[med-svn] r12100 - in trunk/packages/t-coffee/trunk/debian: . patches

Wed Aug 22 16:45:24 UTC 2012

Author: tbooth-guest
Date: 2012-08-22 16:45:24 +0000 (Wed, 22 Aug 2012)
New Revision: 12100

Removed:
   trunk/packages/t-coffee/trunk/debian/t-coffee-doc.docs
Modified:
   trunk/packages/t-coffee/trunk/debian/changelog
   trunk/packages/t-coffee/trunk/debian/control
   trunk/packages/t-coffee/trunk/debian/patches/probconsrna.patch
   trunk/packages/t-coffee/trunk/debian/rules
Log:
Various changes to T-Coffee.  Main one is that the upstream tarball
no longer has docs so the -docs package was empty - I removed it.

Also changed from CDBS to DH - confirmed the same binary is built.



Modified: trunk/packages/t-coffee/trunk/debian/changelog
===================================================================

--- trunk/packages/t-coffee/trunk/debian/changelog	2012-08-21 14:17:10 UTC (rev 12099)
+++ trunk/packages/t-coffee/trunk/debian/changelog	2012-08-22 16:45:24 UTC (rev 12100)
@@ -1,3 +1,16 @@
+t-coffee (9.03.r1318-1ubuntu2) precise; urgency=low
+
+  * Rebuild for Ubuntu with new upstream
+  * Removed the -doc package as it is empty - docs are no longer in
+    tarball but online:
+     http://www.tcoffee.org/Projects/tcoffee/#DOCUMENTATION
+  * Rejigged the rules file to use DH, not CDBS 
+  * Avoid compressing files under t-coffee-examples
+  * Remove TMalign binary on clean (should avoid building it at all)
+  * Fix minor typo flagged by Lintian
+
+ -- Tim Booth <tbooth at ceh.ac.uk>  Wed, 22 Aug 2012 17:33:25 +0100
+
 t-coffee (9.02.r1228-3) UNRELEASED; urgency=low
 
   * debian/upstream: Single Reference field instead of Reference-*

Modified: trunk/packages/t-coffee/trunk/debian/control
===================================================================
--- trunk/packages/t-coffee/trunk/debian/control	2012-08-21 14:17:10 UTC (rev 12099)
+++ trunk/packages/t-coffee/trunk/debian/control	2012-08-22 16:45:24 UTC (rev 12100)
@@ -6,7 +6,7 @@
 Uploaders: Steffen Moeller <moeller at debian.org>,
  Charles Plessy <plessy at debian.org>,
  Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 8), cdbs, quilt, gfortran
+Build-Depends: debhelper (>= 8), gfortran
 Standards-Version: 3.9.3
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/t-coffee/trunk/
 Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/t-coffee/trunk/
@@ -16,7 +16,7 @@
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}
 Recommends: libsoap-lite-perl, libxml-simple-perl, tm-align
-Suggests: boxshade, seaview, t-coffee-doc, t-coffee-examples,
+Suggests: boxshade, seaview, t-coffee-examples,
           dialign-tx, kalign, mafft, muscle, poa, probcons, clustalw,
           amap-align, proda
 Description: Multiple Sequence Alignment
@@ -25,7 +25,7 @@
  alignment. Version 2.00 and higher can mix sequences and structures.
  .
  T-Coffee allows the combination of a collection of multiple/pairwise,
- global or local alignments into a single model. It also allows to
+ global or local alignments into a single model. It can also
  estimate the level of consistency of each position within the new
  alignment with the rest of the alignments. See the pre-print for more
  information
@@ -46,13 +46,3 @@
  To help increasing the proficiency in the use of T-Coffee, this
  package provides examples for input sequences and their proper
  alignment.
-
-Package: t-coffee-doc
-Architecture: all
-Section: doc
-Depends: ${misc:Depends}
-Recommends: t-coffee
-Suggests: t-coffee-examples
-Description: PDF and HTML accompaning documents to T-Coffee
- The tool for multiple sequence alignment, T-Coffee, is explained
- both from the users' perspective and for its technical background.

Modified: trunk/packages/t-coffee/trunk/debian/patches/probconsrna.patch
===================================================================
--- trunk/packages/t-coffee/trunk/debian/patches/probconsrna.patch	2012-08-21 14:17:10 UTC (rev 12099)
+++ trunk/packages/t-coffee/trunk/debian/patches/probconsrna.patch	2012-08-22 16:45:24 UTC (rev 12100)
@@ -1,6 +1,6 @@
 --- a/t_coffee_source/define_header.h
 +++ b/t_coffee_source/define_header.h
-@@ -589,7 +589,7 @@
+@@ -592,7 +592,7 @@
  #define DALILITEc_source "empty"
  #define DALILITEc_update_action "never"
  #define DALILITEc_mode "expresso,3dcoffee"

Modified: trunk/packages/t-coffee/trunk/debian/rules
===================================================================
--- trunk/packages/t-coffee/trunk/debian/rules	2012-08-21 14:17:10 UTC (rev 12099)
+++ trunk/packages/t-coffee/trunk/debian/rules	2012-08-22 16:45:24 UTC (rev 12100)
@@ -1,18 +1,24 @@
 #!/usr/bin/make -f
 
-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
-
 # DEB_SRCDIR		= t_coffee_source
 # Is messing with /usr/share/cdbs/1/rules/patchsys-quilt.mk
 
-DEB_COMPRESS_EXCLUDE = .doc
-
 FCC = gfortran $(shell dpkg-buildflags --get FFLAGS)
 
-DEB_MAKE_BUILD_TARGET	= -C t_coffee_source -i USER_BIN=../bin/ FCC="$(FCC)" all
+%:
+	dh $@ --sourcedirectory=t_coffee_source
 
-clean::
-	dh_clean  t_coffee_source/*.o t_coffee_source/t_coffee bin/t_coffee $(shell find example/ -size 0) bin/t_coffee
+override_dh_auto_build:
+	dh_auto_build -- -i USER_BIN=../bin/ FCC="$(FCC)" all
+
+override_dh_auto_clean:
+	rm -rf t_coffee_source/*.o t_coffee_source/t_coffee bin/t_coffee $(shell find example/ -size 0) bin/t_coffee
+	rm -rf t_coffee_source/TMalign 
 	chmod 644 example/*
+
+override_dh_compress:
+	#Compressing most of the files in examples/ makes them unusable
+	dh_compress -Xt-coffee-examples
+	( cd debian/t-coffee-examples/ && \
+	chmod 644 usr/share/doc/t-coffee-examples/changelog.Debian && \
+	gzip -9 usr/share/doc/t-coffee-examples/changelog.Debian ) || true

Deleted: trunk/packages/t-coffee/trunk/debian/t-coffee-doc.docs
===================================================================
--- trunk/packages/t-coffee/trunk/debian/t-coffee-doc.docs	2012-08-21 14:17:10 UTC (rev 12099)
+++ trunk/packages/t-coffee/trunk/debian/t-coffee-doc.docs	2012-08-22 16:45:24 UTC (rev 12100)
@@ -1 +0,0 @@
-doc/*


