[med-svn] r17757 - in trunk/packages: . R/r-cran-batchjobs/tags fsa fsa/trunk fsa/trunk/debian fsa/trunk/debian/source fsa/trunk/debian/upstream king/tags
Andreas Tille
tille at moszumanska.debian.org
Sat Aug 16 21:56:01 UTC 2014
Author: tille
Date: 2014-08-16 21:56:01 +0000 (Sat, 16 Aug 2014)
New Revision: 17757
Added:
trunk/packages/R/r-cran-batchjobs/tags/1.3-2/
trunk/packages/fsa/
trunk/packages/fsa/trunk/
trunk/packages/fsa/trunk/debian/
trunk/packages/fsa/trunk/debian/changelog
trunk/packages/fsa/trunk/debian/compat
trunk/packages/fsa/trunk/debian/control
trunk/packages/fsa/trunk/debian/copyright
trunk/packages/fsa/trunk/debian/createmanpages
trunk/packages/fsa/trunk/debian/rules
trunk/packages/fsa/trunk/debian/source/
trunk/packages/fsa/trunk/debian/source/format
trunk/packages/fsa/trunk/debian/upstream/
trunk/packages/fsa/trunk/debian/upstream/metadata
trunk/packages/fsa/trunk/debian/watch
trunk/packages/king/tags/2.21.120420+dfsg-1/
Log:
fsa is used by t-coffee
Added: trunk/packages/fsa/trunk/debian/changelog
===================================================================
--- trunk/packages/fsa/trunk/debian/changelog (rev 0)
+++ trunk/packages/fsa/trunk/debian/changelog 2014-08-16 21:56:01 UTC (rev 17757)
@@ -0,0 +1,5 @@
+fsa (1.15.9-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org> Sat, 16 Aug 2014 22:03:17 +0200
Added: trunk/packages/fsa/trunk/debian/compat
===================================================================
--- trunk/packages/fsa/trunk/debian/compat (rev 0)
+++ trunk/packages/fsa/trunk/debian/compat 2014-08-16 21:56:01 UTC (rev 17757)
@@ -0,0 +1 @@
+9
Added: trunk/packages/fsa/trunk/debian/control
===================================================================
--- trunk/packages/fsa/trunk/debian/control (rev 0)
+++ trunk/packages/fsa/trunk/debian/control 2014-08-16 21:56:01 UTC (rev 17757)
@@ -0,0 +1,45 @@
+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>
+Build-Depends: debhelper (>= 9),
+ dh-autoreconf
+Standards-Version: 3.9.5
+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
Added: trunk/packages/fsa/trunk/debian/copyright
===================================================================
--- trunk/packages/fsa/trunk/debian/copyright (rev 0)
+++ trunk/packages/fsa/trunk/debian/copyright 2014-08-16 21:56:01 UTC (rev 17757)
@@ -0,0 +1,29 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: fsl
+Source: http://sourceforge.net/projects/fsa/files/
+
+Files: *
+Copyright: © 2010-2014 Ariel Schwartz, Chuong Do, Robert Bradley, Jaeyoung Do, Colin Dewey, Ian Holmes, Lars Barquist
+License: GPL-2+
+
+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.
+
Added: trunk/packages/fsa/trunk/debian/createmanpages
===================================================================
--- trunk/packages/fsa/trunk/debian/createmanpages (rev 0)
+++ trunk/packages/fsa/trunk/debian/createmanpages 2014-08-16 21:56:01 UTC (rev 17757)
@@ -0,0 +1,16 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name='<optional description of the program>' \
+ --version-string="$VERSION" <programname> > $MANDIR/<programname>.1
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
Property changes on: trunk/packages/fsa/trunk/debian/createmanpages
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/fsa/trunk/debian/rules
===================================================================
--- trunk/packages/fsa/trunk/debian/rules (rev 0)
+++ trunk/packages/fsa/trunk/debian/rules 2014-08-16 21:56:01 UTC (rev 17757)
@@ -0,0 +1,27 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+# some helpful variables - uncomment them if needed
+# shamelessly stolen from http://jmtd.net/log/awk/
+#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
+#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}')
+#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
+#GIT_TAG := $(subst ~,_,$(VERSION))
+
+# alternatively to manually set those variables you can
+# include /usr/share/cdbs/1/rules/buildvars.mk
+# and use what is set there. Any hint whether dh might set variables in
+# a similar manner are welcome.
+
+%:
+ dh $@ --with autoreconf
+
+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."
+
+#get-orig-source:
+# . debian/get-orig-source
Property changes on: trunk/packages/fsa/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/fsa/trunk/debian/source/format
===================================================================
--- trunk/packages/fsa/trunk/debian/source/format (rev 0)
+++ trunk/packages/fsa/trunk/debian/source/format 2014-08-16 21:56:01 UTC (rev 17757)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/fsa/trunk/debian/upstream/metadata
===================================================================
--- trunk/packages/fsa/trunk/debian/upstream/metadata (rev 0)
+++ trunk/packages/fsa/trunk/debian/upstream/metadata 2014-08-16 21:56:01 UTC (rev 17757)
@@ -0,0 +1,7 @@
+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
+
Added: trunk/packages/fsa/trunk/debian/watch
===================================================================
--- trunk/packages/fsa/trunk/debian/watch (rev 0)
+++ trunk/packages/fsa/trunk/debian/watch 2014-08-16 21:56:01 UTC (rev 17757)
@@ -0,0 +1,2 @@
+version=3
+http://sf.net/fsa/fsa-(\d[\d\.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
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