[med-svn] r5713 - in trunk/packages/theseus/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Wed Jan 26 12:19:34 UTC 2011
Author: tille
Date: 2011-01-26 12:19:33 +0000 (Wed, 26 Jan 2011)
New Revision: 5713
Removed:
trunk/packages/theseus/trunk/debian/patches/99-theseus_align.sh.patch
trunk/packages/theseus/trunk/debian/patches/use_muscle_instead_of_clustalw.patch
Modified:
trunk/packages/theseus/trunk/debian/changelog
trunk/packages/theseus/trunk/debian/patches/00-makefile.patch
trunk/packages/theseus/trunk/debian/patches/200-make.inc.patch
trunk/packages/theseus/trunk/debian/patches/series
trunk/packages/theseus/trunk/debian/rules
trunk/packages/theseus/trunk/debian/theseus.install
Log:
Packaging for new upstream version; UNRELEASED because one of the examples segfaults
Modified: trunk/packages/theseus/trunk/debian/changelog
===================================================================
--- trunk/packages/theseus/trunk/debian/changelog 2011-01-26 09:15:44 UTC (rev 5712)
+++ trunk/packages/theseus/trunk/debian/changelog 2011-01-26 12:19:33 UTC (rev 5713)
@@ -1,3 +1,18 @@
+theseus (1.6.0-1) UNRELEASED; urgency=low
+
+UNRELEASED because of segfaulting example
+
+ * New upstream version
+ * debian/patches:
+ - 99-theseus_align.sh.patch:
+ Replaced by sed script in debian/rules which works (hopefully)
+ for future versions as well without manually changing the patch
+ - use_muscle_instead_of_clustalw.patch:
+ Removed because clustalw is no in main and we do not need
+ to actively replace it by muscle
+
+ -- Andreas Tille <tille at debian.org> Wed, 26 Jan 2011 11:39:36 +0100
+
theseus (1.5.5-1) unstable; urgency=low
* New upstream version
Modified: trunk/packages/theseus/trunk/debian/patches/00-makefile.patch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/00-makefile.patch 2011-01-26 09:15:44 UTC (rev 5712)
+++ trunk/packages/theseus/trunk/debian/patches/00-makefile.patch 2011-01-26 12:19:33 UTC (rev 5713)
@@ -2,9 +2,9 @@
Author: Morten Kjeldgaard <mok0 at ubuntu.com>
Switched to quilt: Andreas Tille <tille at debian.org>
---- theseus-1.3.4~/Makefile 2008-04-16 16:13:23.000000000 +0200
-+++ theseus-1.3.4/Makefile 2008-11-17 12:32:24.000000000 +0100
-@@ -145,6 +145,6 @@
+--- theseus_src.orig/Makefile
++++ theseus_src/Makefile
+@@ -149,6 +149,6 @@
cp lib/*.a ${LOCALLIBDIR}
clean:
Modified: trunk/packages/theseus/trunk/debian/patches/200-make.inc.patch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/200-make.inc.patch 2011-01-26 09:15:44 UTC (rev 5712)
+++ trunk/packages/theseus/trunk/debian/patches/200-make.inc.patch 2011-01-26 12:19:33 UTC (rev 5713)
@@ -26,12 +26,12 @@
#OPT = -O0 -ggdb
OPT = -O3 -ffast-math -fstrict-aliasing -funroll-loops -fomit-frame-pointer
WARN = -Werror -Wall -pedantic -std=c99 #-Wstrict-aliasing=2
--CFLAGS = $(WARN) #-force_cpusubtype_ALL -mmacosx-version-min=10.4 -arch ppc -arch i386 -DNDEBUG
+-CFLAGS = $(WARN) #-force_cpusubtype_ALL -mmacosx-version-min=10.4 -arch ppc -arch i386 #-DNDEBUG
+CFLAGS = $(WARN) -DNDEBUG
CC = /usr/bin/gcc
-
-@@ -244,3 +244,16 @@
+ # Intel Xeon Mac OSX
+@@ -243,3 +243,16 @@
# CFLAGS = $(WARN)
# CC = cc
Deleted: trunk/packages/theseus/trunk/debian/patches/99-theseus_align.sh.patch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/99-theseus_align.sh.patch 2011-01-26 09:15:44 UTC (rev 5712)
+++ trunk/packages/theseus/trunk/debian/patches/99-theseus_align.sh.patch 2011-01-26 12:19:33 UTC (rev 5713)
@@ -1,53 +0,0 @@
-Fix path names in shell script to adapt to Debian locations of files
-ANTENTION: This patch is currently not used
-Authors: Morten Kjeldgaard <mok at bioxray.dk>, Andreas Tille <tille at debian.org>
-
---- theseus_src.orig/theseus_align
-+++ theseus_src/theseus_align
-@@ -44,38 +44,38 @@
- CAT="/bin/cat";
- SED="/usr/bin/sed";
- TEE="/usr/bin/tee";
--theseus="/usr/local/bin/theseus"; # where to find the THESEUS binary executable
-+theseus="/usr/bin/theseus"; # where to find the THESEUS binary executable
- fastafile="theseus.fasta";
- filemapfile="theseus.filemap";
- alignmentfile="theseus.aln";
-
- # for MUSCLE -- http://www.drive5.com/muscle/
--#alignprog="/usr/local/bin/muscle";
-+#alignprog="/usr/bin/muscle";
- #align_cmd="${alignprog} -maxiters 32 -in ${fastafile} -out ${alignmentfile} -clwstrict";
-
- # for PROBCONS -- http://probcons.stanford.edu/
--#alignprog="/usr/local/bin/probcons";
-+#alignprog="/usr/bin/probcons";
- #align_cmd="( ${alignprog} -clustalw ${fastafile} | ${SED} 's/PROBCONS/CLUSTALW/' | ${TEE} ${alignmentfile} )";
- #echo $align_cmd
-
- # for CLUSTALW -- ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/
--alignprog="/usr/local/bin/clustalw";
-+alignprog="/usr/bin/clustalw";
- align_cmd="${alignprog} -infile=${fastafile} -outfile=${alignmentfile}";
-
- # for MAFFT -- http://www.biophys.kyoto-u.ac.jp/%7Ekatoh/programs/align/mafft/
--#alignprog="/usr/local/bin/mafft";
-+#alignprog="/usr/bin/mafft";
- #align_cmd="${alignprog} --maxiterate 1000 --localpair --clustalout ${fastafile} > ${alignmentfile}";
-
- # for T_COFFEE -- http://igs-server.cnrs-mrs.fr/%7Ecnotred/Projects_home_page/t_coffee_home_page.html
--#alignprog="/usr/local/bin/t_coffee";
-+#alignprog="/usr/bin/t_coffee";
- #align_cmd="${alignprog} ${fastafile} -outfile=${alignmentfile}";
-
- # for KALIGN -- http://msa.cgb.ki.se/
--#alignprog="/usr/local/bin/kalign"
-+#alignprog="/usr/bin/kalign"
- #align_cmd="${alignprog} -i ${fastafile} -f aln | sed 's/Kalign/CLUSTALW/' > ${alignmentfile}";
-
- # for DIALIGN2 -- http://bibiserv.techfak.uni-bielefeld.de/dialign/
--#alignprog="/usr/local/bin/dialign2"
-+#alignprog="/usr/bin/dialign2"
- #align_cmd="${alignprog} -cw ${fastafile}; sed 's/\/\///' ${fastafile%.*}.cw | sed 's/DIALIGN/CLUSTALW/'";
-
-
Modified: trunk/packages/theseus/trunk/debian/patches/series
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/series 2011-01-26 09:15:44 UTC (rev 5712)
+++ trunk/packages/theseus/trunk/debian/patches/series 2011-01-26 12:19:33 UTC (rev 5713)
@@ -1,5 +1,3 @@
00-makefile.patch
200-make.inc.patch
-99-theseus_align.sh.patch
10_kbsd.patch
-use_muscle_instead_of_clustalw.patch
Deleted: trunk/packages/theseus/trunk/debian/patches/use_muscle_instead_of_clustalw.patch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/use_muscle_instead_of_clustalw.patch 2011-01-26 09:15:44 UTC (rev 5712)
+++ trunk/packages/theseus/trunk/debian/patches/use_muscle_instead_of_clustalw.patch 2011-01-26 12:19:33 UTC (rev 5713)
@@ -1,29 +0,0 @@
-Description: The script thesaus_align says it would use muscle as align program
- but it actually uses clustalw which is in non-free and thus we can
- not recommend it. The patch makes muscle really the default
-Author: Andreas Tille <tille at debian.org>
-
---- theseus_src.orig/theseus_align
-+++ theseus_src/theseus_align
-@@ -50,8 +50,8 @@
- alignmentfile="theseus.aln";
-
- # for MUSCLE -- http://www.drive5.com/muscle/
--#alignprog="/usr/bin/muscle";
--#align_cmd="${alignprog} -maxiters 32 -in ${fastafile} -out ${alignmentfile} -clwstrict";
-+alignprog="/usr/bin/muscle";
-+align_cmd="${alignprog} -maxiters 32 -in ${fastafile} -out ${alignmentfile} -clwstrict";
-
- # for PROBCONS -- http://probcons.stanford.edu/
- #alignprog="/usr/bin/probcons";
-@@ -59,8 +59,8 @@
- #echo $align_cmd
-
- # for CLUSTALW -- ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/
--alignprog="/usr/bin/clustalw";
--align_cmd="${alignprog} -infile=${fastafile} -outfile=${alignmentfile}";
-+# alignprog="/usr/bin/clustalw";
-+# align_cmd="${alignprog} -infile=${fastafile} -outfile=${alignmentfile}";
-
- # for MAFFT -- http://www.biophys.kyoto-u.ac.jp/%7Ekatoh/programs/align/mafft/
- #alignprog="/usr/bin/mafft";
Modified: trunk/packages/theseus/trunk/debian/rules
===================================================================
--- trunk/packages/theseus/trunk/debian/rules 2011-01-26 09:15:44 UTC (rev 5712)
+++ trunk/packages/theseus/trunk/debian/rules 2011-01-26 12:19:33 UTC (rev 5713)
@@ -3,6 +3,8 @@
# Copyright (C) Andreas Tille <tille at debian.org>
# License: GPL
+pkg=theseus
+
%:
dh --with quilt $@
@@ -11,4 +13,8 @@
dh_auto_clean
override_dh_auto_install:
- echo "Do not call make install, use dh_install instead"
+ # Fix wrong path used in upstream script. Fixing it here is safer than
+ # changing the patch for any new upstream release
+ sed -e 's?/usr/local/bin?/usr/bin?' \
+ -e 's?/usr/bin/sed?/bin/sed?' \
+ theseus_align > debian/$(pkg)/usr/bin/theseus_align
Modified: trunk/packages/theseus/trunk/debian/theseus.install
===================================================================
--- trunk/packages/theseus/trunk/debian/theseus.install 2011-01-26 09:15:44 UTC (rev 5712)
+++ trunk/packages/theseus/trunk/debian/theseus.install 2011-01-26 12:19:33 UTC (rev 5713)
@@ -1,2 +1 @@
theseus usr/bin
-theseus_align /usr/bin
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