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 <[email protected]> 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 <[email protected]>, Charles Plessy <[email protected]>, Andreas Tille <[email protected]> -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/* _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
