[med-svn] r15191 - in trunk/packages/glam2/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Wed Nov 20 21:52:14 UTC 2013
Author: tille
Date: 2013-11-20 21:52:14 +0000 (Wed, 20 Nov 2013)
New Revision: 15191
Added:
trunk/packages/glam2/trunk/debian/NEWS.Debian
trunk/packages/glam2/trunk/debian/patches/
trunk/packages/glam2/trunk/debian/patches/hardening.patch
trunk/packages/glam2/trunk/debian/patches/series
Removed:
trunk/packages/glam2/trunk/debian/patches/
trunk/packages/glam2/trunk/debian/reference
Modified:
trunk/packages/glam2/trunk/debian/changelog
trunk/packages/glam2/trunk/debian/compat
trunk/packages/glam2/trunk/debian/control
trunk/packages/glam2/trunk/debian/copyright
trunk/packages/glam2/trunk/debian/rules
Log:
Mass commit changes for 1064-3
Added: trunk/packages/glam2/trunk/debian/NEWS.Debian
===================================================================
--- trunk/packages/glam2/trunk/debian/NEWS.Debian (rev 0)
+++ trunk/packages/glam2/trunk/debian/NEWS.Debian 2013-11-20 21:52:14 UTC (rev 15191)
@@ -0,0 +1,28 @@
+glam2 (1064-3) unstable; urgency=low
+
+ The source of glam2 is now maintained in the MEME software suite at
+
+ http://meme.nbcr.net/meme/
+
+ Since MEME is non-free we are keeping this old source here and once
+ the packaging of MEME is finished (packaging started at
+
+ svn://anonscm.debian.org/debian-med/trunk/packages/meme/trunk/
+
+ by Debian Med team) an alternative might be provided.
+
+ There is an alternative branch
+
+ svn://anonscm.debian.org/debian-med/trunk/packages/glam2/branch/meme
+
+ in SVN which strips the glam2 source from MEME which might or might
+ not be considered free. At least MEME authors agreed on the idea that
+ glam2 license should be valid also at the new place on the Debian Med
+ packaging mailing list in February 2013. However, it has turned out
+ that some additional tools of the MEME suite are needed to successfully
+ build glam2 and this was not yet discussed. If you are interested feel
+ free to test the glam2 packaging in branch/meme and in case the test
+ turns out to be successful please ask the authors for permission for
+ relicensing.
+
+ -- Andreas Tille <tille at debian.org> Fri, 15 Nov 2013 15:07:59 +0100
Modified: trunk/packages/glam2/trunk/debian/changelog
===================================================================
--- trunk/packages/glam2/trunk/debian/changelog 2013-11-20 21:51:23 UTC (rev 15190)
+++ trunk/packages/glam2/trunk/debian/changelog 2013-11-20 21:52:14 UTC (rev 15191)
@@ -1,10 +1,5 @@
-glam2 (1064-3) UNRELEASED; urgency=low
+glam2 (1064-3) unstable; urgency=low
- NOTE: The homepage says:
- GLAM2 is now available as part of the MEME Suite of motif-based
- sequence analysis tools. Currently there is an effort to package
- meme (see SVN)
-
[ Charles Plessy ]
* Documented information in ‘debian/upstream’.
@@ -12,12 +7,15 @@
* debian/upstream: Took over some bit sof information from tasks
file and move DOI+PMID to references
* debian/control:
- - Fixed Vcs fields
- - Standards-Version: 3.9.3 (no changes needed)
+ - canonical Vcs fields
+ - cme fix dpkg-control
* debian/source/format: 3.0 (quilt)
- * debhelper 8 (control+compat)
+ * debhelper 9 (control+compat)
+ * debian/copyright: DEP5
+ * debian/NEWS.Debian: Explain maintenance in MEME
+ * debian/patches/hardening: propagate hardening options
- -- Charles Plessy <plessy at debian.org> Sun, 03 Jan 2010 22:06:20 +0900
+ -- Andreas Tille <tille at debian.org> Fri, 15 Nov 2013 15:07:59 +0100
glam2 (1064-2) unstable; urgency=low
Modified: trunk/packages/glam2/trunk/debian/compat
===================================================================
--- trunk/packages/glam2/trunk/debian/compat 2013-11-20 21:51:23 UTC (rev 15190)
+++ trunk/packages/glam2/trunk/debian/compat 2013-11-20 21:52:14 UTC (rev 15191)
@@ -1 +1 @@
-8
+9
Modified: trunk/packages/glam2/trunk/debian/control
===================================================================
--- trunk/packages/glam2/trunk/debian/control 2013-11-20 21:51:23 UTC (rev 15190)
+++ trunk/packages/glam2/trunk/debian/control 2013-11-20 21:52:14 UTC (rev 15191)
@@ -1,18 +1,21 @@
Source: glam2
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Steffen Moeller <moeller at debian.org>,
+ Charles Plessy <plessy at debian.org>,
+ Andreas Tille <tille at debian.org>
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, quilt, libfftw3-dev
-Standards-Version: 3.9.3
+Build-Depends: debhelper (>= 9),
+ libfftw3-dev
+Standards-Version: 3.9.4
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/glam2/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/glam2/trunk/
Homepage: http://bioinformatics.org.au/glam2/
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/glam2/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/glam2/trunk/
Package: glam2
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
Description: gapped protein motifs from unaligned sequences
GLAM2 is a software package for finding motifs in sequences, typically
amino-acid or nucleotide sequences. A motif is a re-occurring sequence
@@ -25,5 +28,14 @@
masking glam2 motifs out of sequences so that weaker motifs can be found, and
removing highly similar members of a set of sequences.
.
+ The package includes these programs:
+ glam2: discovering motifs shared by a set of sequences;
+ glam2scan: finding matches, in a sequence database, to a motif discovered
+ by glam2;
+ glam2format: converting glam2 motifs to standard alignment formats;
+ glam2mask: masking glam2 motifs out of sequences, so that weaker motifs
+ can be found;
+ glam2-purge: removing highly similar members of a set of sequences.
+ .
In this binary package, the fast Fourier algorithm (FFT) was enabled for the
glam2 program.
Modified: trunk/packages/glam2/trunk/debian/copyright
===================================================================
--- trunk/packages/glam2/trunk/debian/copyright 2013-11-20 21:51:23 UTC (rev 15190)
+++ trunk/packages/glam2/trunk/debian/copyright 2013-11-20 21:52:14 UTC (rev 15191)
@@ -1,16 +1,16 @@
-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=103
-Debianized-By: Steffen Moeller <moeller at debian.org>
-Debianized-Date: Tue, 13 Nov 2007 00:35:50 +0100
-Original-Source-Location: http://bioinformatics.org.au/glam2/archive/glam2-1062.zip
-Original-Source-Depends: unzip
-Original-Source-Command: ./debian/rules get-orig-source
-Upstream-Author: Martin C Frith <martin at cbrc.jp>
- Timothy L Bailey <t.bailey at imb.uq.edu.au>
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Contact: Martin C Frith <martin at cbrc.jp>
+ Timothy L Bailey <t.bailey at imb.uq.edu.au>
+Source: http://bioinformatics.org.au/glam2/archive/glam2-1064.zip
+ Glam2 is now included into the MEME software suite and not
+ maintained separately at this place any more. Since MEME is non-free
+ we are keeping this old version of glam2 in Debian. Se also
+ https://lists.debian.org/debian-med/2013/11/msg00034.html
Files: *
-X-Upstream-Author: 2007 Martin C Frith <martin at cbrc.jp>
- 2007 Timothy L Bailey <t.bailey at imb.uq.edu.au>
-License: PD
+Copyright: 2007 Martin C Frith <martin at cbrc.jp>
+ 2007 Timothy L Bailey <t.bailey at imb.uq.edu.au>
+License: PD_glam
GLAM2 was developed by Martin C Frith, working at the Computational Biology
Research Center in Tokyo, and Timothy L Bailey, working at the Institute for
Molecular Bioscience in Brisbane. The source code and documentation are hereby
@@ -20,8 +20,8 @@
Apr 25;4(4):e1000071.).
Files: purge/*
-X-Upstream-Author: Andrew Neuwald
-License: PD
+Copyright: Andrew Neuwald
+License: PD_ncbi
PUBLIC DOMAIN NOTICE
National Center for Biotechnology Information
.
@@ -61,8 +61,9 @@
by A. F. Neuwald.
Files: debian/*
-Upstream-Author: 2007 Steffen Moeller <moeller at debian.org>
- 2007-2008 Charles Plessy <plessy at debian.org>
+Copyright: 2007 Steffen Moeller <moeller at debian.org>
+ 2007-2008 Charles Plessy <plessy at debian.org>
+ 2011-2013 Andreas Tille <tille at debian.org>
License: PD
The package is in the public domain and so shall then be
the packaging for Debian of Steffen Moeller <moeller at debian.org>
Added: trunk/packages/glam2/trunk/debian/patches/hardening.patch
===================================================================
--- trunk/packages/glam2/trunk/debian/patches/hardening.patch (rev 0)
+++ trunk/packages/glam2/trunk/debian/patches/hardening.patch 2013-11-20 21:52:14 UTC (rev 15191)
@@ -0,0 +1,56 @@
+Author: Andreas Tille <tille at debian.org>
+LastChanged: Fri, 15 Nov 2013 15:07:59 +0100
+Description: propagate hardening options
+
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -24,32 +24,32 @@ FSRC = glam2format.c alignment.c fasta.c
+ MSRC = glam2mask.c alignment.c fasta.c util.c
+
+ # Compiler options:
+-CFLAGS = -Wall -O3
++CFLAGS += -Wall -O3
+
+ # Default action: compile glam2, glam2scan, glam2format, and glam2mask
+ all: glam2 glam2scan glam2format glam2mask
+
+ # Command for compiling glam2:
+ glam2: $(GSRC) *.h Makefile
+- cc $(CFLAGS) -o glam2 $(GSRC) -lm
++ cc $(CFLAGS) -o glam2 $(GSRC) -lm $(LDFLAGS)
+
+ # Command for compiling glam2scan:
+ glam2scan: $(SSRC) *.h Makefile
+- cc $(CFLAGS) -o glam2scan $(SSRC) -lm
++ cc $(CFLAGS) -o glam2scan $(SSRC) -lm $(LDFLAGS)
+
+ # Command for compiling glam2format:
+ glam2format: $(FSRC) *.h Makefile
+- cc $(CFLAGS) -o glam2format $(FSRC) -lm
++ cc $(CFLAGS) -o glam2format $(FSRC) -lm $(LDFLAGS)
+
+ # Command for compiling glam2mask:
+ glam2mask: $(MSRC) *.h Makefile
+- cc $(CFLAGS) -o glam2mask $(MSRC) -lm
++ cc $(CFLAGS) -o glam2mask $(MSRC) -lm $(LDFLAGS)
+
+ # Here follow commands for compiling special versions of the programs
+
+ # Compile glam2 including FFT algorithm (requires FFTW to be installed):
+ glam2fft: $(GSRC) convolve.c *.h Makefile
+- cc $(CFLAGS) -DFFT -o glam2fft $(GSRC) convolve.c -lm -lfftw3
++ cc $(CFLAGS) -DFFT -o glam2fft $(GSRC) convolve.c -lm -lfftw3 $(LDFLAGS)
+
+ # Compile for debugging with gdb or valgrind, with extra compiler warnings:
+ glam2_d: $(GSRC) *.h Makefile
+--- a/purge/Makefile
++++ b/purge/Makefile
+@@ -1,6 +1,6 @@
+ # Compiler options:
+-CFLAGS = -Wall -O3
++CFLAGS += -Wall -O3
+
+ # Command for compiling purge:
+ purge: *.c *.h Makefile
+- cc $(CFLAGS) -o purge *.c -lm
++ cc $(CFLAGS) -o purge *.c -lm $(LDFLAGS)
Added: trunk/packages/glam2/trunk/debian/patches/series
===================================================================
--- trunk/packages/glam2/trunk/debian/patches/series (rev 0)
+++ trunk/packages/glam2/trunk/debian/patches/series 2013-11-20 21:52:14 UTC (rev 15191)
@@ -0,0 +1 @@
+hardening.patch
Deleted: trunk/packages/glam2/trunk/debian/reference
===================================================================
--- trunk/packages/glam2/trunk/debian/reference 2013-11-20 21:51:23 UTC (rev 15190)
+++ trunk/packages/glam2/trunk/debian/reference 2013-11-20 21:52:14 UTC (rev 15191)
@@ -1,13 +0,0 @@
- at article{10.1371/journal.pcbi.1000071,
- author = {Frith, Martin C. AND Saunders, Neil F. W. AND Kobe, Bostjan AND Bailey, Timothy L.},
- journal = {PLoS Comput Biol},
- publisher = {Public Library of Science},
- title = {Discovering Sequence Motifs with Arbitrary Insertions and Deletions},
- year = {2008},
- month = {05},
- volume = {4},
- url = {http://dx.plos.org/10.1371%2Fjournal.pcbi.1000071},
- pages = {e1000071},
- number = {5},
- doi = {10.1371/journal.pcbi.1000071}
-}
Modified: trunk/packages/glam2/trunk/debian/rules
===================================================================
--- trunk/packages/glam2/trunk/debian/rules 2013-11-20 21:51:23 UTC (rev 15190)
+++ trunk/packages/glam2/trunk/debian/rules 2013-11-20 21:52:14 UTC (rev 15191)
@@ -1,28 +1,31 @@
#!/usr/bin/make -f
-DEB_COMPRESS_EXCLUDE := .pdf # The PDF doc will not be compressed
+DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+BINDIR = $(CURDIR)/debian/$(DEBPKGNAME)/usr/bin
+SRCDIR=src
-include /usr/share/cdbs/1/rules/patchsys-quilt.mk
-include /usr/share/cdbs/1/rules/debhelper.mk
-include /usr/share/cdbs/1/class/makefile.mk
+%:
+ dh $@ --sourcedirectory=$(SRCDIR) --parallel
-DEB_MAKE_BUILD_TARGET = --directory src all glam2fft
-build/glam2::
- $(DEB_MAKE_INVOKE) --directory purge
+override_dh_auto_build:
+ dh_auto_build
+ make --directory=$(SRCDIR) glam2fft
+ make --directory=purge
-BINDIR = $(CURDIR)/debian/glam2/usr/bin
-binary-fixup/glam2::
+override_dh_compress:
+ dh_compress --exclude=.pdf
+
+override_dh_install:
+ dh_install
# purge is renamed glam2-purge to avoid namespace problems.
mv $(BINDIR)/purge $(BINDIR)/glam2-purge
# FFT is enabled by default in Debian.
mv $(BINDIR)/glam2fft $(BINDIR)/glam2
-clean::
- rm -f purge/*.o purge/purge src/*.o src/glam2, src/glam2mask, scr/glam2format src/glam2scan src/glam2fft
+override_dh_clean:
+ dh_clean
+ rm -f purge/*.o purge/purge src/*.o src/glam2 src/glam2mask scr/glam2format src/glam2scan src/glam2fft src/glam2format
get-orig-source:
- # The unzip command from the unzip package is needed for this one.
- # Please update debian/changelog before calling this target.
- [ -f ../glam2-$(DEB_UPSTREAM_VERSION).zip ] || uscan --force-download
- unzip ../glam2-$(DEB_UPSTREAM_VERSION).zip -d..
- tar --create --gzip --file ../glam2_$(DEB_UPSTREAM_VERSION).orig.tar.gz ../glam2-$(DEB_UPSTREAM_VERSION)
+ mkdir -p ../tarballs
+ uscan --verbose --force-download --repack --destdir=../tarballs
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