Author: tille Date: 2011-02-02 16:28:20 +0000 (Wed, 02 Feb 2011) New Revision: 5861
Added: trunk/packages/boxshade/tags/3.3.1-5/ trunk/packages/mosaik-aligner/ trunk/packages/mosaik-aligner/trunk/ trunk/packages/mosaik-aligner/trunk/debian/ trunk/packages/mosaik-aligner/trunk/debian/changelog trunk/packages/mosaik-aligner/trunk/debian/compat trunk/packages/mosaik-aligner/trunk/debian/control trunk/packages/mosaik-aligner/trunk/debian/install trunk/packages/mosaik-aligner/trunk/debian/rules trunk/packages/mosaik-aligner/trunk/debian/watch trunk/packages/mothur/tags/ trunk/packages/mothur/tags/1.15.0-1/ trunk/packages/probalign/ trunk/packages/probalign/trunk/ trunk/packages/probalign/trunk/debian/ trunk/packages/probalign/trunk/debian/changelog trunk/packages/probalign/trunk/debian/compat trunk/packages/probalign/trunk/debian/control trunk/packages/probalign/trunk/debian/copyright trunk/packages/probalign/trunk/debian/dirs trunk/packages/probalign/trunk/debian/docs trunk/packages/probalign/trunk/debian/install trunk/packages/probalign/trunk/debian/patches/ trunk/packages/probalign/trunk/debian/patches/gcc_fixes.patch trunk/packages/probalign/trunk/debian/patches/series trunk/packages/probalign/trunk/debian/rules trunk/packages/probalign/trunk/debian/source/ trunk/packages/probalign/trunk/debian/source/format trunk/packages/probalign/trunk/debian/watch Modified: trunk/packages/R/r-other-mott-happy/trunk/debian/changelog Log: Added probalign (packaging finished, ITP will be just issued), added mosaik-aligner (packaging needs further work) Modified: trunk/packages/R/r-other-mott-happy/trunk/debian/changelog =================================================================== --- trunk/packages/R/r-other-mott-happy/trunk/debian/changelog 2011-02-02 15:12:33 UTC (rev 5860) +++ trunk/packages/R/r-other-mott-happy/trunk/debian/changelog 2011-02-02 16:28:20 UTC (rev 5861) @@ -1,34 +1,37 @@ r-other-mott-happy (2.3~beta-1) UNRELEASED; urgency=low - * debian/control: - - Added myself to uploaders - - Standards-Version: 3.9.1 (no changes needed) - - debhelper 7 - - Added missing (Build-)Depends: r-cran-mass - * Added watch file + [Steffen Moeller] + * debian/README.Debian + ???????????? please comment here - it seems to contradict what + you said on the mailing list + + [Andreas Tille] + * New upstream beta release * Source Format 3.0 (quilt) -- Andreas Tille <[email protected]> Mon, 24 Jan 2011 14:52:31 +0100 -r-other-mott-happy (2.2.hbrem~beta-2) UNRELEASED; urgency=low +r-other-mott-happy (2.1-5) unstable; urgency=low - * patch to happyplot + [Charles Plessy] + * Documented information in ‘debian/upstream-metadata.yaml’. + * Removed mention of the bibliographic reference in ‘debian/control’. - -- Steffen Moeller <[email protected]> Wed, 28 Apr 2010 18:24:05 +0200 + [Andreas Tille] + * debian/control: + - Build-Depends r-base-dev (>= 2.10), Depends r-core (>= 2.10) and + rebuild on current Squeeze system + Closes: #611008 + - Added myself to uploaders + - Standards-Version: 3.9.1 (no changes needed) + - Fixed name of Debian Med team + - Debhelper 7 + - Replaced (Build-)Depends r-cran-vr by r-cran-mass + - Recommends: r-cran-vr, r-cran-multicore + * Added watch file -r-other-mott-happy (2.2.hbrem~beta-1) UNRELEASED; urgency=low + -- Andreas Tille <[email protected]> Tue, 25 Jan 2011 08:17:57 +0100 - * New upstream release. - - -- Steffen Moeller <[email protected]> Tue, 09 Mar 2010 11:27:05 +0100 - -r-other-mott-happy (2.1-5) UNRELEASED; urgency=low - - * Documented informations in ‘debian/upstream-metadata.yaml’. - * Removed mention of the bibliographic reference in ‘debian/control’. - - -- Charles Plessy <[email protected]> Sun, 03 Jan 2010 23:24:11 +0900 - r-other-mott-happy (2.1-4) unstable; urgency=low * Rebuilt for R 2.10. Added: trunk/packages/mosaik-aligner/trunk/debian/changelog =================================================================== --- trunk/packages/mosaik-aligner/trunk/debian/changelog (rev 0) +++ trunk/packages/mosaik-aligner/trunk/debian/changelog 2011-02-02 16:28:20 UTC (rev 5861) @@ -0,0 +1,5 @@ +mosaik-aligner (1.1.0021-1) unstable; urgency=low + + * Initial release (Closes: #????) + + -- Andreas Tille <[email protected]> Sun, 30 Jan 2011 18:41:07 +0100 Added: trunk/packages/mosaik-aligner/trunk/debian/compat =================================================================== --- trunk/packages/mosaik-aligner/trunk/debian/compat (rev 0) +++ trunk/packages/mosaik-aligner/trunk/debian/compat 2011-02-02 16:28:20 UTC (rev 5861) @@ -0,0 +1 @@ +7 Added: trunk/packages/mosaik-aligner/trunk/debian/control =================================================================== --- trunk/packages/mosaik-aligner/trunk/debian/control (rev 0) +++ trunk/packages/mosaik-aligner/trunk/debian/control 2011-02-02 16:28:20 UTC (rev 5861) @@ -0,0 +1,21 @@ +Source: mosaik-aligner +Section: science +Priority: extra +Maintainer: Debian Med Packaging Team <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Andreas Tille <[email protected]> +Build-Depends: debhelper (>= 7.1), zlib1g-dev, help2man +Standards-Version: 3.9.1 +Homepage: http://code.google.com/p/mosaik-aligner/ +Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mosaik-aligner/trunk +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mosaik-aligner/trunk/?rev=0&sc=0 + +Package: mosaik-aligner +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: reference-guided aligner for next-generation sequencing technologies + MosaikBuild converts various sequence formats into Mosaik’s native read + format. MosaikAligner pairwise aligns each read to a specified series of + reference sequences. MosaikSort resolves paired-end reads and sorts the + alignments by the reference sequence coordinates. Finally, MosaikText + converts alignments to different text-based formats. Added: trunk/packages/mosaik-aligner/trunk/debian/install =================================================================== --- trunk/packages/mosaik-aligner/trunk/debian/install (rev 0) +++ trunk/packages/mosaik-aligner/trunk/debian/install 2011-02-02 16:28:20 UTC (rev 5861) @@ -0,0 +1 @@ +bin/* usr/bin Added: trunk/packages/mosaik-aligner/trunk/debian/rules =================================================================== --- trunk/packages/mosaik-aligner/trunk/debian/rules (rev 0) +++ trunk/packages/mosaik-aligner/trunk/debian/rules 2011-02-02 16:28:20 UTC (rev 5861) @@ -0,0 +1,22 @@ +#!/usr/bin/make -f +# debian/rules for mosaik-aligner +# Andreas Tille <[email protected]> +# GPL + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +pkg=mosaik-aligner + +%: + dh $@ + +override_dh_auto_build: + cd src; $(MAKE) + mkdir -p $(CURDIR)/debian/$(pkg)/usr/share/man/man1/ + for bin in MosaikAligner MosaikMerge MosaikSort ; do \ + help2man $(CURDIR)/bin/$${bin} > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/$${bin}.1 ; \ + done + +override_dh_auto_clean: + cd src; $(MAKE) clean Property changes on: trunk/packages/mosaik-aligner/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/mosaik-aligner/trunk/debian/watch =================================================================== --- trunk/packages/mosaik-aligner/trunk/debian/watch (rev 0) +++ trunk/packages/mosaik-aligner/trunk/debian/watch 2011-02-02 16:28:20 UTC (rev 5861) @@ -0,0 +1,2 @@ +version=3 +http://googlecode.debian.net/p/mosaik-aligner/Mosaik-([\d\.]+)-source\.tar\.bz2 Added: trunk/packages/probalign/trunk/debian/changelog =================================================================== --- trunk/packages/probalign/trunk/debian/changelog (rev 0) +++ trunk/packages/probalign/trunk/debian/changelog 2011-02-02 16:28:20 UTC (rev 5861) @@ -0,0 +1,5 @@ +probalign (1.4-1) unstable; urgency=low + + * Initial release (Closes: ????) + + -- Andreas Tille <[email protected]> Wed, 02 Feb 2011 15:45:54 +0100 Added: trunk/packages/probalign/trunk/debian/compat =================================================================== --- trunk/packages/probalign/trunk/debian/compat (rev 0) +++ trunk/packages/probalign/trunk/debian/compat 2011-02-02 16:28:20 UTC (rev 5861) @@ -0,0 +1 @@ +7 Added: trunk/packages/probalign/trunk/debian/control =================================================================== --- trunk/packages/probalign/trunk/debian/control (rev 0) +++ trunk/packages/probalign/trunk/debian/control 2011-02-02 16:28:20 UTC (rev 5861) @@ -0,0 +1,26 @@ +Source: probalign +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Andreas Tille <[email protected]> +Build-Depends: debhelper (>= 7.1), quilt (>= 0.47), help2man +Standards-Version: 3.9.1 +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/probalign/trunk/?rev=0&sc=0 +Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/probalign/trunk/ +Homepage: http://cs.njit.edu/usman/probalign/ + +Package: probalign +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: multiple sequence alignment using partition function posterior probabilities + Probalign uses partition function posterior probability estimates to + compute maximum expected accuracy multiple sequence alignments. It + performs statistically significantly better than the leading alignment + programs Probcons v1.1, MAFFT v5.851, and MUSCLE v3.6 on BAliBASE 3.0, + HOMSTRAD, and OXBENCH benchmarks. Probalign improvements are largest on + datasets containing N/C terminal extensions and on datasets with long + and heterogeneous length sequences. On heteregeneous length datasets + containing repeats Probalign alignment accuracy is 10% and 15% than the + other three methods when standard deviation of length is at least 300 + and 400. Added: trunk/packages/probalign/trunk/debian/copyright =================================================================== --- trunk/packages/probalign/trunk/debian/copyright (rev 0) +++ trunk/packages/probalign/trunk/debian/copyright 2011-02-02 16:28:20 UTC (rev 5861) @@ -0,0 +1,24 @@ +Format: http://dep.debian.net/deps/dep5/ +Upstream-Name: Probalign +Upstream-Contact: Usman Roshan <[email protected]> +Source: http://cs.njit.edu/usman/probalign/ + +Files: * +Copyright: © 2010 Satish Chikkagoudar and Usman Roshan + © 2005 Chuong Dousing (PROBCONS 1.1) + © 2002 Ulrike Muckstein (probA) + +License: Public Domain + PROBALIGN has been made freely available as PUBLIC DOMAIN + software and hence is not subject to copyright in the United + States. This system and/or any portion of the source code + may be used, modified, or redistributed without restrictions... + PROBALIGN is distributed WITHOUT WARRANTY, express or implied. + The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for + loss due to reliance on the program. + + +Files: debian/* +Copyright: © 2011 Andreas Tille <[email protected]> +License: The Debian packaging is licensed under the same terms + as probalign. Added: trunk/packages/probalign/trunk/debian/dirs =================================================================== --- trunk/packages/probalign/trunk/debian/dirs (rev 0) +++ trunk/packages/probalign/trunk/debian/dirs 2011-02-02 16:28:20 UTC (rev 5861) @@ -0,0 +1 @@ +usr/share/man/man1 Added: trunk/packages/probalign/trunk/debian/docs =================================================================== --- trunk/packages/probalign/trunk/debian/docs (rev 0) +++ trunk/packages/probalign/trunk/debian/docs 2011-02-02 16:28:20 UTC (rev 5861) @@ -0,0 +1 @@ +README Added: trunk/packages/probalign/trunk/debian/install =================================================================== --- trunk/packages/probalign/trunk/debian/install (rev 0) +++ trunk/packages/probalign/trunk/debian/install 2011-02-02 16:28:20 UTC (rev 5861) @@ -0,0 +1 @@ +probalign usr/bin Added: trunk/packages/probalign/trunk/debian/patches/gcc_fixes.patch =================================================================== --- trunk/packages/probalign/trunk/debian/patches/gcc_fixes.patch (rev 0) +++ trunk/packages/probalign/trunk/debian/patches/gcc_fixes.patch 2011-02-02 16:28:20 UTC (rev 5861) @@ -0,0 +1,14 @@ +Author: Andreas Tille <[email protected]> +Date: Wed, 02 Feb 2011 15:45:54 +0100 +Description: Patches to compile with gcc-4.4 +--- probalign1.4.orig/Main.cc ++++ probalign1.4/Main.cc +@@ -15,6 +15,8 @@ + #include <iostream> + #include <cerrno> + #include <time.h> ++#include <climits> ++#include <cstring> + + //struct for column reliability + Added: trunk/packages/probalign/trunk/debian/patches/series =================================================================== --- trunk/packages/probalign/trunk/debian/patches/series (rev 0) +++ trunk/packages/probalign/trunk/debian/patches/series 2011-02-02 16:28:20 UTC (rev 5861) @@ -0,0 +1 @@ +gcc_fixes.patch Added: trunk/packages/probalign/trunk/debian/rules =================================================================== --- trunk/packages/probalign/trunk/debian/rules (rev 0) +++ trunk/packages/probalign/trunk/debian/rules 2011-02-02 16:28:20 UTC (rev 5861) @@ -0,0 +1,21 @@ +#!/usr/bin/make -f +# debian/rules for probalign +# Andreas Tille <[email protected]> +# GPL + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +VERSION := $(shell dpkg-parsechangelog | sed -ne 's/^Version: \(\([0-9]\+\):\)\?\(.*\)-.*/\3/p') +PKG := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p') + +%: + dh $@ --with quilt + +override_dh_auto_install: + help2man --name="Align sequences in MFAFILE(s) and print result to standard output" \ + --no-discard-stderr \ + --version-string=$(VERSION) \ + --help-option=" " \ + --no-info \ + $(CURDIR)/probalign > $(CURDIR)/debian/$(PKG)/usr/share/man/man1/probalign.1 Property changes on: trunk/packages/probalign/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/probalign/trunk/debian/source/format =================================================================== --- trunk/packages/probalign/trunk/debian/source/format (rev 0) +++ trunk/packages/probalign/trunk/debian/source/format 2011-02-02 16:28:20 UTC (rev 5861) @@ -0,0 +1 @@ +3.0 (quilt) Added: trunk/packages/probalign/trunk/debian/watch =================================================================== --- trunk/packages/probalign/trunk/debian/watch (rev 0) +++ trunk/packages/probalign/trunk/debian/watch 2011-02-02 16:28:20 UTC (rev 5861) @@ -0,0 +1,2 @@ +version=3 +http://cs.njit.edu/usman/probalign/probalign([\d\.]+)\.tgz _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
