[med-svn] r1308 - in trunk/packages/muscle/trunk/debian: . patches
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Wed Feb 6 11:04:48 UTC 2008
Author: charles-guest
Date: 2008-02-06 11:04:48 +0000 (Wed, 06 Feb 2008)
New Revision: 1308
Added:
trunk/packages/muscle/trunk/debian/muscle.doc-base
trunk/packages/muscle/trunk/debian/muscle.docs
trunk/packages/muscle/trunk/debian/muscle.install
trunk/packages/muscle/trunk/debian/muscle.manpages
Removed:
trunk/packages/muscle/trunk/debian/compat
trunk/packages/muscle/trunk/debian/muscle-doc.dirs
trunk/packages/muscle/trunk/debian/patches/Makefile
trunk/packages/muscle/trunk/debian/patches/series
Modified:
trunk/packages/muscle/trunk/debian/README.Debian
trunk/packages/muscle/trunk/debian/changelog
trunk/packages/muscle/trunk/debian/control
trunk/packages/muscle/trunk/debian/copyright
trunk/packages/muscle/trunk/debian/muscle.1
trunk/packages/muscle/trunk/debian/muscle.1.xml
trunk/packages/muscle/trunk/debian/rules
Log:
New upstream release that builds with GCC 4.3; Switched the source package to CDBS
Modified: trunk/packages/muscle/trunk/debian/README.Debian
===================================================================
--- trunk/packages/muscle/trunk/debian/README.Debian 2008-02-06 11:03:15 UTC (rev 1307)
+++ trunk/packages/muscle/trunk/debian/README.Debian 2008-02-06 11:04:48 UTC (rev 1308)
@@ -1,9 +1,6 @@
muscle for Debian
-----------------
-The license was not found in the source but only on the web site. I will
-contact the author to include this information with the source.
-
Please cite
Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with
@@ -14,3 +11,13 @@
Steffen
-- Steffen Moeller <steffen_moeller at gmx.de>, Sun, 19 Sep 2004 00:51:19 +0200
+
+
+
+There has been two different upstream releases with the same name,
+muscle3.7_src.tar.gz, the second one being corrected for building with GCC 4.3.
+The Debian package 3.70-1 contained the first release (md5sum:
+55c9fe99b9c0bccd41e3ed18f8b9d0d99). The Debian package 3.70+fix1-1 contains the
+corrected release (md5sum: 45930141f334b89d927b3cfee6fc7857).
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Wed, 06 Feb 2008 12:04:31 +0900
Modified: trunk/packages/muscle/trunk/debian/changelog
===================================================================
--- trunk/packages/muscle/trunk/debian/changelog 2008-02-06 11:03:15 UTC (rev 1307)
+++ trunk/packages/muscle/trunk/debian/changelog 2008-02-06 11:04:48 UTC (rev 1308)
@@ -1,12 +1,16 @@
-muscle (3.70-2) UNRELEASED; urgency=low
+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.
[ Nelson A. de Oliveira ]
* Fixed watch file (Closes: #462827)
- -- Nelson A. de Oliveira <naoliv at debian.org> Tue, 29 Jan 2008 12:04:35 -0200
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Wed, 06 Feb 2008 12:04:31 +0900
muscle (3.70-1) unstable; urgency=low
Deleted: trunk/packages/muscle/trunk/debian/compat
===================================================================
--- trunk/packages/muscle/trunk/debian/compat 2008-02-06 11:03:15 UTC (rev 1307)
+++ trunk/packages/muscle/trunk/debian/compat 2008-02-06 11:04:48 UTC (rev 1308)
@@ -1 +0,0 @@
-5
Modified: trunk/packages/muscle/trunk/debian/control
===================================================================
--- trunk/packages/muscle/trunk/debian/control 2008-02-06 11:03:15 UTC (rev 1307)
+++ trunk/packages/muscle/trunk/debian/control 2008-02-06 11:04:48 UTC (rev 1308)
@@ -2,11 +2,11 @@
Section: science
Priority: optional
Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-XS-DM-Upload-Allowed: yes
+DM-Upload-Allowed: yes
Uploaders: Steffen Moeller <moeller at debian.org>,
Charles Plessy <charles-debian-nospam at plessy.org>,
David Paleino <d.paleino at gmail.com>
-Build-Depends: debhelper (>= 5.0.0), quilt
+Build-Depends: debhelper (>= 5.0.0), cdbs
Standards-Version: 3.7.3
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/muscle/trunk/
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/muscle
@@ -15,7 +15,7 @@
Package: muscle
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
-Suggests: muscle-doc
+Provides: muscle-doc
Enhances: seaview
Description: Multiple alignment program of protein sequences
MUSCLE is a multiple alignment program for protein sequences. MUSCLE
@@ -23,10 +23,3 @@
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.
-
-Package: muscle-doc
-Architecture: all
-Section: doc
-Suggests: muscle
-Description: Documentation to sequence alignment program
- The manual to MUSCLE as an HTML file.
Modified: trunk/packages/muscle/trunk/debian/copyright
===================================================================
--- trunk/packages/muscle/trunk/debian/copyright 2008-02-06 11:03:15 UTC (rev 1307)
+++ trunk/packages/muscle/trunk/debian/copyright 2008-02-06 11:04:48 UTC (rev 1308)
@@ -25,7 +25,7 @@
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
Deleted: trunk/packages/muscle/trunk/debian/muscle-doc.dirs
===================================================================
--- trunk/packages/muscle/trunk/debian/muscle-doc.dirs 2008-02-06 11:03:15 UTC (rev 1307)
+++ trunk/packages/muscle/trunk/debian/muscle-doc.dirs 2008-02-06 11:04:48 UTC (rev 1308)
@@ -1,2 +0,0 @@
-/usr/share/doc/muscle
-/usr/share/doc/muscle-doc
Modified: trunk/packages/muscle/trunk/debian/muscle.1
===================================================================
--- trunk/packages/muscle/trunk/debian/muscle.1 2008-02-06 11:03:15 UTC (rev 1307)
+++ trunk/packages/muscle/trunk/debian/muscle.1 2008-02-06 11:04:48 UTC (rev 1308)
@@ -1,11 +1,11 @@
.\" Title: MUSCLE
.\" Author: Robert Elgar
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 11/18/2007
+.\" Date: 02/06/2008
.\" Manual: Muscle Manual
-.\" Source: muscle 3.6
+.\" Source: muscle 3.7
.\"
-.TH "MUSCLE" "1" "11/18/2007" "muscle 3.6" "Muscle Manual"
+.TH "MUSCLE" "1" "02/06/2008" "muscle 3.7" "Muscle Manual"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
@@ -22,7 +22,7 @@
command\.
.PP
\fBmuscle\fR
-aligns protein sequences and is considered superior and faster than clustalw\.
+aligns protein sequences and is considered superior and faster than Clustal\ W\.
.SH "OPTIONS"
.PP
\fB\-in \fR\fB\fIinput file\fR\fR
@@ -32,9 +32,14 @@
.PP
\fB\-out \fR\fB\fIoutput file\fR\fR
.RS 4
-Path to output file, FASTA formatted by default\.
+Path to output file, FASTA formatted by default
.RE
.PP
+\fB\-diags\fR
+.RS 4
+Find diagonals (faster for similar sequences)
+.RE
+.PP
\fB\-maxiters \fR\fB\fIn\fR\fR
.RS 4
Maximum number of iterations (integer, default 16)
@@ -62,7 +67,7 @@
.PP
\fB\-clw\fR
.RS 4
-Write output in CLUSTALW format (default FASTA)
+Write output in Clustal\ W format (default FASTA)
.RE
.PP
\fB\-clwstrict\fR
@@ -98,7 +103,8 @@
.PP
\fBclustalw\fR(1),
-\fBseaview\fR(1)\.
+\fBseaview\fR(1),
+\fBt_coffee\fR(1)\.
.SH "AUTHORS"
.PP
\fBRobert Elgar\fR
@@ -118,7 +124,7 @@
.SH "COPYRIGHT"
Copyright \(co 2003, 2004 Steffen Moeller (manpage)
.br
-Copyright \(co 2007 Charles Plessy (manpage)
+Copyright \(co 2007, 2008 Charles Plessy (manpage)
.br
.PP
Muscle is in the public domain, and therefore not subjected to copyright\.
Modified: trunk/packages/muscle/trunk/debian/muscle.1.xml
===================================================================
--- trunk/packages/muscle/trunk/debian/muscle.1.xml 2008-02-06 11:03:15 UTC (rev 1307)
+++ trunk/packages/muscle/trunk/debian/muscle.1.xml 2008-02-06 11:04:48 UTC (rev 1308)
@@ -38,7 +38,7 @@
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
- <!ENTITY dhrelease "3.6">
+ <!ENTITY dhrelease "3.7">
<!ENTITY dhtitle "Muscle Manual">
]>
@@ -74,6 +74,7 @@
</copyright>
<copyright>
<year>2007</year>
+ <year>2008</year>
<holder>Charles Plessy (manpage)</holder>
</copyright>
<legalnotice>
@@ -82,7 +83,7 @@
</para>
<para>
- This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document as if it were in public domain.
+ This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others). Permission is granted to copy, distribute and/or modify this document as if it were in public domain.
</para>
</legalnotice>
</refentryinfo>
@@ -126,7 +127,7 @@
<command>&dhpackage;</command> command.
</para>
- <para><command>&dhpackage;</command> aligns protein sequences and is considered superior and faster than clustalw.</para>
+ <para><command>&dhpackage;</command> aligns protein sequences and is considered superior and faster than Clustal W.</para>
</refsect1>
<refsect1>
@@ -144,11 +145,19 @@
<term><option>-out <replaceable>output file</replaceable></option>
</term>
<listitem>
- <para>Path to output file, FASTA formatted by default.
+ <para>Path to output file, FASTA formatted by default
</para>
</listitem>
</varlistentry>
<varlistentry>
+ <term><option>-diags</option>
+ </term>
+ <listitem>
+ <para>Find diagonals (faster for similar sequences)
+ </para>
+ </listitem>
+ </varlistentry>
+ <varlistentry>
<term><option>-maxiters <replaceable>n</replaceable></option>
</term>
<listitem>
@@ -191,7 +200,7 @@
<term><option>-clw</option>
</term>
<listitem>
- <para>Write output in CLUSTALW format (default FASTA)</para>
+ <para>Write output in Clustal W format (default FASTA)</para>
</listitem>
</varlistentry>
<varlistentry>
@@ -250,6 +259,11 @@
<citerefentry>
<refentrytitle>seaview</refentrytitle>
<manvolnum>1</manvolnum>
+ </citerefentry>,
+
+ <citerefentry>
+ <refentrytitle>t_coffee</refentrytitle>
+ <manvolnum>1</manvolnum>
</citerefentry>.
</para>
</refsect1>
Added: trunk/packages/muscle/trunk/debian/muscle.doc-base
===================================================================
--- trunk/packages/muscle/trunk/debian/muscle.doc-base (rev 0)
+++ trunk/packages/muscle/trunk/debian/muscle.doc-base 2008-02-06 11:04:48 UTC (rev 1308)
@@ -0,0 +1,15 @@
+Document: muscle-manual
+Title: MUSCLE User Guide 3.5
+Author: Robert C. Edgar
+Abstract: MUSCLE is a program for creating multiple alignments of amino acid or
+ nucleotide sequences. A range of options is provided that give you the choice
+ of optimizing accuracy, speed, or some compromise between the two. Default
+ parameters are those that give the best average accuracy in our tests. Using
+ versions current at the time of writing, my tests show that MUSCLE can achieve
+ both better average accuracy and better speed than Clustal W or T‑Coffee,
+ depending on the chosen options.
+Section: Applications/Science/Biology
+
+Format: HTML
+Index: /usr/share/doc/muscle/muscle.html
+Files: /usr/share/doc/muscle/muscle.html
Added: trunk/packages/muscle/trunk/debian/muscle.docs
===================================================================
--- trunk/packages/muscle/trunk/debian/muscle.docs (rev 0)
+++ trunk/packages/muscle/trunk/debian/muscle.docs 2008-02-06 11:04:48 UTC (rev 1308)
@@ -0,0 +1 @@
+debian/muscle.html
Added: trunk/packages/muscle/trunk/debian/muscle.install
===================================================================
--- trunk/packages/muscle/trunk/debian/muscle.install (rev 0)
+++ trunk/packages/muscle/trunk/debian/muscle.install 2008-02-06 11:04:48 UTC (rev 1308)
@@ -0,0 +1 @@
+muscle /usr/bin
Added: trunk/packages/muscle/trunk/debian/muscle.manpages
===================================================================
--- trunk/packages/muscle/trunk/debian/muscle.manpages (rev 0)
+++ trunk/packages/muscle/trunk/debian/muscle.manpages 2008-02-06 11:04:48 UTC (rev 1308)
@@ -0,0 +1 @@
+debian/muscle.1
Deleted: trunk/packages/muscle/trunk/debian/patches/Makefile
===================================================================
--- trunk/packages/muscle/trunk/debian/patches/Makefile 2008-02-06 11:03:15 UTC (rev 1307)
+++ trunk/packages/muscle/trunk/debian/patches/Makefile 2008-02-06 11:04:48 UTC (rev 1308)
@@ -1,37 +0,0 @@
-Index: muscle3.6_src/Makefile
-===================================================================
---- muscle3.6_src.orig/Makefile
-+++ muscle3.6_src/Makefile
-@@ -9,9 +9,9 @@
- # On OSX, using -static gives the error "ld: can't locate file for: -lcrt0.o",
- # this is fixed by deleting "-static" from the LDLIBS line.
-
--CFLAGS = -O3 -funroll-loops -Winline -DNDEBUG=1
--LDLIBS = -lm -static
--# LDLIBS = -lm
-+CFLAGS = -O2 -funroll-loops -Winline -DNDEBUG=1
-+# LDLIBS = -lm -static
-+LDLIBS = -lm
-
- OBJ = .o
- EXE =
-@@ -34,3 +34,19 @@
- muscle: $(CPPOBJ)
- $(LD) -o muscle $(CPPOBJ) $(LDLIBS)
- strip muscle
-+
-+DESTDIR=""
-+
-+install: muscle
-+ if [ ! -x $(DESTDIR)/usr/bin ]; then mkdir -p $(DESTDIR)/usr/bin; fi
-+ cp muscle $(DESTDIR)/usr/bin/muscle
-+
-+install-doc: debian/muscle.html
-+ if [ ! -x $(DESTDIR)/usr/share/doc/muscle ]; then mkdir -p $(DESTDIR)/usr/share/doc/muscle; fi
-+ if [ ! -x $(DESTDIR)/usr/share/doc/muscle-doc ]; then mkdir -p $(DESTDIR)/usr/share/doc/muscle-doc; fi
-+ cp debian/muscle.html $(DESTDIR)/usr/share/doc/muscle/
-+ (cd $(DESTDIR)/usr/share/doc/muscle-doc/ && ln -s ../muscle/muscle.html* . )
-+
-+clean:
-+ $(RM) *.o make.err make.out
-+ $(RM) muscle
Deleted: trunk/packages/muscle/trunk/debian/patches/series
===================================================================
--- trunk/packages/muscle/trunk/debian/patches/series 2008-02-06 11:03:15 UTC (rev 1307)
+++ trunk/packages/muscle/trunk/debian/patches/series 2008-02-06 11:04:48 UTC (rev 1308)
@@ -1 +0,0 @@
-Makefile
Modified: trunk/packages/muscle/trunk/debian/rules
===================================================================
--- trunk/packages/muscle/trunk/debian/rules 2008-02-06 11:03:15 UTC (rev 1307)
+++ trunk/packages/muscle/trunk/debian/rules 2008-02-06 11:04:48 UTC (rev 1308)
@@ -1,95 +1,12 @@
#!/usr/bin/make -f
-# -*- makefile -*-
-# Sample debian/rules that uses debhelper.
-# GNU copyright 1997 to 1999 by Joey Hess.
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/makefile.mk
-include /usr/share/quilt/quilt.make
+DEB_MAKE_BUILD_TARGET = all
+DEB_MAKE_INVOKE += -e
+DEB_MAKE_ENVVARS = LDLIBS=-lm
-CFLAGS = -Wall -g
-
-ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
- CFLAGS += -O0
-else
- CFLAGS += -O2
-endif
-
-CFLAGS += -funroll-loops
-CFLAGS += -Winline
-CFLAGS += -DNDEBUG=1
-
-DB2MAN=/usr/share/sgml/docbook/stylesheet/xsl/nwalsh/manpages/docbook.xsl
-XP=xsltproc -''-nonet -o debian/
-
-muscle.1: debian/muscle.1.xml
- $(XP) $<
-
-build: patch build-stamp
-build-stamp:
- dh_testdir
-
- $(MAKE) CFLAGS="$(CFLAGS)"
- touch $@
-
-clean: patch clean-patched unpatch
-clean-patched:
- dh_testdir
- dh_testroot
- rm -f build-stamp
-
- [ ! -f Makefile ] || $(MAKE) clean
-
- dh_clean
-
-install: build
- dh_testdir
- dh_testroot
- dh_clean -k
- dh_installdirs -a
-
- $(MAKE) install DESTDIR=$(CURDIR)/debian/muscle
-
-install-indep:
- dh_testdir
- dh_testroot
- dh_installdirs -i
-
- $(MAKE) install-doc DESTDIR=$(CURDIR)/debian/muscle-doc
-
-
-binary-indep: install-indep
- dh_testdir -i
- dh_testroot -i
- dh_installchangelogs -i
- dh_installdocs -i
- dh_link -i
- dh_strip -i
- dh_compress -i
- dh_fixperms -i
- dh_installdeb -i
- dh_shlibdeps -i
- dh_gencontrol -i
- dh_md5sums -i
- dh_builddeb -i
-
-binary-arch: build install
- dh_testdir -a
- dh_testroot -a
- dh_installchangelogs -a
- dh_installdocs -a
- dh_installexamples -a
- dh_installman -a debian/muscle.1
- dh_link -a
- dh_strip -a
- dh_compress -a
- dh_fixperms -a
- dh_installdeb -a
- dh_shlibdeps -a
- dh_gencontrol -a
- dh_md5sums -a
- dh_builddeb -a
-
-binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install configure
+clean::
+ $(RM) *.o make.err make.out
+ $(RM) muscle
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