[med-svn] [fsa] 05/10: COnsidering we want to touch t-coffee again which could profit from fsa we do another try on this
Andreas Tille
tille at debian.org
Mon Dec 21 18:43:32 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository fsa.
commit c69e712186a34121ab609727109a928e94e8dc7e
Author: Andreas Tille <tille at debian.org>
Date: Mon Dec 21 15:52:54 2015 +0000
COnsidering we want to touch t-coffee again which could profit from fsa we do another try on this
---
debian/changelog | 4 ++--
debian/control | 11 +++++++----
debian/copyright | 27 +++++++++++++++++++++------
debian/patches/no-display.patch | 17 +++++++++++++++++
debian/patches/series | 1 +
debian/rules | 5 +++++
debian/upstream/metadata | 17 +++++++++++------
7 files changed, 64 insertions(+), 18 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 9296ec5..6276e6d 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -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 @@ fsa (1.15.9-1) UNRELEASED; urgency=low
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
diff --git a/debian/control b/debian/control
index 110b64e..82a5f64 100644
--- a/debian/control
+++ b/debian/control
@@ -1,19 +1,22 @@
Source: fsa
-Section: science
-Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
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
diff --git a/debian/copyright b/debian/copyright
index 923e792..b3441a5 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -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+
diff --git a/debian/patches/no-display.patch b/debian/patches/no-display.patch
new file mode 100644
index 0000000..7de4a54
--- /dev/null
+++ b/debian/patches/no-display.patch
@@ -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 = $(ALWAYS_BUILT)
+
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..b1c458c
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+no-display.patch
diff --git a/debian/rules b/debian/rules
index c950af8..3fddf01 100755
--- a/debian/rules
+++ b/debian/rules
@@ -13,6 +13,11 @@ HELP2MAN = help2man --no-info --version-string="$(VERSION)"
%:
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."
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
index ab92e46..7b5b080 100644
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -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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