is not in actual fact a program\&. This manual
+ page documents the behaviour and options of the clm program when
+Index: mcl-09-261/doc/clmmate.1
+===================================================================
+--- mcl-09-261.orig/doc/clmmate.1	2009-06-28 14:20:17.000000000 +0000
++++ mcl-09-261/doc/clmmate.1	2009-06-28 14:20:24.000000000 +0000
+@@ -1,5 +1,5 @@
+ .\" Copyright (c) 2009 Stijn van Dongen
+-.TH "clm mate" 1 "18 Sep 2009" "clm mate 1\&.008, 09-261" "USER COMMANDS "
++.TH "clmmate" 1 "18 Sep 2009" "clm mate 1\&.008, 09-261" "USER COMMANDS "
+ .po 2m
+ .de ZI
+ .\" Zoem Indent/Itemize macro I.
+@@ -28,7 +28,7 @@
+ .el .in 8m
+ ..
+ .SH NAME
+-clm mate \- compute best matches between two clusterings
++clmmate \- compute best matches between two clusterings
+ 
+ clmmate is not in actual fact a program\&. This manual
+ page documents the behaviour and options of the clm program when
+Index: mcl-09-261/doc/clmmeet.1
+===================================================================
+--- mcl-09-261.orig/doc/clmmeet.1	2009-06-28 14:20:31.000000000 +0000
++++ mcl-09-261/doc/clmmeet.1	2009-06-28 14:20:36.000000000 +0000
+@@ -1,5 +1,5 @@
+ .\" Copyright (c) 2009 Stijn van Dongen
+-.TH "clm meet" 1 "18 Sep 2009" "clm meet 1\&.008, 09-261" "USER COMMANDS "
++.TH "clmmeet" 1 "18 Sep 2009" "clm meet 1\&.008, 09-261" "USER COMMANDS "
+ .po 2m
+ .de ZI
+ .\" Zoem Indent/Itemize macro I.
+@@ -28,7 +28,7 @@
+ .el .in 8m
+ ..
+ .SH NAME
+-clm meet \- compute the intersection of a set of clusterings\&.
++clmmeet \- compute the intersection of a set of clusterings\&.
+ 
+ clmmeet is not in actual fact a program\&. This manual
+ page documents the behaviour and options of the clm program when
+Index: mcl-09-261/doc/clmorder.1
+===================================================================
+--- mcl-09-261.orig/doc/clmorder.1	2009-06-28 14:20:41.000000000 +0000
++++ mcl-09-261/doc/clmorder.1	2009-06-28 14:20:46.000000000 +0000
+@@ -1,5 +1,5 @@
+ .\" Copyright (c) 2009 Stijn van Dongen
+-.TH "clm order" 1 "18 Sep 2009" "clm order 1\&.008, 09-261" "USER COMMANDS "
++.TH "clmorder" 1 "18 Sep 2009" "clm order 1\&.008, 09-261" "USER COMMANDS "
+ .po 2m
+ .de ZI
+ .\" Zoem Indent/Itemize macro I.
+@@ -28,7 +28,7 @@
+ .el .in 8m
+ ..
+ .SH NAME
+-clm order \- reorder indices to represent blocks from different clusterings\&.
++clmorder \- reorder indices to represent blocks from different clusterings\&.
+ 
+ clmorder is not in actual fact a program\&. This manual
+ page documents the behaviour and options of the clm program when
+Index: mcl-09-261/doc/clmresidue.1
+===================================================================
+--- mcl-09-261.orig/doc/clmresidue.1	2009-06-28 14:20:51.000000000 +0000
++++ mcl-09-261/doc/clmresidue.1	2009-06-28 14:20:57.000000000 +0000
+@@ -1,5 +1,5 @@
+ .\" Copyright (c) 2009 Stijn van Dongen
+-.TH "clm residue" 1 "18 Sep 2009" "clm residue 1\&.008, 09-261" "USER COMMANDS "
++.TH "clmresidue" 1 "18 Sep 2009" "clm residue 1\&.008, 09-261" "USER COMMANDS "
+ .po 2m
+ .de ZI
+ .\" Zoem Indent/Itemize macro I.
+@@ -28,7 +28,7 @@
+ .el .in 8m
+ ..
+ .SH NAME
+-clm residue \- extend clustering of subgraph to clustering of graph\&.
++clmresidue \- extend clustering of subgraph to clustering of graph\&.
+ 
+ clmresidue is not in actual fact a program\&. This manual
+ page documents the behaviour and options of the clm program when
+Index: mcl-09-261/doc/clmvol.1
+===================================================================
+--- mcl-09-261.orig/doc/clmvol.1	2009-06-28 14:21:02.000000000 +0000
++++ mcl-09-261/doc/clmvol.1	2009-06-28 14:21:07.000000000 +0000
+@@ -1,5 +1,5 @@
+ .\" Copyright (c) 2009 Stijn van Dongen
+-.TH "clm vol" 1 "18 Sep 2009" "clm vol 1\&.008, 09-261" "USER COMMANDS "
++.TH "clmvol" 1 "18 Sep 2009" "clm vol 1\&.008, 09-261" "USER COMMANDS "
+ .po 2m
+ .de ZI
+ .\" Zoem Indent/Itemize macro I.
+@@ -28,7 +28,7 @@
+ .el .in 8m
+ ..
+ .SH NAME
+-clm vol \- compute volatile nodes from a set of clusterings
++clmvol \- compute volatile nodes from a set of clusterings
+ 
+ clmvol is not in actual fact a program\&. This manual
+ page documents the behaviour and options of the clm program when
+Index: mcl-09-261/doc/mcxclcf.1
+===================================================================
+--- mcl-09-261.orig/doc/mcxclcf.1	2009-06-28 14:21:17.000000000 +0000
++++ mcl-09-261/doc/mcxclcf.1	2009-06-28 14:21:22.000000000 +0000
+@@ -1,5 +1,5 @@
+ .\" Copyright (c) 2009 Stijn van Dongen
+-.TH "mcx clcf" 1 "18 Sep 2009" "mcx clcf 1\&.008, 09-261" "USER COMMANDS "
++.TH "mcxclcf" 1 "18 Sep 2009" "mcx clcf 1\&.008, 09-261" "USER COMMANDS "
+ .po 2m
+ .de ZI
+ .\" Zoem Indent/Itemize macro I.
+@@ -28,7 +28,7 @@
+ .el .in 8m
+ ..
+ .SH NAME
+-mcx clcf \- compute the clustering coefficient of a graph
++mcxclcf \- compute the clustering coefficient of a graph
+ .SH SYNOPSIS
+ 
+ \fBmcx clcf\fP [options] [matrix-file]
+Index: mcl-09-261/doc/mcxconvert.1
+===================================================================
+--- mcl-09-261.orig/doc/mcxconvert.1	2009-06-28 14:21:30.000000000 +0000
++++ mcl-09-261/doc/mcxconvert.1	2009-06-28 14:21:37.000000000 +0000
+@@ -1,5 +1,5 @@
+ .\" Copyright (c) 2009 Stijn van Dongen
+-.TH "mcx convert" 1 "18 Sep 2009" "mcx convert 1\&.008, 09-261" "USER COMMANDS "
++.TH "mcxconvert" 1 "18 Sep 2009" "mcx convert 1\&.008, 09-261" "USER COMMANDS "
+ .po 2m
+ .de ZI
+ .\" Zoem Indent/Itemize macro I.
+@@ -28,7 +28,7 @@
+ .el .in 8m
+ ..
+ .SH NAME
+-mcx convert \- convert between mcx storage types
++mcxconvert \- convert between mcx storage types
+ .SH SYNOPSIS
+ 
+ \fBmcx convert\fP <matrix-file-in> <matrix-file-out>
+Index: mcl-09-261/doc/mcxctty.1
+===================================================================
+--- mcl-09-261.orig/doc/mcxctty.1	2009-06-28 14:21:49.000000000 +0000
++++ mcl-09-261/doc/mcxctty.1	2009-06-28 14:21:53.000000000 +0000
+@@ -1,5 +1,5 @@
+ .\" Copyright (c) 2009 Stijn van Dongen
+-.TH "mcx ctty" 1 "18 Sep 2009" "mcx ctty 1\&.008, 09-261" "USER COMMANDS "
++.TH "mcxctty" 1 "18 Sep 2009" "mcx ctty 1\&.008, 09-261" "USER COMMANDS "
+ .po 2m
+ .de ZI
+ .\" Zoem Indent/Itemize macro I.
+@@ -28,7 +28,7 @@
+ .el .in 8m
+ ..
+ .SH NAME
+-mcx ctty \- compute the clustering coefficient of a graph
++mcxctty \- compute the clustering coefficient of a graph
+ .SH SYNOPSIS
+ 
+ \fBmcx ctty\fP [options] [matrix-file]
+Index: mcl-09-261/doc/mcxdiameter.1
+===================================================================
+--- mcl-09-261.orig/doc/mcxdiameter.1	2009-06-28 14:21:59.000000000 +0000
++++ mcl-09-261/doc/mcxdiameter.1	2009-06-28 14:22:04.000000000 +0000
+@@ -1,5 +1,5 @@
+ .\" Copyright (c) 2009 Stijn van Dongen
+-.TH "mcx diameter" 1 "18 Sep 2009" "mcx diameter 1\&.008, 09-261" "USER COMMANDS "
++.TH "mcxdiameter" 1 "18 Sep 2009" "mcx diameter 1\&.008, 09-261" "USER COMMANDS "
+ .po 2m
+ .de ZI
+ .\" Zoem Indent/Itemize macro I.
+@@ -28,7 +28,7 @@
+ .el .in 8m
+ ..
+ .SH NAME
+-mcx diameter \- compute the diameter of a graph
++mcxdiameter \- compute the diameter of a graph
+ .SH SYNOPSIS
+ 
+ \fBmcx diameter\fP [options]

Added: trunk/mcl/trunk/debian/patches/02-wrong-interpreter-path.patch
===================================================================
--- trunk/mcl/trunk/debian/patches/02-wrong-interpreter-path.patch	                        (rev 0)
+++ trunk/mcl/trunk/debian/patches/02-wrong-interpreter-path.patch	2009-11-24 20:14:45 UTC (rev 4401)
@@ -0,0 +1,10 @@
+Index: mcl-09-149/src/alien/oxygen/src/mcxdeblast
+===================================================================
+--- mcl-09-149.orig/src/alien/oxygen/src/mcxdeblast	2009-06-28 14:27:45.000000000 +0000
++++ mcl-09-149/src/alien/oxygen/src/mcxdeblast	2009-06-28 14:27:48.000000000 +0000
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/perl -w
+ 
+ use Getopt::Long;
+ 

Added: trunk/mcl/trunk/debian/patches/series
===================================================================
--- trunk/mcl/trunk/debian/patches/series	                        (rev 0)
+++ trunk/mcl/trunk/debian/patches/series	2009-11-24 20:14:45 UTC (rev 4401)
@@ -0,0 +1,2 @@
+01-manpage-errors.patch
+02-wrong-interpreter-path.patch

Added: trunk/mcl/trunk/debian/rules
===================================================================
--- trunk/mcl/trunk/debian/rules	                        (rev 0)
+++ trunk/mcl/trunk/debian/rules	2009-11-24 20:14:45 UTC (rev 4401)
@@ -0,0 +1,188 @@
+#!/usr/bin/make -f
+
+# based upon sample debian/rules that uses debhelper.
+# GNU copyright 1997 to 1999 by Joey Hess.
+
+# Uncomment this to turn on verbose mode.
+# export DH_VERBOSE=1
+
+include /usr/share/quilt/quilt.make
+
+# allow bashism's in commandlines
+SHELL = /bin/bash
+
+# Debian Policy 10.1
+CFLAGS = -g -Wall
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+CFLAGS += -O0
+else
+CFLAGS += -O2
+endif
+INSTALL = install
+INSTALL_PROGRAM = $(INSTALL) -p    -o root -g root  -m  755
+ifeq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS)))
+INSTALL_PROGRAM += -s
+endif
+
+# variables to be used in configure invocation. see
+# autotools-dev/README.Debian.gz
+export DEB_HOST_GNU_TYPE  ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE)
+export DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
+
+# use autoconf 2.52 or newer
+ifeq ($(DEB_BUILD_GNU_TYPE), $(DEB_HOST_GNU_TYPE))
+  confflags += --build $(DEB_HOST_GNU_TYPE)
+else
+  confflags += --build $(DEB_BUILD_GNU_TYPE) --host $(DEB_HOST_GNU_TYPE)
+endif
+
+## Build BLAST parsing script mcxdeblast and the pipeline script mclblastline
+## (sources in src/alien/oxygen).  It encapsulates all the stages of parsing,
+## matrix creation, running mcl, and formatting the result
+## into a single application.
+confflags += --enable-blast
+
+## add --enable-tribe to confflags to add the upstreams supplied tribe tools
+## (protein clustering stuff).  This builds and installs the tools
+##
+##  tribe-families  tribe-matrix  tribemcl  tribe-parse
+##
+## We're not doing it since tribe-matrix segfaults, and the tools lackproper
+## manpages.  Furthermore, the BLAST parsing scripts can be used in place of
+## the tribe module.
+
+# confflags += --enable-tribe
+
+## If you really want to suppress the citation reference printed by MCL (the
+## one which looks like
+##
+##  Please cite:
+##    Stijn van Dongen, Graph Clustering by Flow Simulation.  PhD thesis,
+##    University of Utrecht, May 2000.
+##       (  http://www.library.uu.nl/digiarchief/dip/diss/1895620/full.pdf
+##       or  http://micans.org/mcl/lit/svdthesis.pdf.gz)
+##  OR
+##    Stijn van Dongen, A cluster algorithm for graphs. Technical
+##    Report INS-R0010, National Research Institute for Mathematics
+##    and Computer Science in the Netherlands, Amsterdam, May 2000.
+##       (  http://www.cwi.nl/ftp/CWIreports/INS/INS-R0010.ps.Z
+##       or  http://micans.org/mcl/lit/INS-R0010.ps.Z)
+##
+## ), then this is the place to do it.  Of course we honor the choice of
+## upstream here, and build as suggested by upsteam.
+
+# confflags += --disable-helpful-reminder
+
+config: config-stamp
+config-stamp:
+	dh_testdir
+
+#	# Make sure we have fresh config.{sub,guess}, in order to make life
+#	# more easy for porters to new architectures. See
+#	# autotools-dev/README.Debian.gz
+	if [ -r /usr/share/misc/config.sub ] && [ ! -f autofoo/config.sub.backup ]; then \
+		mv -v autofoo/config.sub autofoo/config.sub.backup; \
+		cp -f /usr/share/misc/config.sub autofoo/config.sub; \
+	fi
+
+	if [ -r /usr/share/misc/config.guess ] && [ ! -f autofoo/config.guess.backup ]; then \
+		mv -v autofoo/config.guess autofoo/config.guess.backup; \
+		cp -f /usr/share/misc/config.guess autofoo/config.guess; \
+	fi
+
+	touch $@
+
+config-clean:
+	dh_testdir
+	dh_testroot
+
+	if [ -f autofoo/config.sub.backup ]; then \
+		mv -fv autofoo/config.sub.backup autofoo/config.sub; \
+	fi
+
+	if [ -f autofoo/config.guess.backup ]; then \
+		mv -fv autofoo/config.guess.backup autofoo/config.guess; \
+	fi
+
+	$(RM) config-stamp
+
+
+configure: config configure-stamp
+configure-stamp:
+	dh_testdir
+
+	./configure \
+           $(confflags) \
+           --prefix=/usr \
+           --mandir=\$${prefix}/share/man \
+           --infodir=\$${prefix}/share/info
+
+	touch configure-stamp
+
+build: patch configure build-stamp
+build-stamp: $(QUILT_STAMPFN)
+	dh_testdir
+
+	$(MAKE)
+
+	touch build-stamp
+
+clean: unpatch config-clean
+	dh_testdir
+	dh_testroot
+	$(RM) -f build-stamp configure-stamp
+
+	[ ! -f Makefile ] || $(MAKE) distclean
+
+	dh_clean
+
+install: build
+	dh_testdir
+	dh_testroot
+	dh_clean -k
+	dh_installdirs
+
+	$(MAKE) install DESTDIR=$(CURDIR)/debian/mcl
+#	# install some extra stuff not installed by upstream
+	install -c -m 644 $(CURDIR)/{AUTHORS,README,THANKS} $(CURDIR)/debian/mcl/usr/share/doc/mcl/
+	mkdir $(CURDIR)/debian/mcl/usr/share/doc/mcl/scripts
+	install -c -m 644 $(CURDIR)/scripts/clx* $(CURDIR)/debian/mcl/usr/share/doc/mcl/scripts/
+#	# clean up unneeded docs
+	$(RM) $(CURDIR)/debian/mcl/usr/share/doc/mcl/*txt
+#	# process mcl-doc.install
+	dh_install --sourcedir=debian/mcl
+	dh_installdocs
+#	# clean up files just copied to mcl-doc
+	$(RM) $(CURDIR)/debian/mcl/usr/share/doc/mcl/{AUTHORS,README,THANKS}
+	$(RM) $(CURDIR)/debian/mcl/usr/share/doc/mcl/*{html,ps,minimcl}
+	$(RM) -r $(CURDIR)/debian/mcl/usr/share/doc/mcl/examples
+	$(RM) -r $(CURDIR)/debian/mcl/usr/share/man/man[5,7]
+
+binary-indep: build install
+	dh_installman
+	dh_installchangelogs ChangeLog
+	dh_compress
+	dh_fixperms
+	dh_installdeb
+	dh_shlibdeps
+	dh_gencontrol
+	dh_md5sums
+	dh_builddeb -pmcl-doc
+
+
+binary-arch: build install
+#	no need to call dh_installexamples: upstream takes care of
+#        this in 'make install'
+	dh_installman
+	dh_installchangelogs ChangeLog
+	dh_strip
+	dh_compress
+	dh_fixperms
+	dh_installdeb
+	dh_shlibdeps
+	dh_gencontrol
+	dh_md5sums
+	dh_builddeb -pmcl
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install configure config config-clean


Property changes on: trunk/mcl/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/mcl/trunk/debian/watch
===================================================================
--- trunk/mcl/trunk/debian/watch	                        (rev 0)
+++ trunk/mcl/trunk/debian/watch	2009-11-24 20:14:45 UTC (rev 4401)
@@ -0,0 +1,3 @@
+version=3
+
+http://micans.org/mcl/src/mcl-(..-.*)\.tar\.gz debian uupdate




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