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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> -Forwarded: Cédric Notredame <[email protected]> -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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
