[med-svn] [t-coffee] 01/05: Executable in clustalw 2.x package is named clustalw
Andreas Tille
tille at debian.org
Sat Dec 17 17:48:38 UTC 2016
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 <tille at debian.org>
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 <tille at debian.org> 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 <tille at debian.org>
+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
--
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