[med-svn] r18693 - in trunk/community/edam/test: . test_muscle test_muscle/debian test_muscle/debian/upstream
Steffen Möller
moeller at moszumanska.debian.org
Sat Jan 31 21:25:06 UTC 2015
Author: moeller
Date: 2015-01-31 21:25:05 +0000 (Sat, 31 Jan 2015)
New Revision: 18693
Added:
trunk/community/edam/test/test_muscle/
trunk/community/edam/test/test_muscle/debian/
trunk/community/edam/test/test_muscle/debian/README.source
trunk/community/edam/test/test_muscle/debian/changelog
trunk/community/edam/test/test_muscle/debian/control
trunk/community/edam/test/test_muscle/debian/copyright
trunk/community/edam/test/test_muscle/debian/upstream/
trunk/community/edam/test/test_muscle/debian/upstream/edam
trunk/community/edam/test/test_muscle/debian/upstream/metadata
Modified:
trunk/community/edam/test/test_01.sh
Log:
Adding local instructions for testing
Modified: trunk/community/edam/test/test_01.sh
===================================================================
--- trunk/community/edam/test/test_01.sh 2015-01-31 21:25:01 UTC (rev 18692)
+++ trunk/community/edam/test/test_01.sh 2015-01-31 21:25:05 UTC (rev 18693)
@@ -1 +1,2 @@
-../debian2edam ../../../packages/muscle/trunk/debian/upstream/edam
+#../debian2edam ../../../packages/muscle/trunk/debian/upstream/edam
+../debian2edam ./test_muscle/debian
Added: trunk/community/edam/test/test_muscle/debian/README.source
===================================================================
--- trunk/community/edam/test/test_muscle/debian/README.source (rev 0)
+++ trunk/community/edam/test/test_muscle/debian/README.source 2015-01-31 21:25:05 UTC (rev 18693)
@@ -0,0 +1 @@
+This is not real - testing the EDAM ontology parsing only.
Added: trunk/community/edam/test/test_muscle/debian/changelog
===================================================================
--- trunk/community/edam/test/test_muscle/debian/changelog (rev 0)
+++ trunk/community/edam/test/test_muscle/debian/changelog 2015-01-31 21:25:05 UTC (rev 18693)
@@ -0,0 +1,110 @@
+muscle (1:3.8.31-2) UNRELEASED; urgency=low
+
+ * debian/upstream: Added citations
+ * debian/control:
+ - Fixed Vcs-Svn
+ - Standards-Version: 3.9.3 (no changes needed)
+
+ -- Andreas Tille <tille at debian.org> Sat, 05 May 2012 08:09:12 +0200
+
+muscle (1:3.8.31-1) unstable; urgency=low
+
+ [ Charles Plessy ]
+ * New upstream release (Closes: #643443).
+ * debian/control: Enhances: t-coffee.
+ * Changed the doc-base section according to the new policy.
+ * Updated my email address.
+ * Updated debian/watch to new version scheme and download location.
+ * Repack usptream archive and implemented a get-orig-source target
+ (debian/rules, debian/README.source, debian/copyright).
+ * Use Debhelper 8 (debian/control, debian/compat).
+ * Build directly from debian/rules targets.
+ * Corrected VCS URLs in debian/control.
+ * Conforms to Debian Policy 3.9.2 (debian/control, no changes needed).
+
+ [ David Paleino ]
+ * removed myself from Uploaders (debian/control).
+
+ -- Charles Plessy <plessy at debian.org> Sun, 13 Nov 2011 18:38:06 +0900
+
+muscle (3.70+fix1-2) unstable; urgency=low
+
+ * debian/control Conflicts: and Replaces: muscle-doc (Closes: #465607)
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Thu, 14 Feb 2008 10:44:17 +0900
+
+muscle (3.70+fix1-1) unstable; urgency=low
+
+ [ Charles Plessy ]
+ * New upstream version, buildable with GCC 4.3 (Closes: #462707)
+ The version number was not increased upstream when the sources were
+ changed. We name this new version in Debian "3.70+fix1".
+ * Updated manual page.
+ * Converted the source package to CDBS, dropped Makefile patch.
+ * Fused muscle and muscle-doc.
+
+ [ Nelson A. de Oliveira ]
+ * Fixed watch file (Closes: #462827)
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Wed, 06 Feb 2008 12:04:31 +0900
+
+muscle (3.70-1) unstable; urgency=low
+
+ [ Charles Plessy ]
+ * New upstream release (bugfixes plus undocumented new features).
+ * debian/control:
+ - Add Subversion repository.
+ - Swiched to quilt.
+ - Enhaces: seaview because SeaView can call muscle to re-align sequences.
+ - Moved the Homepage: field out from the package's description.
+ - Using debhelper 5.
+ - Removed [Biology] from package description as there are Debtags now.
+ - Checked that muscle conforms to Policy 3.7.3.
+ - Updated Steffen's email address.
+ * Handling nostrip build option (policy 10.1) (Closes: #437599).
+ * Updated manpage.
+ * debian/copyright made machine-readable.
+
+ [ Nelson A. de Oliveira ]
+ * Added watch file.
+
+ [ David Paleino ]
+ * debian/manpage.xml moved to debian/muscle.1.xml
+ * debian/muscle.1 added - statically built
+ * debian/manpages removed - passing arguments to dh_installman
+ directly
+ * debian/control:
+ - B-D updated (see above)
+ - added myself to Uploaders
+ - moved XS-Vcs-* to Vcs-*
+ * debian/rules:
+ - manpages statically built
+ - minor changes
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 12 Jan 2008 16:55:48 +0900
+
+muscle (3.60-1) unstable; urgency=low
+
+ * New upstram release (Closes: Bug#361742).
+ * New maintainers email addresses.
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 5 Aug 2006 09:57:27 +0900
+
+muscle (3.52-2) unstable; urgency=low
+
+ * Added missing build dependencies (Closes: Bug#287684).
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Wed, 29 Dec 2004 21:50:47 +0200
+
+muscle (3.52-1) unstable; urgency=low
+
+ * New upstream version.
+ * Fix build on arch other than Pentium (Closes: Bug#285000).
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Sun, 18 Dec 2004 00:06:00 +0200
+
+muscle (3.51-1) unstable; urgency=low
+
+ * Initial Release (Closes: Bug#280411).
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Sun, 19 Sep 2004 00:51:19 +0200
Added: trunk/community/edam/test/test_muscle/debian/control
===================================================================
--- trunk/community/edam/test/test_muscle/debian/control (rev 0)
+++ trunk/community/edam/test/test_muscle/debian/control 2015-01-31 21:25:05 UTC (rev 18693)
@@ -0,0 +1,26 @@
+Source: muscle
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Steffen Moeller <moeller at debian.org>,
+ Charles Plessy <plessy at debian.org>
+Build-Depends: debhelper (>= 8), cdbs
+Standards-Version: 3.9.3
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/muscle
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/muscle/trunk/
+Homepage: http://www.drive5.com/muscle/
+
+Package: muscle
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Conflicts: muscle-doc
+Replaces: muscle-doc
+Provides: muscle-doc
+Enhances: seaview, t-coffee
+Description: Multiple alignment program of protein sequences
+ MUSCLE is a multiple alignment program for protein sequences. MUSCLE
+ stands for multiple sequence comparison by log-expectation. In the
+ authors tests, MUSCLE achieved the highest scores of all tested
+ programs on several alignment accuracy benchmarks, and is also one of
+ the fastest programs out there.
Added: trunk/community/edam/test/test_muscle/debian/copyright
===================================================================
--- trunk/community/edam/test/test_muscle/debian/copyright (rev 0)
+++ trunk/community/edam/test/test_muscle/debian/copyright 2015-01-31 21:25:05 UTC (rev 18693)
@@ -0,0 +1,24 @@
+Format: http://dep.debian.net/deps/dep5/
+Source: http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_src.tar.gz
+Comment: This release contains a potentially sourceless binary file, muscle21, that was removed.
+
+Files: *
+Copyright: © Robert C. Edgar "Bob" <muscle at drive5.com>
+License: PD-dedication
+ MUSCLE is public domain software
+ The MUSCLE software, including object and source code, is hereby donated
+ to the public domain.
+ .
+ Disclaimer of warranty
+ THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER
+ EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION IMPLIED WARRANTIES OF
+ MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+
+Files: debian/*
+Copyright: © 2004 Steffen Moeller <steffen_moeller at gmx.de>
+ © 2007 Nelson A. de Oliveira <naoliv at debian.org>
+ © 2007 David Paleino <d.paleino at gmail.com>
+ © 2006-2008 Charles Plessy <charles-debian-nospam at plessy.org>
+License: PD-dedication
+ Please treat this work as if it were in public domain.
+
Added: trunk/community/edam/test/test_muscle/debian/upstream/edam
===================================================================
--- trunk/community/edam/test/test_muscle/debian/upstream/edam (rev 0)
+++ trunk/community/edam/test/test_muscle/debian/upstream/edam 2015-01-31 21:25:05 UTC (rev 18693)
@@ -0,0 +1,9 @@
+topic: topic_0182 Sequence alignment
+scope: summary
+ function: operation_0492 Multiple Sequence Alignment
+ input: data_2044 Sequence
+ input: format_1929 FASTA
+ output: data_1916 Alignment
+ output: format_1984 FASTA-aln
+ output: format_1982 Clustalw format
+ output: format_1997 Phylip format
Added: trunk/community/edam/test/test_muscle/debian/upstream/metadata
===================================================================
--- trunk/community/edam/test/test_muscle/debian/upstream/metadata (rev 0)
+++ trunk/community/edam/test/test_muscle/debian/upstream/metadata 2015-01-31 21:25:05 UTC (rev 18693)
@@ -0,0 +1,23 @@
+Reference:
+ - Author: Robert C. Edgar
+ Title: "MUSCLE: multiple sequence alignment with high accuracy and high throughput"
+ Journal: Nucleic Acids Research
+ Year: 2004
+ Volume: 32
+ Number: 5
+ Pages: 1792-1797
+ DOI: 10.1093/nar/gkh340
+ PMID: 15034147
+ URL: http://nar.oxfordjournals.org/content/32/5/1792
+ eprint: http://nar.oxfordjournals.org/content/32/5/1792.full.pdf+html
+ - Author: Robert C. Edgar
+ Title: "MUSCLE: a multiple sequence alignment method with reduced time and space complexity"
+ Journal: BMC Bioinformatics
+ Year: 2004
+ Volume: 19
+ Number: 5
+ Pages: 113
+ DOI: 10.1186/1471-2105-5-113
+ PMID: 15318951
+ URL: http://www.biomedcentral.com/1471-2105/5/113
+ eprint: http://www.biomedcentral.com/content/pdf/1471-2105-5-113.pdf
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