[med-svn] r2111 - in trunk/packages/t-coffee/trunk/debian: . patches
plessy at alioth.debian.org
plessy at alioth.debian.org
Mon Jun 30 14:52:17 UTC 2008
Author: plessy
Date: 2008-06-30 14:52:16 +0000 (Mon, 30 Jun 2008)
New Revision: 2111
Removed:
trunk/packages/t-coffee/trunk/debian/patches/unicode.diff
Modified:
trunk/packages/t-coffee/trunk/debian/changelog
trunk/packages/t-coffee/trunk/debian/patches/dmcoffee.patch
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
Log:
Updated the patch. Will upload tomorrow.
Modified: trunk/packages/t-coffee/trunk/debian/changelog
===================================================================
--- trunk/packages/t-coffee/trunk/debian/changelog 2008-06-30 13:54:55 UTC (rev 2110)
+++ trunk/packages/t-coffee/trunk/debian/changelog 2008-06-30 14:52:16 UTC (rev 2111)
@@ -1,4 +1,4 @@
-t-coffee (5.65-1) UNRELEASED; urgency=low
+t-coffee (5.72-1) unstable; urgency=low
[ David Paleino ]
* New upstream release
@@ -6,12 +6,12 @@
[ Charles Plessy ]
* Switched to CDBS.
* debian/patches:
- - Unicode conversions.
- - Upated the dm-coffee patch because dialign-t was renamed dialign-tx
- * Changed the doc-base section according to the new policy.
+ - Upated the dm-coffee patch because dialign-t was renamed dialign-tx.
+ - Dropped the unicode conversion patch.
+ - Dropped the manpage patch (implements the clear rule through CDBS).
* Updated my email address.
- -- David Paleino <d.paleino at gmail.com> Sat, 31 May 2008 19:27:36 +0200
+ -- Charles Plessy <plessy at debian.org> Mon, 30 Jun 2008 23:34:32 +0900
t-coffee (5.31-1) unstable; urgency=low
Modified: trunk/packages/t-coffee/trunk/debian/patches/dmcoffee.patch
===================================================================
--- trunk/packages/t-coffee/trunk/debian/patches/dmcoffee.patch 2008-06-30 13:54:55 UTC (rev 2110)
+++ trunk/packages/t-coffee/trunk/debian/patches/dmcoffee.patch 2008-06-30 14:52:16 UTC (rev 2111)
@@ -1,13 +1,13 @@
Author: Charles Plessy <plessy at debian.org>
-Forwarded: Soon
-Description: To make (D)M-COFFEE work out of the bok on Debian.
+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
-@@ -1368,13 +1368,13 @@
+@@ -1397,13 +1397,13 @@
else if ( lstrstr ( method, "dialignt_pair"))
{
@@ -23,7 +23,7 @@
fprintf ( fp, "IN_FLAG &bnsp\n");
fprintf ( fp, "OUT_FLAG &bnsp\n");
fprintf ( fp, "PARAM >/dev/null&bnsp2>/dev/null\n");
-@@ -1387,12 +1387,12 @@
+@@ -1416,12 +1416,12 @@
else if ( lstrstr ( method, "dialignt_msa"))
{
@@ -38,7 +38,7 @@
fprintf ( fp, "IN_FLAG &bnsp\n");
fprintf ( fp, "OUT_FLAG &bnsp\n");
fprintf ( fp, "PARAM >/dev/null&bnsp2>/dev/null\n");
-@@ -1414,7 +1414,7 @@
+@@ -1443,7 +1443,7 @@
fprintf ( fp, "PARAM1 -toupper \n");
fprintf ( fp, "IN_FLAG -read_fasta&bnsp\n");
fprintf ( fp, "OUT_FLAG -clustal&bnsp\n");
@@ -47,7 +47,7 @@
fprintf ( fp, "SEQ_TYPE S\n");
vfclose (fp);
-@@ -1432,7 +1432,7 @@
+@@ -1461,7 +1461,7 @@
fprintf ( fp, "PARAM1 -toupper \n");
fprintf ( fp, "IN_FLAG -read_fasta&bnsp\n");
fprintf ( fp, "OUT_FLAG -clustal&bnsp\n");
@@ -56,3 +56,16 @@
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"
Modified: trunk/packages/t-coffee/trunk/debian/patches/series
===================================================================
--- trunk/packages/t-coffee/trunk/debian/patches/series 2008-06-30 13:54:55 UTC (rev 2110)
+++ trunk/packages/t-coffee/trunk/debian/patches/series 2008-06-30 14:52:16 UTC (rev 2111)
@@ -1,2 +1 @@
dmcoffee.patch
-unicode.diff
Deleted: trunk/packages/t-coffee/trunk/debian/patches/unicode.diff
===================================================================
--- trunk/packages/t-coffee/trunk/debian/patches/unicode.diff 2008-06-30 13:54:55 UTC (rev 2110)
+++ trunk/packages/t-coffee/trunk/debian/patches/unicode.diff 2008-06-30 14:52:16 UTC (rev 2111)
@@ -1,98 +0,0 @@
-Author: Charles Plessy <plessy at debian.org>
-Forwarded: Soon
-Description: converts the encoding of some output of T-COFFEE to Unicode
- (Unicode is now the default encoding in Debian).
-License: Same as t-coffee itself.
---- a/doc/t_coffee_technical.txt
-+++ b/doc/t_coffee_technical.txt
-@@ -4,7 +4,7 @@
- Centre National De LA Recherche scientifique (France)
-
- CeNTRO De REGULACIO GENOMICA (SPAIN)
--Cédric Notredame
-+Cédric Notredame
-
- www.tcoffee.org
-
-@@ -32,7 +32,7 @@
-
- APDB and iRMSD
-
-- ( Cédric Notredame and Centre National de la Recherche Scientifique, France
-+ ( Cédric Notredame and Centre National de la Recherche Scientifique, France
- License and Terms of Use 5
- T-Coffee is distributed under the Gnu Public License 5
- T-Coffee code can be re-used freely 5
-@@ -302,7 +302,7 @@
- T-coffee is developed, maintained, monitored, used and debugged by a
- dedicated team that include:
-
-- Cédric Notredame
-+ Cédric Notredame
-
- Fabrice Armougom
-
-@@ -1315,7 +1315,7 @@
- Forces t_coffee to identify the sequences type (PROTEIN, DNA).
-
- -type [cw]
-- Usage: -type=DNA ¦ PROTEIN¦ DNA_PROTEIN
-+ Usage: -type=DNA Å PROTEINÅ DNA_PROTEIN
- Default: -type=<automatically set>
-
- This flag sets the type of the sequences. If omitted, the type is
---- a/doc/t_coffee_tutorial.txt
-+++ b/doc/t_coffee_tutorial.txt
-@@ -2,7 +2,7 @@
- T-coffee Tutorial
-
- Centre National De LA Recherche scientifique
--Cédric Notredame
-+Cédric Notredame
-
- www.tcoffee.org
-
-@@ -26,7 +26,7 @@
-
- APDB and iRMSD
-
-- ( Cédric Notredame and Centre National de la Recherche Scientifique, France
-+ ( Cédric Notredame and Centre National de la Recherche Scientifique, France
- Before You Start. 5
- Foreword 5
- Pre-Requisite 5
-@@ -1693,11 +1693,11 @@
- each of these applications with T-Coffee.
-
- | |Muscle |Mafft |
--|Expresso |sproteases_small.expresso|1.33 Å |
--|T-Coffee |sproteases_small.tc_aln |1.35 Å |
--|ClustalW |sproteases_small.cw_aln |1.52 Å |
--|Mafft |sproteases_small.mafft |1.36 Å |
--|Muscle |sproteases_small.muscle |1.34 Å |
-+|Expresso |sproteases_small.expresso|1.33 Ã… |
-+|T-Coffee |sproteases_small.tc_aln |1.35 Ã… |
-+|ClustalW |sproteases_small.cw_aln |1.52 Ã… |
-+|Mafft |sproteases_small.mafft |1.36 Ã… |
-+|Muscle |sproteases_small.muscle |1.34 Ã… |
-
-
- As expected, Expresso delivers the best alignment from a structural
-@@ -2112,7 +2112,7 @@
- This special method (em, external method) uses the following syntax:
-
-
-- em@<method>@<aln_mode:pairwise¦s_pairwise|multiple>
-+ em@<method>@<aln_mode:pairwiseÅ s_pairwise|multiple>
-
-
- 2 Customizing an external method (with parameters) for T-Coffee
-@@ -3307,7 +3307,7 @@
- T-coffee is developed, maintained, monitored, used and debugged by a
- dedicated team that include:
-
-- Cédric Notredame
-+ Cédric Notredame
-
- Fabrice Armougom
-
Modified: trunk/packages/t-coffee/trunk/debian/rules
===================================================================
--- trunk/packages/t-coffee/trunk/debian/rules 2008-06-30 13:54:55 UTC (rev 2110)
+++ trunk/packages/t-coffee/trunk/debian/rules 2008-06-30 14:52:16 UTC (rev 2111)
@@ -1,7 +1,5 @@
#!/usr/bin/make -f
-DEB_COMPRESS_EXCLUDE := l.txt # These are indexed by doc-base
-
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
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 2008-06-30 13:54:55 UTC (rev 2110)
+++ trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base.technical 2008-06-30 14:52:16 UTC (rev 2111)
@@ -6,7 +6,7 @@
Section: Science/Biology
Format: Text
-Files: /usr/share/doc/t-coffee-doc/t_coffee_technical.txt
+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
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 2008-06-30 13:54:55 UTC (rev 2110)
+++ trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base.tutorial 2008-06-30 14:52:16 UTC (rev 2111)
@@ -10,7 +10,7 @@
Section: Science/Biology
Format: Text
-Files: /usr/share/doc/t-coffee-doc/t_coffee_tutorial.txt
+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
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