[med-svn] r15313 - in trunk/packages/t-coffee/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Fri Nov 29 09:34:53 UTC 2013
Author: tille
Date: 2013-11-29 09:34:53 +0000 (Fri, 29 Nov 2013)
New Revision: 15313
Added:
trunk/packages/t-coffee/trunk/debian/patches/ncbi-blast++_has_dropped_pl_extension.patch
Modified:
trunk/packages/t-coffee/trunk/debian/changelog
trunk/packages/t-coffee/trunk/debian/patches/series
Log:
Cope with renamings of *.pl scripts in ncbi-blast++
Modified: trunk/packages/t-coffee/trunk/debian/changelog
===================================================================
--- trunk/packages/t-coffee/trunk/debian/changelog 2013-11-29 09:33:51 UTC (rev 15312)
+++ trunk/packages/t-coffee/trunk/debian/changelog 2013-11-29 09:34:53 UTC (rev 15313)
@@ -1,9 +1,18 @@
-t-coffee (10.00.r1613-2) UNRELEASED; urgency=low
+t-coffee (10.00.r1613-1) UNRELEASED; urgency=low
+ [ Charles Plessy ]
* Suggest ncbi-blast+.
- -- Charles Plessy <plessy at debian.org> Fri, 29 Nov 2013 07:59:07 +0900
+ [ Andreas Tille ]
+ * debian/patches/ncbi-blast++_has_dropped_pl_extension.patch:
+ since ncbi-blast++ has renamed some perl scripts according to
+ Debian policy t-coffee needs to be adapted:
+ s/legacy_blast\.pl/legacy_blast/
+ s/blastpgp\.pl/blastpgp/
+ Closes: #730722
+ -- Andreas Tille <tille at debian.org> Fri, 29 Nov 2013 10:27:47 +0100
+
t-coffee (10.00.r1613-1) unstable; urgency=low
* New upstream release.
Added: trunk/packages/t-coffee/trunk/debian/patches/ncbi-blast++_has_dropped_pl_extension.patch
===================================================================
--- trunk/packages/t-coffee/trunk/debian/patches/ncbi-blast++_has_dropped_pl_extension.patch (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/patches/ncbi-blast++_has_dropped_pl_extension.patch 2013-11-29 09:34:53 UTC (rev 15313)
@@ -0,0 +1,241 @@
+Author: Andreas Tille <tille at debian.org>
+LastChanged: Fri, 29 Nov 2013 10:27:47 +0100
+BugsDebian: http://bugs.debian.org/730722
+Description: Cope with renaming of scripts in ncbi-blast++
+ Since ncbi-blast++ has renamed some perl scripts according to
+ Debian policy (section 10.4) t-coffee needs to be adapted:
+ s/legacy_blast\.pl/legacy_blast/
+ s/blastpgp\.pl/blastpgp/
+
+--- a/t_coffee_source/define_header.h
++++ b/t_coffee_source/define_header.h
+@@ -651,7 +651,7 @@
+ #define EBIWUBLASTc_source "empty"
+ #define EBIWUBLASTc_update_action "never"
+ #define EBIWUBLASTc_mode "psicoffee,expresso,accurate"
+-#define EBIBLASTPGPc_4_TCOFFEE "blastpgp.pl"
++#define EBIBLASTPGPc_4_TCOFFEE "blastpgp"
+ #define EBIBLASTPGPc_type "protein_homology_predictor"
+ #define EBIBLASTPGPc_ADDRESS "built_in"
+ #define EBIBLASTPGPc_ADDRESS2 "http://www.ebi.ac.uk/Tools/webservices/services/blastpgp"
+@@ -676,7 +676,7 @@
+ #define blastall_source "empty"
+ #define blastall_update_action "never"
+ #define blastall_mode "psicoffee,expresso,3dcoffee"
+-#define NCBIBLAST_4_TCOFFEE "legacy_blast.pl"
++#define NCBIBLAST_4_TCOFFEE "legacy_blast"
+ #define NCBIBLAST_type "protein_homology_predictor"
+ #define NCBIBLAST_ADDRESS "ftp://ftp.ncbi.nih.gov/blast/executables/LATEST"
+ #define NCBIBLAST_language "C"
+--- a/t_coffee_source/perl_header_lib.h
++++ b/t_coffee_source/perl_header_lib.h
+@@ -4,7 +4,7 @@ msa2bootstrap.pl","t_coffee_dpa","t_coff
+ tc_generic_method.pl","generic_method.tc_method","\
+ clustalw_method.tc_method","extract_from_pdb","ins\
+ tall.pl","clean_cache.pl","nature_protocol.pl","mo\
+-cca","dalilite.pl","wublast.pl","blastpgp.pl","ncb\
++cca","dalilite.pl","wublast.pl","blastpgp","ncb\
+ iblast_lwp.pl","wublast_lwp.pl","RNAplfold2tclib.p\
+ l","fasta_seq2RNAplfold_templatefile.pl","fasta_se\
+ q2hmmtop_fasta.pl","fasta_seq2consan_aln.pl","clus\
+@@ -2379,7 +2379,7 @@ se lock\n\n if ( $debug_lock ){print
+ ;\n }\n\nsub blast_com2new_blast_com\n {\n \
+ my $com=shift;\n if ($ENV{\"NCBI_BLAST_4_TC\
+ OFFEE\"} eq \"OLD\"){return $com;}\n elsif (!\
+-&pg_is_installed(\"legacy_blast.pl\")){return $com\
++&pg_is_installed(\"legacy_blast\")){return $com\
+ ;}\n else\n {\n if ($com=~/formatdb/)\n \
+ {\n $com=~s/formatdb/makeblastdb/;\n \
+ $com=~s/\\-i/\\-in/;\n if ($com =~/pF/){$com\
+@@ -2390,13 +2390,13 @@ n }\n elsif ($com =~/^blastn/){ret
+ \n elsif (&is_blast_package($com))\n {\n \
+ my $path;\n\n if ( $ENV{\"NCBI_BIN_4_TCOF\
+ FEE\"}){$path=$ENV{\"NCBI_BLAST_4_TCOFFEE\"};}\n \
+- else\n {\n $path=`which legacy_blast.pl`;\
++ else\n {\n $path=`which legacy_blast`;\
+ \n $path=~s/\\/legacy_blast\\.pl//;\n chomp \
+ ($path);\n }\n $path=\"--path $path\";\n \
+ if ( $com=~/\\>\\>/){$com=~s/\\>\\>/ $path \\>\
+ \\>/;}\n elsif ( $com=~/\\>/){$com=~s/\\>/ $\
+ path \\>/;}\n else {$com.=\" $path\";}\n \
+- $com=\"legacy_blast.pl $com\";\n\n return\
++ $com=\"legacy_blast $com\";\n\n return\
+ $com;\n }\n }\n }\nsub safe_system\n{\n m\
+ y $com=shift;\n my $ntry=shift;\n my $ctry=shift\
+ ;\n my $pid;\n my $status;\n my $ppid=getppid()\
+@@ -5571,16 +5571,16 @@ ervices/wublast\";\n$PG{\"wublast.pl\"}{
+ \"Perl\";\n$PG{\"wublast.pl\"}{\"source\"}=\"empty\
+ \";\n$PG{\"wublast.pl\"}{\"update_action\"}=\"neve\
+ r\";\n$PG{\"wublast.pl\"}{\"mode\"}=\"psicoffee,ex\
+-presso,accurate\";\n$PG{\"blastpgp.pl\"}{\"4_TCOFF\
+-EE\"}=\"EBIBLASTPGPc\";\n$PG{\"blastpgp.pl\"}{\"ty\
++presso,accurate\";\n$PG{\"blastpgp\"}{\"4_TCOFF\
++EE\"}=\"EBIBLASTPGPc\";\n$PG{\"blastpgp\"}{\"ty\
+ pe\"}=\"protein_homology_predictor\";\n$PG{\"blast\
+ pgp.pl\"}{\"ADDRESS\"}=\"built_in\";\n$PG{\"blastp\
+ gp.pl\"}{\"ADDRESS2\"}=\"http://www.ebi.ac.uk/Tool\
+ s/webservices/services/blastpgp\";\n$PG{\"blastpgp\
+-.pl\"}{\"language\"}=\"Perl\";\n$PG{\"blastpgp.pl\\
+-"}{\"language2\"}=\"Perl\";\n$PG{\"blastpgp.pl\"}{\
+-\"source\"}=\"empty\";\n$PG{\"blastpgp.pl\"}{\"upd\
+-ate_action\"}=\"never\";\n$PG{\"blastpgp.pl\"}{\"m\
++.pl\"}{\"language\"}=\"Perl\";\n$PG{\"blastpgp\\
++"}{\"language2\"}=\"Perl\";\n$PG{\"blastpgp\"}{\
++\"source\"}=\"empty\";\n$PG{\"blastpgp\"}{\"upd\
++ate_action\"}=\"never\";\n$PG{\"blastpgp\"}{\"m\
+ ode\"}=\"psicoffee,expresso,accurate\";\n$PG{\"bla\
+ stcl3\"}{\"4_TCOFFEE\"}=\"NCBIWEBBLAST\";\n$PG{\"b\
+ lastcl3\"}{\"type\"}=\"protein_homology_predictor\\
+@@ -5599,15 +5599,15 @@ ables/LATEST\";\n$PG{\"blastall\"}{\"lan
+ G{\"blastall\"}{\"source\"}=\"empty\";\n$PG{\"blas\
+ tall\"}{\"update_action\"}=\"never\";\n$PG{\"blast\
+ all\"}{\"mode\"}=\"psicoffee,expresso,3dcoffee\";\\
+-n$PG{\"legacy_blast.pl\"}{\"4_TCOFFEE\"}=\"NCBIBLA\
+-ST\";\n$PG{\"legacy_blast.pl\"}{\"type\"}=\"protei\
+-n_homology_predictor\";\n$PG{\"legacy_blast.pl\"}{\
++n$PG{\"legacy_blast\"}{\"4_TCOFFEE\"}=\"NCBIBLA\
++ST\";\n$PG{\"legacy_blast\"}{\"type\"}=\"protei\
++n_homology_predictor\";\n$PG{\"legacy_blast\"}{\
+ \"ADDRESS\"}=\"ftp://ftp.ncbi.nih.gov/blast/execut\
+-ables/LATEST\";\n$PG{\"legacy_blast.pl\"}{\"langua\
+-ge\"}=\"C\";\n$PG{\"legacy_blast.pl\"}{\"language2\
+-\"}=\"C\";\n$PG{\"legacy_blast.pl\"}{\"source\"}=\\
+-"empty\";\n$PG{\"legacy_blast.pl\"}{\"update_actio\
+-n\"}=\"never\";\n$PG{\"legacy_blast.pl\"}{\"mode\"\
++ables/LATEST\";\n$PG{\"legacy_blast\"}{\"langua\
++ge\"}=\"C\";\n$PG{\"legacy_blast\"}{\"language2\
++\"}=\"C\";\n$PG{\"legacy_blast\"}{\"source\"}=\\
++"empty\";\n$PG{\"legacy_blast\"}{\"update_actio\
++n\"}=\"never\";\n$PG{\"legacy_blast\"}{\"mode\"\
+ }=\"psicoffee,expresso,3dcoffee\";\n$PG{\"SOAP::Li\
+ te\"}{\"4_TCOFFEE\"}=\"SOAPLITE\";\n$PG{\"SOAP::Li\
+ te\"}{\"type\"}=\"library\";\n$PG{\"SOAP::Lite\"}{\
+@@ -6432,7 +6432,7 @@ sults should be written to\n
+ ile is written)\n --trace : : \
+ show SOAP messages being interchanged\n\nSynchrono\
+ us job:\n\n The results/errors are returned as so\
+-on as the job is finished.\n Usage: blastpgp.pl -\
++on as the job is finished.\n Usage: blastpgp -\
+ -email <your at email> [options...] seqfile\n Return\
+ s: saves the results to disk\n\nAsynchronous job:\\
+ n\n Use this if you want to retrieve the results \
+@@ -6442,7 +6442,7 @@ s recommended when users are submitting\
+ obs or large database searches\n Usage: blastpgp.\
+ pl --email <your at email> --async [options...] seqFi\
+ le\n Returns: jobid\n\n Use the jobid to query f\
+-or the status of the job.\n Usage: blastpgp.pl --\
++or the status of the job.\n Usage: blastpgp --\
+ status --jobid <jobId>\n Returns: string indicati\
+ ng the status of the job\n DONE - job has finis\
+ hed\n RUNNING - job is running\n NOT_FOUND -\
+--- a/install
++++ b/install
+@@ -1795,15 +1795,15 @@ $PG{"wublast.pl"}{"language2"}="Perl";
+ $PG{"wublast.pl"}{"source"}="empty";
+ $PG{"wublast.pl"}{"update_action"}="never";
+ $PG{"wublast.pl"}{"mode"}="psicoffee,expresso,accurate";
+-$PG{"blastpgp.pl"}{"4_TCOFFEE"}="EBIBLASTPGPc";
+-$PG{"blastpgp.pl"}{"type"}="protein_homology_predictor";
+-$PG{"blastpgp.pl"}{"ADDRESS"}="built_in";
+-$PG{"blastpgp.pl"}{"ADDRESS2"}="http://www.ebi.ac.uk/Tools/webservices/services/blastpgp";
+-$PG{"blastpgp.pl"}{"language"}="Perl";
+-$PG{"blastpgp.pl"}{"language2"}="Perl";
+-$PG{"blastpgp.pl"}{"source"}="empty";
+-$PG{"blastpgp.pl"}{"update_action"}="never";
+-$PG{"blastpgp.pl"}{"mode"}="psicoffee,expresso,accurate";
++$PG{"blastpgp"}{"4_TCOFFEE"}="EBIBLASTPGPc";
++$PG{"blastpgp"}{"type"}="protein_homology_predictor";
++$PG{"blastpgp"}{"ADDRESS"}="built_in";
++$PG{"blastpgp"}{"ADDRESS2"}="http://www.ebi.ac.uk/Tools/webservices/services/blastpgp";
++$PG{"blastpgp"}{"language"}="Perl";
++$PG{"blastpgp"}{"language2"}="Perl";
++$PG{"blastpgp"}{"source"}="empty";
++$PG{"blastpgp"}{"update_action"}="never";
++$PG{"blastpgp"}{"mode"}="psicoffee,expresso,accurate";
+ $PG{"blastcl3"}{"4_TCOFFEE"}="NCBIWEBBLAST";
+ $PG{"blastcl3"}{"type"}="protein_homology_predictor";
+ $PG{"blastcl3"}{"ADDRESS"}="ftp://ftp.ncbi.nih.gov/blast/executables/LATEST";
+@@ -1820,14 +1820,14 @@ $PG{"blastall"}{"language2"}="C";
+ $PG{"blastall"}{"source"}="empty";
+ $PG{"blastall"}{"update_action"}="never";
+ $PG{"blastall"}{"mode"}="psicoffee,expresso,3dcoffee";
+-$PG{"legacy_blast.pl"}{"4_TCOFFEE"}="NCBIBLAST";
+-$PG{"legacy_blast.pl"}{"type"}="protein_homology_predictor";
+-$PG{"legacy_blast.pl"}{"ADDRESS"}="ftp://ftp.ncbi.nih.gov/blast/executables/LATEST";
+-$PG{"legacy_blast.pl"}{"language"}="C";
+-$PG{"legacy_blast.pl"}{"language2"}="C";
+-$PG{"legacy_blast.pl"}{"source"}="empty";
+-$PG{"legacy_blast.pl"}{"update_action"}="never";
+-$PG{"legacy_blast.pl"}{"mode"}="psicoffee,expresso,3dcoffee";
++$PG{"legacy_blast"}{"4_TCOFFEE"}="NCBIBLAST";
++$PG{"legacy_blast"}{"type"}="protein_homology_predictor";
++$PG{"legacy_blast"}{"ADDRESS"}="ftp://ftp.ncbi.nih.gov/blast/executables/LATEST";
++$PG{"legacy_blast"}{"language"}="C";
++$PG{"legacy_blast"}{"language2"}="C";
++$PG{"legacy_blast"}{"source"}="empty";
++$PG{"legacy_blast"}{"update_action"}="never";
++$PG{"legacy_blast"}{"mode"}="psicoffee,expresso,3dcoffee";
+ $PG{"SOAP::Lite"}{"4_TCOFFEE"}="SOAPLITE";
+ $PG{"SOAP::Lite"}{"type"}="library";
+ $PG{"SOAP::Lite"}{"ADDRESS"}="http://cpansearch.perl.org/src/MKUTTER/SOAP-Lite-0.710.08/Makefile.PL";
+--- a/tclinkdb.txt
++++ b/tclinkdb.txt
+@@ -292,15 +292,15 @@ PG wublast.pl source empty
+ PG wublast.pl update_action never
+ PG wublast.pl mode psicoffee,expresso,accurate
+
+-PG blastpgp.pl 4_TCOFFEE EBIBLASTPGPc
+-PG blastpgp.pl type protein_homology_predictor
+-PG blastpgp.pl ADDRESS built_in
+-PG blastpgp.pl ADDRESS2 http://www.ebi.ac.uk/Tools/webservices/services/blastpgp
+-PG blastpgp.pl language Perl
+-PG blastpgp.pl language2 Perl
+-PG blastpgp.pl source empty
+-PG blastpgp.pl update_action never
+-PG blastpgp.pl mode psicoffee,expresso,accurate
++PG blastpgp 4_TCOFFEE EBIBLASTPGPc
++PG blastpgp type protein_homology_predictor
++PG blastpgp ADDRESS built_in
++PG blastpgp ADDRESS2 http://www.ebi.ac.uk/Tools/webservices/services/blastpgp
++PG blastpgp language Perl
++PG blastpgp language2 Perl
++PG blastpgp source empty
++PG blastpgp update_action never
++PG blastpgp mode psicoffee,expresso,accurate
+
+
+ PG blastcl3 4_TCOFFEE NCBIWEBBLAST
+@@ -321,14 +321,14 @@ PG blastall source empty
+ PG blastall update_action never
+ PG blastall mode psicoffee,expresso,3dcoffee
+
+-PG legacy_blast.pl 4_TCOFFEE NCBIBLAST
+-PG legacy_blast.pl type protein_homology_predictor
+-PG legacy_blast.pl ADDRESS ftp://ftp.ncbi.nih.gov/blast/executables/LATEST
+-PG legacy_blast.pl language C
+-PG legacy_blast.pl language2 C
+-PG legacy_blast.pl source empty
+-PG legacy_blast.pl update_action never
+-PG legacy_blast.pl mode psicoffee,expresso,3dcoffee
++PG legacy_blast 4_TCOFFEE NCBIBLAST
++PG legacy_blast type protein_homology_predictor
++PG legacy_blast ADDRESS ftp://ftp.ncbi.nih.gov/blast/executables/LATEST
++PG legacy_blast language C
++PG legacy_blast language2 C
++PG legacy_blast source empty
++PG legacy_blast update_action never
++PG legacy_blast mode psicoffee,expresso,3dcoffee
+
+ PG SOAP::Lite 4_TCOFFEE SOAPLITE
+ PG SOAP::Lite type library
+--- a/t_coffee_source/util_constraints_list.c
++++ b/t_coffee_source/util_constraints_list.c
+@@ -6340,7 +6340,7 @@ char *** produce_method_file ( char *met
+ sprintf (list[n][0], "blastpgp_client");
+ 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 blastpgp.pl \n");
++ fprintf ( fp, "EXECUTABLE blastpgp \n");
+ fprintf ( fp, "ALN_MODE predict\n");
+ fprintf ( fp, "SEQ_TYPE PROTEIN\n");
+
Modified: trunk/packages/t-coffee/trunk/debian/patches/series
===================================================================
--- trunk/packages/t-coffee/trunk/debian/patches/series 2013-11-29 09:33:51 UTC (rev 15312)
+++ trunk/packages/t-coffee/trunk/debian/patches/series 2013-11-29 09:34:53 UTC (rev 15313)
@@ -1 +1,2 @@
probconsrna.patch
+ncbi-blast++_has_dropped_pl_extension.patch
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