This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository t-coffee.
commit 53660abc92e9615ebf5a3356166f6d7caa54d622 Author: Andreas Tille <[email protected]> Date: Sat Dec 17 18:39:06 2016 +0100 Executable in clustalw 2.x package is named clustalw --- debian/changelog | 8 ++ debian/patches/clustalw2.patch | 175 +++++++++++++++++++++++++++++++++++++++++ debian/patches/series | 1 + 3 files changed, 184 insertions(+) diff --git a/debian/changelog b/debian/changelog index 91cf3ee..e071eee 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,11 @@ +t-coffee (11.00.8cbe486-5) UNRELEASED; urgency=medium + + * When using bioperl-run test suite it is uncovered that t-coffee is + wrongly seeking for a clustalw2 executable. A patch is applied to + rather seek for clustalw. + + -- Andreas Tille <[email protected]> Fri, 16 Dec 2016 15:00:58 +0100 + t-coffee (11.00.8cbe486-4) unstable; urgency=medium * Team upload diff --git a/debian/patches/clustalw2.patch b/debian/patches/clustalw2.patch new file mode 100644 index 0000000..c78c5fb --- /dev/null +++ b/debian/patches/clustalw2.patch @@ -0,0 +1,175 @@ +Description: Executable in clustalw 2.x package is named clustalw + When using bioperl-run test suite it is uncovered that t-coffee is + wrongly seeking for a clustalw2 executable. A patch is applied to + rather seek for clustalw. +Author: Andreas Tille <[email protected]> +Last-Update: Fri, 16 Dec 2016 15:00:58 +0100 + +--- a/t_coffee_source/perl_header_lib.h ++++ b/t_coffee_source/perl_header_lib.h +@@ -5177,7 +5177,7 @@ po_store(\"./src/$pg\");\n }\n else\n + h_command (\"make $arguments sap\");\n &check_\ + cp ($pg, \"$BIN\");\n repo_store($pg);\n }\n\ + }\n \n #\n # CLUSTALW2 module\n \ +-#\n elsif ($pg eq \"clustalw2\")\n {\n &fl\ ++#\n elsif ($pg eq \"clustalw\")\n {\n &fl\ + ush_command(\"./configure\");\n &flush_command(\"m\ + ake $arguments\");\n &check_cp (\"./src/$pg\", \"$\ + BIN\");\n repo_store(\"./src/$pg\");\n }\n\n \ +@@ -5534,16 +5534,16 @@ trike/index.html\";\n$PG{\"strike\"}{\"l + \n$PG{\"strike\"}{\"source\"}=\"http://www.tcoffee\ + .org/Projects/strike/strike_v1.2.tar.bz2\";\n$PG{\\ + "strike\"}{\"mode\"}=\"tcoffee,expresso\";\n$PG{\"\ +-strike\"}{\"version\"}=\"1.2\";\n$PG{\"clustalw2\"\ +-}{\"4_TCOFFEE\"}=\"CLUSTALW2\";\n$PG{\"clustalw2\"\ ++strike\"}{\"version\"}=\"1.2\";\n$PG{\"clustalw\"\ ++}{\"4_TCOFFEE\"}=\"CLUSTALW2\";\n$PG{\"clustalw\"\ + }{\"type\"}=\"sequence_multiple_aligner\";\n$PG{\"\ +-clustalw2\"}{\"ADDRESS\"}=\"http://www.clustal.org\ +-\";\n$PG{\"clustalw2\"}{\"language\"}=\"C++\";\n$P\ +-G{\"clustalw2\"}{\"language2\"}=\"CXX\";\n$PG{\"cl\ ++clustalw\"}{\"ADDRESS\"}=\"http://www.clustal.org\ ++\";\n$PG{\"clustalw\"}{\"language\"}=\"C++\";\n$P\ ++G{\"clustalw\"}{\"language2\"}=\"CXX\";\n$PG{\"cl\ + ustalw2\"}{\"source\"}=\"http://www.clustal.org/do\ + wnload/2.0.10/clustalw-2.0.10-src.tar.gz\";\n$PG{\\ +-"clustalw2\"}{\"mode\"}=\"mcoffee,rcoffee\";\n$PG{\ +-\"clustalw2\"}{\"version\"}=\"2.0.10\";\n$PG{\"clu\ ++"clustalw\"}{\"mode\"}=\"mcoffee,rcoffee\";\n$PG{\ ++\"clustalw\"}{\"version\"}=\"2.0.10\";\n$PG{\"clu\ + stalw\"}{\"4_TCOFFEE\"}=\"CLUSTALW\";\n$PG{\"clust\ + alw\"}{\"type\"}=\"sequence_multiple_aligner\";\n$\ + PG{\"clustalw\"}{\"ADDRESS\"}=\"http://www.clustal\ +--- a/t_coffee_source/util_lib/util_constraints_list.c ++++ b/t_coffee_source/util_lib/util_constraints_list.c +@@ -5677,7 +5677,7 @@ char *** produce_method_file ( char *met + sprintf (list[n][1], "%s", vtmpnam(NULL)); + n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w"); + fprintf ( fp, "EXECUTABLE profile_pair\n"); +- fprintf ( fp, "EXECUTABLE2 clustalw2\n"); ++ fprintf ( fp, "EXECUTABLE2 clustalw\n"); + fprintf ( fp, "ALN_MODE pairwise\n"); + fprintf ( fp, "OUT_MODE fL\n"); + fprintf ( fp, "IN_FLAG -profile1=\n"); +@@ -5917,7 +5917,7 @@ char *** produce_method_file ( char *met + sprintf (list[n][1], "%s", vtmpnam(NULL)); + n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w"); + fprintf ( fp, "DOC: clustalw [%s]\n", CLUSTALW2_ADDRESS); +- fprintf ( fp, "EXECUTABLE clustalw2\n"); ++ fprintf ( fp, "EXECUTABLE clustalw\n"); + fprintf ( fp, "ALN_MODE pairwise\n"); + fprintf ( fp, "OUT_MODE aln\n"); + fprintf ( fp, "IN_FLAG %sINFILE=\n",CWF); +@@ -5932,7 +5932,7 @@ char *** produce_method_file ( char *met + sprintf (list[n][1], "%s", vtmpnam(NULL)); + n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w"); + fprintf ( fp, "DOC clustalw[%s]\n", CLUSTALW2_ADDRESS); +- fprintf ( fp, "EXECUTABLE clustalw2\n"); ++ fprintf ( fp, "EXECUTABLE clustalw\n"); + fprintf ( fp, "ALN_MODE multiple\n"); + fprintf ( fp, "OUT_MODE aln\n"); + fprintf ( fp, "IN_FLAG %sINFILE=\n",CWF); +@@ -5947,7 +5947,7 @@ char *** produce_method_file ( char *met + sprintf (list[n][1], "%s", vtmpnam(NULL)); + n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w"); + fprintf ( fp, "DOC: clustalw [%s]\n", CLUSTALW_ADDRESS); +- fprintf ( fp, "EXECUTABLE clustalw2\n"); ++ fprintf ( fp, "EXECUTABLE clustalw\n"); + fprintf ( fp, "ALN_MODE pairwise\n"); + fprintf ( fp, "OUT_MODE aln\n"); + fprintf ( fp, "IN_FLAG %sINFILE=\n", CWF); +@@ -5962,7 +5962,7 @@ char *** produce_method_file ( char *met + sprintf (list[n][1], "%s", vtmpnam(NULL)); + n++;if (method==NULL || strm (method, list[n-1][0])){fp=vfopen (list[n-1][1], "w"); + fprintf ( fp, "DOC clustalw[%s]\n", CLUSTALW_ADDRESS); +- fprintf ( fp, "EXECUTABLE clustalw2\n"); ++ fprintf ( fp, "EXECUTABLE clustalw\n"); + fprintf ( fp, "ALN_MODE multiple\n"); + fprintf ( fp, "OUT_MODE aln\n"); + fprintf ( fp, "IN_FLAG %sINFILE=\n", CWF); +--- a/t_coffee_source/data_headers/programmes_define.h ++++ b/t_coffee_source/data_headers/programmes_define.h +@@ -56,7 +56,7 @@ + #define CLUSTALW_4_TCOFFEE "clustalw" + #define CLUSTALW_ADDRESS "ftp://www.ebi.ac.uk/pub/clustalw"; + +-#define CLUSTALW2_4_TCOFFEE "clustalw2" ++#define CLUSTALW2_4_TCOFFEE "clustalw" + #define CLUSTALW2_ADDRESS "http://www.clustal.org"; + + #define CLUSTALO_ADDRESS "http://www.clustal.org/omega/"; +--- a/install ++++ b/install +@@ -798,7 +798,7 @@ sub install_source_package + # + # CLUSTALW2 module + # +- elsif ($pg eq "clustalw2") ++ elsif ($pg eq "clustalw") + { + &flush_command("./configure"); + &flush_command("make $arguments"); +@@ -1577,22 +1577,14 @@ $PG{"strike"}{"language2"}="CXX"; + $PG{"strike"}{"source"}="http://www.tcoffee.org/Projects/strike/strike_v1.2.tar.bz2";; + $PG{"strike"}{"mode"}="tcoffee,expresso"; + $PG{"strike"}{"version"}="1.2"; +-$PG{"clustalw2"}{"4_TCOFFEE"}="CLUSTALW2"; +-$PG{"clustalw2"}{"type"}="sequence_multiple_aligner"; +-$PG{"clustalw2"}{"ADDRESS"}="http://www.clustal.org";; +-$PG{"clustalw2"}{"language"}="C++"; +-$PG{"clustalw2"}{"language2"}="CXX"; +-$PG{"clustalw2"}{"source"}="http://www.clustal.org/download/2.0.10/clustalw-2.0.10-src.tar.gz";; +-$PG{"clustalw2"}{"mode"}="mcoffee,rcoffee"; +-$PG{"clustalw2"}{"version"}="2.0.10"; +-$PG{"clustalw"}{"4_TCOFFEE"}="CLUSTALW"; ++$PG{"clustalw"}{"4_TCOFFEE"}="CLUSTALW2"; + $PG{"clustalw"}{"type"}="sequence_multiple_aligner"; + $PG{"clustalw"}{"ADDRESS"}="http://www.clustal.org";; +-$PG{"clustalw"}{"language"}="C"; +-$PG{"clustalw"}{"language2"}="C"; +-$PG{"clustalw"}{"source"}="http://www.clustal.org/download/1.X/ftp-igbmc.u-strasbg.fr/pub/ClustalW/clustalw1.82.UNIX.tar.gz";; ++$PG{"clustalw"}{"language"}="C++"; ++$PG{"clustalw"}{"language2"}="CXX"; ++$PG{"clustalw"}{"source"}="http://www.clustal.org/download/2.0.10/clustalw-2.0.10-src.tar.gz";; + $PG{"clustalw"}{"mode"}="mcoffee,rcoffee"; +-$PG{"clustalw"}{"version"}="1.82"; ++$PG{"clustalw"}{"version"}="2.0.10"; + $PG{"dialign-t"}{"4_TCOFFEE"}="DIALIGNT"; + $PG{"dialign-t"}{"type"}="sequence_multiple_aligner"; + $PG{"dialign-t"}{"ADDRESS"}="http://dialign-tx.gobics.de/";; +--- a/t_coffee_source/programmes_define.h ++++ b/t_coffee_source/programmes_define.h +@@ -60,7 +60,7 @@ + #define STRIKE_source "http://www.tcoffee.org/Projects/strike/strike_v1.2.tar.bz2"; + #define STRIKE_mode "tcoffee,expresso" + #define STRIKE_version "1.2" +-#define CLUSTALW2_4_TCOFFEE "clustalw2" ++#define CLUSTALW2_4_TCOFFEE "clustalw" + #define CLUSTALW2_type "sequence_multiple_aligner" + #define CLUSTALW2_ADDRESS "http://www.clustal.org"; + #define CLUSTALW2_language "C++" +--- a/tclinkdb.txt ++++ b/tclinkdb.txt +@@ -25,14 +25,14 @@ PG strike source http://www.tcoffee.org + PG strike mode tcoffee,expresso + PG strike version 1.2 + +-PG clustalw2 4_TCOFFEE CLUSTALW2 +-PG clustalw2 type sequence_multiple_aligner +-PG clustalw2 ADDRESS http://www.clustal.org +-PG clustalw2 language C++ +-PG clustalw2 language2 CXX +-PG clustalw2 source http://www.clustal.org/download/2.0.10/clustalw-2.0.10-src.tar.gz +-PG clustalw2 mode mcoffee,rcoffee +-PG clustalw2 version 2.0.10 ++PG clustalw 4_TCOFFEE CLUSTALW2 ++PG clustalw type sequence_multiple_aligner ++PG clustalw ADDRESS http://www.clustal.org ++PG clustalw language C++ ++PG clustalw language2 CXX ++PG clustalw source http://www.clustal.org/download/2.0.10/clustalw-2.0.10-src.tar.gz ++PG clustalw mode mcoffee,rcoffee ++PG clustalw version 2.0.10 + + PG clustalw 4_TCOFFEE CLUSTALW + PG clustalw type sequence_multiple_aligner diff --git a/debian/patches/series b/debian/patches/series index 3d413c2..53d7fb7 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -5,3 +5,4 @@ hardening.patch set_proper_dir_permissions.patch mayhem.patch stable-linking-inputs.patch +clustalw2.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/t-coffee.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
