[med-svn] [fsa] 09/10: Re-add debian dir
Andreas Tille
tille at debian.org
Mon Dec 21 18:43:35 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 43c8b631008ad30b969f71f2b953600b8a8ef32e
Author: Andreas Tille <tille at debian.org>
Date: Mon Dec 21 19:41:37 2015 +0100
Re-add debian dir
---
debian/changelog | 10 ++++++
debian/compat | 1 +
debian/control | 50 ++++++++++++++++++++++++++++
debian/copyright | 53 ++++++++++++++++++++++++++++++
debian/docs | 3 ++
debian/examples | 1 +
debian/patches/no-display.patch | 17 ++++++++++
debian/patches/removed-pdf-only-docs.patch | 22 +++++++++++++
debian/patches/series | 2 ++
debian/rules | 50 ++++++++++++++++++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 12 +++++++
debian/watch | 2 ++
13 files changed, 224 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..6276e6d
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,10 @@
+fsa (1.15.9+dfsg-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+ 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
+
+ -- Andreas Tille <tille at debian.org> Mon, 21 Dec 2015 16:49:55 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..d24d2fe
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,50 @@
+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
+Build-Depends: debhelper (>= 9),
+ dh-autoreconf,
+ mummer,
+ exonerate,
+# htcondor is a bit complex to be configured and thus we delay this one: htcondor,
+ help2man
+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}
+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
+ sequences. Much as distance-based phylogenetic reconstruction methods
+ like Neighbor-Joining build a phylogeny using only pairwise divergence
+ estimates, FSA builds a multiple alignment using only pairwise
+ estimations of homology. This is made possible by the sequence annealing
+ technique for constructing a multiple alignment from pairwise
+ comparisons, developed by Ariel Schwartz.
+ .
+ FSA brings the high accuracies previously available only for
+ small-scale analyses of proteins or RNAs to large-scale problems such as
+ aligning thousands of sequences or megabase-long sequences. FSA
+ introduces several novel methods for constructing better alignments:
+ * FSA uses machine-learning techniques to estimate gap and
+ substitution parameters on the fly for each set of input sequences.
+ This "query-specific learning" alignment method makes FSA very robust:
+ it can produce superior alignments of sets of homologous sequences
+ which are subject to very different evolutionary constraints.
+ * FSA is capable of aligning hundreds or even thousands of sequences
+ using a randomized inference algorithm to reduce the computational
+ cost of multiple alignment. This randomized inference can be over ten
+ times faster than a direct approach with little loss of accuracy.
+ * FSA can quickly align very long sequences using the "anchor
+ annealing" technique for resolving anchors and projecting them with
+ transitive anchoring. It then stitches together the alignment between
+ the anchors using the methods described above.
+ * The included GUI, MAD (Multiple Alignment Display), can display the
+ intermediate alignments produced by FSA, where each character is
+ colored according to the probability that it is correctly aligned
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..ac05452
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,53 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: fsl
+Source: http://sourceforge.net/projects/fsa/files/
+Files-Excluded: */*.jar
+ */*.class
+ display/JMF-2.1.1e
+ display/jai-1_1_3
+ doc
+
+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+
+
+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 3 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, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General General
+ Public License can be found at /usr/share/common-licenses/GPL-2.
+
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..6e7abe4
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,3 @@
+README
+html/*.html
+html/*.css
diff --git a/debian/examples b/debian/examples
new file mode 100644
index 0000000..6947f9d
--- /dev/null
+++ b/debian/examples
@@ -0,0 +1 @@
+examples/[N-Za-z]*
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/removed-pdf-only-docs.patch b/debian/patches/removed-pdf-only-docs.patch
new file mode 100644
index 0000000..975f33d
--- /dev/null
+++ b/debian/patches/removed-pdf-only-docs.patch
@@ -0,0 +1,22 @@
+--- 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 perl examples doc html tests
++ALWAYS_BUILT = src/util src/math src/seq src/manager src/fsa src/annealing src/main perl examples html tests
+ SUBDIRS = $(MAYBE_MW) $(ALWAYS_BUILT)
+ DIST_SUBDIRS = $(ALWAYS_BUILT)
+
+--- a/configure.ac
++++ b/configure.ac
+@@ -273,8 +273,6 @@ AC_CONFIG_FILES([Makefile
+ display/mad/manifest.mf
+ perl/Makefile
+ examples/Makefile
+- doc/Makefile
+- doc/version.tex
+ html/Makefile
+ tests/Makefile])
+
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..7032061
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+no-display.patch
+removed-pdf-only-docs.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..c0f6e8b
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,50 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+VERSION := $(shell dpkg-parsechangelog | grep Version: | cut -f2 -d' ' | cut -f1 -d- )
+DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+
+mandir=$(CURDIR)/debian/$(DEBPKGNAME)/usr/share/man/man1
+bindir=$(CURDIR)/debian/$(DEBPKGNAME)/usr/bin
+
+HELP2MAN = help2man --no-info --version-string="$(VERSION)"
+
+%:
+ dh $@ --with autoreconf
+
+#override_dh_auto_configure:
+# htcondor is a bit complex to be configured and thus we delay this one
+# dh_auto_configure -- --enable-condor-compile
+ # found automatically: --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."
+
+override_dh_installman:
+ # try to create man pages whereever possible
+ mkdir -p $(mandir)
+ $(HELP2MAN) \
+ --name='Distance-based alignment of DNA, RNA and proteins' \
+ $(bindir)/fsa > $(mandir)/fsa.1
+ $(HELP2MAN) \
+ --name='Find the most-parsimonious ordering of indels' \
+ $(bindir)/gapcleaner > $(mandir)/gapcleaner.1
+ $(HELP2MAN) \
+ --name='Calculate the percentage identity of the passed alignment' \
+ $(bindir)/percentid > $(mandir)/percentid.1
+ $(HELP2MAN) \
+ --name='Find the codon alignment corresponding to the given protein alignment' \
+ $(bindir)/prot2codon > $(mandir)/prot2codon.1
+ $(HELP2MAN) \
+ --name='Slice a subsequence from an input FASTA file' \
+ $(bindir)/slice_fasta > $(mandir)/slice_fasta.1
+ $(HELP2MAN) \
+ --name='Slice subsequences from an input FASTA file' \
+ $(bindir)/slice_fasta_gff > $(mandir)/slice_fasta_gff.1
+ $(HELP2MAN) \
+ --name='Translate input nucleotide sequences into protein sequence.' \
+ $(bindir)/translate > $(mandir)/translate.1
+
+
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..7b5b080
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+ 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
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..2b4ced5
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,2 @@
+version=3
+http://sf.net/fsa/fsa-(\d[\d\.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
--
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