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 <[email protected]> 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 <[email protected]> +Uploaders: Andreas Tille <[email protected]> +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 <[email protected]> +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))) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
