[med-svn] r865 - trunk/packages/glam2/trunk/debian

[charles-guest at alioth.debian.org]

Author: charles-guest
Date: 2007-11-26 14:00:16 +0000 (Mon, 26 Nov 2007)
New Revision: 865

Added:
   trunk/packages/glam2/trunk/debian/glam2.dirs
   trunk/packages/glam2/trunk/debian/purge-fasta.dirs
   trunk/packages/glam2/trunk/debian/purge-fasta.install
Removed:
   trunk/packages/glam2/trunk/debian/dirs
Modified:
   trunk/packages/glam2/trunk/debian/control
   trunk/packages/glam2/trunk/debian/docs
   trunk/packages/glam2/trunk/debian/glam2.install
   trunk/packages/glam2/trunk/debian/rules
Log:
[svn-inject] Applying Debian modifications to trunk

Modified: trunk/packages/glam2/trunk/debian/control
===================================================================
--- trunk/packages/glam2/trunk/debian/control	2007-11-26 10:58:42 UTC (rev 864)
+++ trunk/packages/glam2/trunk/debian/control	2007-11-26 14:00:16 UTC (rev 865)
@@ -1,14 +1,35 @@
 Source: glam2
 Section: science
 Priority: optional
-Maintainer: Steffen Moeller <moeller at debian.org>
-Build-Depends: debhelper (>= 5)
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Steffen Moeller <moeller at debian.org>, Charles Plessy <charles-debian-nospam at plessy.org>
+Build-Depends: debhelper (>= 5), libfftw3-dev
 Standards-Version: 3.7.2
 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/svn/debian-med/trunk/packages/glam2
 
 Package: glam2
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: purge-fasta
 Description: gapped protein motifs from unaligned sequences
- GLAM2 detects gapped motifs in unaligned sequences of
- protein or DNA.
+ GLAM2 is a software package for finding motifs in sequences, typically
+ amino-acid or nucleotide sequences. A motif is a re-occurring sequence
+ pattern: typical examples are the TATA box and the CAAX prenylation motif. The
+ main innovation of GLAM2 is that it allows insertions and deletions in motifs.
+ .
+ The package includes these programs: glam2 — for discovering motifs shared by
+ a set of sequences; glam2scan — for finding matches, in a sequence database,
+ to a motif discovered by glam2; glam2format — for converting glam2 motifs to
+ standard alignment formats; glam2mask — for masking glam2 motifs out of
+ sequences, so that weaker motifs can be found. The program `purge' is
+ distributed in a separate package, purge-fasta.
+ .
+ In this package, the fast Fourier algorithm (FFT) was enabled in glam2.
+
+Package: purge-fasta
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Provisional description
+ Unsure if purge-fasta deserves its own package

Deleted: trunk/packages/glam2/trunk/debian/dirs
===================================================================
--- trunk/packages/glam2/trunk/debian/dirs	2007-11-26 10:58:42 UTC (rev 864)
+++ trunk/packages/glam2/trunk/debian/dirs	2007-11-26 14:00:16 UTC (rev 865)
@@ -1,2 +0,0 @@
-usr/bin
-usr/sbin

Modified: trunk/packages/glam2/trunk/debian/docs
===================================================================
--- trunk/packages/glam2/trunk/debian/docs	2007-11-26 10:58:42 UTC (rev 864)
+++ trunk/packages/glam2/trunk/debian/docs	2007-11-26 14:00:16 UTC (rev 865)
@@ -1,3 +1,4 @@
 README
 doc/*.html
 doc/*.css
+doc/*.pdf

Added: trunk/packages/glam2/trunk/debian/glam2.dirs
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2.dirs	                        (rev 0)
+++ trunk/packages/glam2/trunk/debian/glam2.dirs	2007-11-26 14:00:16 UTC (rev 865)
@@ -0,0 +1 @@
+usr/bin

Modified: trunk/packages/glam2/trunk/debian/glam2.install
===================================================================
--- trunk/packages/glam2/trunk/debian/glam2.install	2007-11-26 10:58:42 UTC (rev 864)
+++ trunk/packages/glam2/trunk/debian/glam2.install	2007-11-26 14:00:16 UTC (rev 865)
@@ -1,4 +1,4 @@
 src/glam2format /usr/bin/
 src/glam2mask /usr/bin/
 src/glam2scan /usr/bin/
-src/glam2 /usr/bin/
+src/glam2fft /usr/bin/

Added: trunk/packages/glam2/trunk/debian/purge-fasta.dirs
===================================================================
--- trunk/packages/glam2/trunk/debian/purge-fasta.dirs	                        (rev 0)
+++ trunk/packages/glam2/trunk/debian/purge-fasta.dirs	2007-11-26 14:00:16 UTC (rev 865)
@@ -0,0 +1 @@
+usr/bin

Added: trunk/packages/glam2/trunk/debian/purge-fasta.install
===================================================================
--- trunk/packages/glam2/trunk/debian/purge-fasta.install	                        (rev 0)
+++ trunk/packages/glam2/trunk/debian/purge-fasta.install	2007-11-26 14:00:16 UTC (rev 865)
@@ -0,0 +1 @@
+purge/purge /usr/bin

Modified: trunk/packages/glam2/trunk/debian/rules
===================================================================
--- trunk/packages/glam2/trunk/debian/rules	2007-11-26 10:58:42 UTC (rev 864)
+++ trunk/packages/glam2/trunk/debian/rules	2007-11-26 14:00:16 UTC (rev 865)
@@ -15,6 +15,8 @@
 build-stamp: 
 	dh_testdir
 	$(MAKE) -C src
+	$(MAKE) -C src glam2fft
+	$(MAKE) -C purge
 	#(cd debian; for i in  glam2format.1 glam2mask.1 glam2scan.1; do ln -s glam2.1 $$i; done)
 	touch $@
 
@@ -23,9 +25,12 @@
 	dh_testroot
 	rm -f build-stamp configure-stamp
 
-	dh_clean  src/*.o src/{glam2,glam2mask,glam2format,glam2scan}
+	dh_clean  purge/*.o purge/purge src/*.o src/{glam2,glam2mask,glam2format,glam2scan}
 
 install: build
+	dh_install
+	mv $(CURDIR)/debian/glam2/usr/bin/glam2fft $(CURDIR)/debian/glam2/usr/bin/glam2
+	mv $(CURDIR)/debian/purge-fasta/usr/bin/purge $(CURDIR)/debian/purge-fasta/usr/bin/purge-fasta
 
 binary-indep: build install
 
@@ -35,11 +40,10 @@
 	dh_installchangelogs ChangeLog
 	dh_installdocs
 	dh_installexamples examples/*
-	dh_install 
+	dh_installman debian/glam2.1
 	for i in format scan mask; do \
 	  dh_link /usr/share/man/man1/glam2.1.gz /usr/share/man/man1/glam2$$i.1.gz; \
 	done
-	dh_installman debian/glam2.1
 	dh_strip
 	dh_compress
 	dh_fixperms