[med-svn] r20851 - in trunk/packages/fsa/trunk/debian: . patches upstream
Andreas Tille
tille at moszumanska.debian.org
Mon Dec 21 15:52:55 UTC 2015
Author: tille
Date: 2015-12-21 15:52:54 +0000 (Mon, 21 Dec 2015)
New Revision: 20851
Added:
trunk/packages/fsa/trunk/debian/patches/
trunk/packages/fsa/trunk/debian/patches/no-display.patch
trunk/packages/fsa/trunk/debian/patches/series
Modified:
trunk/packages/fsa/trunk/debian/changelog
trunk/packages/fsa/trunk/debian/control
trunk/packages/fsa/trunk/debian/copyright
trunk/packages/fsa/trunk/debian/rules
trunk/packages/fsa/trunk/debian/upstream/metadata
Log:
COnsidering we want to touch t-coffee again which could profit from fsa we do another try on this
Modified: trunk/packages/fsa/trunk/debian/changelog
===================================================================
--- trunk/packages/fsa/trunk/debian/changelog 2015-12-21 14:10:22 UTC (rev 20850)
+++ trunk/packages/fsa/trunk/debian/changelog 2015-12-21 15:52:54 UTC (rev 20851)
@@ -1,4 +1,4 @@
-fsa (1.15.9-1) UNRELEASED; urgency=low
+fsa (1.15.9+dfsg-1) UNRELEASED; urgency=low
* Initial release (Closes: #<bug>)
Question to upstream was repeated here
@@ -7,4 +7,4 @@
Final-Recipient: rfc822; rbradley at mit.edu
Diagnostic-Code: smtp; 550 5.1.1 <rbradley at mit.edu>... User unknown
- -- Andreas Tille <tille at debian.org> Sat, 16 Aug 2014 22:03:17 +0200
+ -- Andreas Tille <tille at debian.org> Mon, 21 Dec 2015 16:49:55 +0100
Modified: trunk/packages/fsa/trunk/debian/control
===================================================================
--- trunk/packages/fsa/trunk/debian/control 2015-12-21 14:10:22 UTC (rev 20850)
+++ trunk/packages/fsa/trunk/debian/control 2015-12-21 15:52:54 UTC (rev 20851)
@@ -1,19 +1,22 @@
Source: fsa
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
Build-Depends: debhelper (>= 9),
dh-autoreconf,
+ mummer,
+ exonerate,
help2man
-Standards-Version: 3.9.5
+Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/fsa/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/fsa/trunk/
Homepage: http://fsa.sourceforge.net/
Package: fsa
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
Description: Fast Statistical Alignment of protein, RNA or DNA sequences
FSA is a probabilistic multiple sequence alignment algorithm which uses
a "distance-based" approach to aligning homologous protein, RNA or DNA
Modified: trunk/packages/fsa/trunk/debian/copyright
===================================================================
--- trunk/packages/fsa/trunk/debian/copyright 2015-12-21 14:10:22 UTC (rev 20850)
+++ trunk/packages/fsa/trunk/debian/copyright 2015-12-21 15:52:54 UTC (rev 20851)
@@ -1,17 +1,32 @@
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: fsl
-Upstream-Contact: fsa at math.berkeley.edu
- Question to upstream was repeated here
- https://lists.debian.org/debian-med/2015/10/msg00068.html
- but the mail bounced with
- Final-Recipient: rfc822; rbradley at mit.edu
- Diagnostic-Code: smtp; 550 5.1.1 <rbradley at mit.edu>... User unknown
Source: http://sourceforge.net/projects/fsa/files/
+Files-Excluded: */*.jar
+ */*.class
Files: *
Copyright: © 2010-2014 Ariel Schwartz, Chuong Do, Robert Bradley, Jaeyoung Do, Colin Dewey, Ian Holmes, Lars Barquist
License: GPL-2+
+Files: MW/*
+Copyright: 1990-2004, Condor Team, Computer Sciences Department,
+ University of Wisconsin-Madison, WI.
+License: Condor-1.1
+ This source code is covered by the Condor Public License, which can
+ be found in the accompanying LICENSE.TXT file, or online at
+ www.condorproject.org.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ AND THE UNIVERSITY OF WISCONSIN-MADISON "AS IS" AND ANY EXPRESS OR
+ IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY, OF SATISFACTORY QUALITY, AND FITNESS
+ FOR A PARTICULAR PURPOSE OR USE ARE DISCLAIMED. THE COPYRIGHT
+ HOLDERS AND CONTRIBUTORS AND THE UNIVERSITY OF WISCONSIN-MADISON
+ MAKE NO MAKE NO REPRESENTATION THAT THE SOFTWARE, MODIFICATIONS,
+ ENHANCEMENTS OR DERIVATIVE WORKS THEREOF, WILL NOT INFRINGE ANY
+ PATENT, COPYRIGHT, TRADEMARK, TRADE SECRET OR OTHER PROPRIETARY
+ RIGHT.
+
Files: debian/*
Copyright: 2014 Andreas Tille <tille at debian.org>
License: GPL-2+
Added: trunk/packages/fsa/trunk/debian/patches/no-display.patch
===================================================================
--- trunk/packages/fsa/trunk/debian/patches/no-display.patch (rev 0)
+++ trunk/packages/fsa/trunk/debian/patches/no-display.patch 2015-12-21 15:52:54 UTC (rev 20851)
@@ -0,0 +1,17 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 21 Dec 2015 16:49:55 +0100
+Description: The GUI comes with several JARs without source including
+ JAI which makes it definitely non-free - so simply do not build the GUI
+ and go with the command line only
+
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -2,7 +2,7 @@ if HAVE_CONDOR
+ MAYBE_MW = MW
+ endif
+
+-ALWAYS_BUILT = src/util src/math src/seq src/manager src/fsa src/annealing src/main display perl examples doc html tests
++ALWAYS_BUILT = src/util src/math src/seq src/manager src/fsa src/annealing src/main perl examples doc html tests
+ SUBDIRS = $(MAYBE_MW) $(ALWAYS_BUILT)
+ DIST_SUBDIRS = $(ALWAYS_BUILT)
+
Added: trunk/packages/fsa/trunk/debian/patches/series
===================================================================
--- trunk/packages/fsa/trunk/debian/patches/series (rev 0)
+++ trunk/packages/fsa/trunk/debian/patches/series 2015-12-21 15:52:54 UTC (rev 20851)
@@ -0,0 +1 @@
+no-display.patch
Modified: trunk/packages/fsa/trunk/debian/rules
===================================================================
--- trunk/packages/fsa/trunk/debian/rules 2015-12-21 14:10:22 UTC (rev 20850)
+++ trunk/packages/fsa/trunk/debian/rules 2015-12-21 15:52:54 UTC (rev 20851)
@@ -13,6 +13,11 @@
%:
dh $@ --with autoreconf
+## should be found due to Build-Depends
+override_dh_auto_configure:
+ dh_auto_configure -- --enable-condor-compile
+ # --with-mummer=/usr/bin/mummer --with-exonerate=/usr/bin/exonerate
+
override_dh_auto_test:
echo "Tests seem to miss some files:"
echo "make[4]: *** No rule to make target 'apps/isect_d.unmappable.bash', needed by 'apps/isect_d.unmappable.bash.log'. Stop."
Modified: trunk/packages/fsa/trunk/debian/upstream/metadata
===================================================================
--- trunk/packages/fsa/trunk/debian/upstream/metadata 2015-12-21 14:10:22 UTC (rev 20850)
+++ trunk/packages/fsa/trunk/debian/upstream/metadata 2015-12-21 15:52:54 UTC (rev 20851)
@@ -1,7 +1,12 @@
Reference:
- Author: Ariel Shaul Schwartz
- Title: Posterior Decoding Methods for Optimization and Accuracy Control of Multiple Alignments
- Year: 2007
- URL: http://www.eecs.berkeley.edu/Pubs/TechRpts/2007/EECS-2007-39.html
- eprint: http://www.eecs.berkeley.edu/Pubs/TechRpts/2007/EECS-2007-39.pdf
-
+ Author: Robert K. Bradley and Adam Roberts and Michael Smoot and Sudeep Juvekar and Jaeyoung Do and Colin Dewey and Ian Holmes and Lior Pachter
+ Title: Fast Statistical Alignment
+ Journal: PLoS Comput Biol.
+ Year: 2009
+ Volume: 5
+ Number: 5
+ Pages: e1000392
+ DOI: 10.1371/journal.pcbi.1000392
+ PMID: 19478997
+ URL: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000392
+ eprint: http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1000392.PDF
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