[med-svn] r5825 - in trunk/packages/t-coffee/trunk/debian: . patches
Timothy Booth
tbooth-guest at alioth.debian.org
Sun Jan 30 15:15:06 UTC 2011
Author: tbooth-guest
Date: 2011-01-30 15:15:03 +0000 (Sun, 30 Jan 2011)
New Revision: 5825
Added:
trunk/packages/t-coffee/trunk/debian/patches/probconsrna.patch
Removed:
trunk/packages/t-coffee/trunk/debian/patches/dmcoffee.patch
Modified:
trunk/packages/t-coffee/trunk/debian/changelog
trunk/packages/t-coffee/trunk/debian/control
trunk/packages/t-coffee/trunk/debian/patches/series
trunk/packages/t-coffee/trunk/debian/rules
trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base.technical
trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base.tutorial
trunk/packages/t-coffee/trunk/debian/watch
Log:
Updated to latest upstream, some tweaks for lintian, test built on lucid
Modified: trunk/packages/t-coffee/trunk/debian/changelog
===================================================================
--- trunk/packages/t-coffee/trunk/debian/changelog 2011-01-30 14:26:33 UTC (rev 5824)
+++ trunk/packages/t-coffee/trunk/debian/changelog 2011-01-30 15:15:03 UTC (rev 5825)
@@ -1,3 +1,23 @@
+t-coffee (8.99-0ubuntu1) lucid; urgency=low
+
+ * Rebuild for new upstream release.
+ * There is no changelog from upstream to read.
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Sat, 29 Jan 2011 15:18:01 +0000
+
+t-coffee (8.97-0ubuntu2) lucid; urgency=low
+
+ * New upstream release, changed watch file and auto rebuild using uupdate
+ * Cleared out old patch - apparently unneeded or else needs total re-write
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Tue, 23 Nov 2010 14:01:22 +0000
+
+t-coffee (8.95-1) lucid; urgency=low
+
+ * New upstream version, rebuild by Tim for Bio-Linux/Lucid
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Mon, 01 Nov 2010 15:05:07 +0000
+
t-coffee (8.84-1) unstable; urgency=low
* New upstream version
Modified: trunk/packages/t-coffee/trunk/debian/control
===================================================================
--- trunk/packages/t-coffee/trunk/debian/control 2011-01-30 14:26:33 UTC (rev 5824)
+++ trunk/packages/t-coffee/trunk/debian/control 2011-01-30 15:15:03 UTC (rev 5825)
@@ -15,9 +15,10 @@
Package: t-coffee
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
-Recommends: libsoap-lite-perl
+Recommends: libsoap-lite-perl, libxml-simple-perl
Suggests: boxshade, seaview, t-coffee-doc, t-coffee-examples,
- dialign-tx, kalign, mafft, muscle, poa, probcons, clustalw
+ dialign-tx, kalign, mafft, muscle, poa, probcons, clustalw,
+ amap-align, proda
Description: Multiple Sequence Alignment
T-Coffee is a multiple sequence alignment package. Given a set of
sequences (Proteins or DNA), T-Coffee generates a multiple sequence
Deleted: trunk/packages/t-coffee/trunk/debian/patches/dmcoffee.patch
===================================================================
--- trunk/packages/t-coffee/trunk/debian/patches/dmcoffee.patch 2011-01-30 14:26:33 UTC (rev 5824)
+++ trunk/packages/t-coffee/trunk/debian/patches/dmcoffee.patch 2011-01-30 15:15:03 UTC (rev 5825)
@@ -1,71 +0,0 @@
-Author: Charles Plessy <plessy at debian.org>
-Forwarded: Cédric Notredame <cedric.notredame at europe.com>
-Description: To make (D)M-COFFEE work out of the box on Debian.
- The path to dialign-tx and to the blosum matrix of POA are hardcoded
- through this patch, so that (D)M-COFFEE work without manual copying
- and/or linking.
-License: Same as T-COFFEE itself.
---- a/t_coffee_source/util_constraints_list.c
-+++ b/t_coffee_source/util_constraints_list.c
-@@ -1397,13 +1397,13 @@
- else if ( lstrstr ( method, "dialignt_pair"))
- {
-
-- check_program_is_installed ("dialign-t", NULL, NULL, "http://dialign-t.gobics.de/", IS_FATAL);
-+ check_program_is_installed ("dialign-tx", NULL, NULL, "http://dialign-tx.gobics.de/", IS_FATAL);
-
- fp=vfopen (fname, "w");
- fprintf ( fp, "EXECUTABLE %s\n",(getenv("DIALIGNT_4_TCOFFEE"))?getenv("DIALIGNT_4_TCOFFEE"):DIALIGNT_4_TCOFFEE );
- fprintf ( fp, "ALN_MODE pairwise\n");
- fprintf ( fp, "OUT_MODE aln\n");
-- fprintf ( fp, "PARAM1 %s \n", get_mcoffee_4_tcoffee());
-+ fprintf ( fp, "PARAM1 /usr/share/dialign-tx \n", get_mcoffee_4_tcoffee());
- fprintf ( fp, "IN_FLAG &bnsp\n");
- fprintf ( fp, "OUT_FLAG &bnsp\n");
- fprintf ( fp, "PARAM >/dev/null&bnsp2>/dev/null\n");
-@@ -1416,12 +1416,12 @@
- else if ( lstrstr ( method, "dialignt_msa"))
- {
-
-- check_program_is_installed ("dialign-t", NULL, NULL, "http://dialign-t.gobics.de/", IS_FATAL);
-+ check_program_is_installed ("dialign-tx", NULL, NULL, "http://dialign-tx.gobics.de/", IS_FATAL);
- fp=vfopen (fname, "w");
- fprintf ( fp, "EXECUTABLE %s\n",(getenv("DIALIGNT_4_TCOFFEE"))?getenv("DIALIGNT_4_TCOFFEE"):DIALIGNT_4_TCOFFEE );
- fprintf ( fp, "ALN_MODE multiple\n");
- fprintf ( fp, "OUT_MODE aln\n");
-- fprintf ( fp, "PARAM1 %s \n", get_mcoffee_4_tcoffee());
-+ fprintf ( fp, "PARAM1 /usr/share/dialign-tx \n", get_mcoffee_4_tcoffee());
- fprintf ( fp, "IN_FLAG &bnsp\n");
- fprintf ( fp, "OUT_FLAG &bnsp\n");
- fprintf ( fp, "PARAM >/dev/null&bnsp2>/dev/null\n");
-@@ -1443,7 +1443,7 @@
- fprintf ( fp, "PARAM1 -toupper \n");
- fprintf ( fp, "IN_FLAG -read_fasta&bnsp\n");
- fprintf ( fp, "OUT_FLAG -clustal&bnsp\n");
-- fprintf ( fp, "PARAM %s/blosum80.mat&bnsp2>/dev/null\n", get_mcoffee_4_tcoffee());
-+ fprintf ( fp, "PARAM /usr/share/blosum80.mat&bnsp2>/dev/null\n", get_mcoffee_4_tcoffee());
- fprintf ( fp, "SEQ_TYPE S\n");
-
- vfclose (fp);
-@@ -1461,7 +1461,7 @@
- fprintf ( fp, "PARAM1 -toupper \n");
- fprintf ( fp, "IN_FLAG -read_fasta&bnsp\n");
- fprintf ( fp, "OUT_FLAG -clustal&bnsp\n");
-- fprintf ( fp, "PARAM %s/blosum80.mat&bnsp2>/dev/null\n", get_mcoffee_4_tcoffee());
-+ fprintf ( fp, "PARAM /usr/share/poa/blosum80.mat&bnsp2>/dev/null\n", get_mcoffee_4_tcoffee());
- fprintf ( fp, "SEQ_TYPE S\n");
-
- vfclose (fp);
---- a/t_coffee_source/define_header.h
-+++ b/t_coffee_source/define_header.h
-@@ -331,8 +331,8 @@
- #define CLUSTALW_4_TCOFFEE "clustalw"
- #define POA_4_TCOFFEE "poa"
- #define PROBCONS_4_TCOFFEE "probcons"
--#define PROBCONSRNA_4_TCOFFEE "probconsRNA"
--#define DIALIGNT_4_TCOFFEE "dialign-t"
-+#define PROBCONSRNA_4_TCOFFEE "probcons-RNA"
-+#define DIALIGNT_4_TCOFFEE "dialign-tx"
- #define MAFFT_4_TCOFFEE "mafft"
- #define MUSCLE_4_TCOFFEE "muscle"
- #define TCOFFEE_4_TCOFFEE "t_coffee"
Added: trunk/packages/t-coffee/trunk/debian/patches/probconsrna.patch
===================================================================
--- trunk/packages/t-coffee/trunk/debian/patches/probconsrna.patch (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/patches/probconsrna.patch 2011-01-30 15:15:03 UTC (rev 5825)
@@ -0,0 +1,11 @@
+--- a/t_coffee_source/define_header.h
++++ b/t_coffee_source/define_header.h
+@@ -589,7 +589,7 @@
+ #define DALILITEc_source "empty"
+ #define DALILITEc_update_action "never"
+ #define DALILITEc_mode "expresso,3dcoffee"
+-#define PROBCONSRNA_4_TCOFFEE "probconsRNA"
++#define PROBCONSRNA_4_TCOFFEE "probcons-RNA"
+ #define PROBCONSRNA_type "RNA_multiple_aligner"
+ #define PROBCONSRNA_ADDRESS "http://probcons.stanford.edu/"
+ #define PROBCONSRNA_language "C++"
Modified: trunk/packages/t-coffee/trunk/debian/patches/series
===================================================================
--- trunk/packages/t-coffee/trunk/debian/patches/series 2011-01-30 14:26:33 UTC (rev 5824)
+++ trunk/packages/t-coffee/trunk/debian/patches/series 2011-01-30 15:15:03 UTC (rev 5825)
@@ -1 +1 @@
-#dmcoffee.patch
+probconsrna.patch
Modified: trunk/packages/t-coffee/trunk/debian/rules
===================================================================
--- trunk/packages/t-coffee/trunk/debian/rules 2011-01-30 14:26:33 UTC (rev 5824)
+++ trunk/packages/t-coffee/trunk/debian/rules 2011-01-30 15:15:03 UTC (rev 5825)
@@ -7,6 +7,8 @@
# DEB_SRCDIR = t_coffee_source
# Is messing with /usr/share/cdbs/1/rules/patchsys-quilt.mk
+DEB_COMPRESS_EXCLUDE = .doc
+
DEB_MAKE_BUILD_TARGET = -C t_coffee_source -i USER_BIN=../bin/ all
clean::
Modified: trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base.technical
===================================================================
--- trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base.technical 2011-01-30 14:26:33 UTC (rev 5824)
+++ trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base.technical 2011-01-30 15:15:03 UTC (rev 5825)
@@ -5,9 +5,6 @@
and provides a reference manual for all its options.
Section: Science/Biology
-Format: Text
-Files: /usr/share/doc/t-coffee-doc/t_coffee_technical.txt.gz
-
Format: HTML
Index: /usr/share/doc/t-coffee-doc/t_coffee_technical.htm
Files: /usr/share/doc/t-coffee-doc/t_coffee_technical.htm
Modified: trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base.tutorial
===================================================================
--- trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base.tutorial 2011-01-30 14:26:33 UTC (rev 5824)
+++ trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base.tutorial 2011-01-30 15:15:03 UTC (rev 5825)
@@ -9,9 +9,6 @@
is the only way.
Section: Science/Biology
-Format: Text
-Files: /usr/share/doc/t-coffee-doc/t_coffee_tutorial.txt.gz
-
Format: HTML
Index: /usr/share/doc/t-coffee-doc/t_coffee_tutorial.htm
Files: /usr/share/doc/t-coffee-doc/t_coffee_tutorial.htm
Modified: trunk/packages/t-coffee/trunk/debian/watch
===================================================================
--- trunk/packages/t-coffee/trunk/debian/watch 2011-01-30 14:26:33 UTC (rev 5824)
+++ trunk/packages/t-coffee/trunk/debian/watch 2011-01-30 15:15:03 UTC (rev 5825)
@@ -1,2 +1,2 @@
version=3
-http://www.tcoffee.org/Packages/ T-COFFEE_distribution_Version_(.*)\.tar\.gz
+http://www.tcoffee.org/Packages/Stable/Latest/T-COFFEE_distribution_Version_([^_]*).*\.tar\.gz
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