[med-svn] r5861 - in trunk/packages: . R/r-other-mott-happy/trunk/debian boxshade/tags mosaik-aligner mosaik-aligner/trunk mosaik-aligner/trunk/debian mothur mothur/tags probalign probalign/trunk probalign/trunk/debian probalign/trunk/debian/patches probalign/trunk/debian/source
Andreas Tille
tille at alioth.debian.org
Wed Feb 2 16:28:31 UTC 2011
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 <tille at debian.org> 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 <moeller at debian.org> 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 <tille at debian.org> Tue, 25 Jan 2011 08:17:57 +0100
- * New upstream release.
-
- -- Steffen Moeller <moeller at debian.org> 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 <plessy at debian.org> 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 <tille at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>
+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 <tille at debian.org>
+# 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 <tille at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>
+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 <usman at cs.njit.edu>
+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 <tille at debian.org>
+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 <tille at debian.org>
+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 <tille at debian.org>
+# 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
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