[med-svn] [Git][med-team/t-coffee][master] Better way to deal with .pl extension in blast tools

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / t-coffee


Commits:
773699b7 by Andreas Tille at 2020-04-20T17:44:30+02:00
Better way to deal with .pl extension in blast tools

- - - - -


4 changed files:

- debian/changelog
- + debian/patches/bypass_legacy_blast.patch
- debian/patches/probconsrna.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+t-coffee (13.41.0.28bdc39+dfsg-2) UNRELEASED; urgency=medium
+
+  [ Aaron M. Ucko ]
+  * Better way to deal with .pl extension in blast tools
+
+ -- Andreas Tille <tille at debian.org>  Mon, 20 Apr 2020 17:43:49 +0200
+
 t-coffee (13.41.0.28bdc39+dfsg-1) unstable; urgency=medium
 
   [ Michael R. Crusoe ]


=====================================
debian/patches/bypass_legacy_blast.patch
=====================================
@@ -0,0 +1,49 @@
+Date: Mon, 20 Apr 2020 10:52:40 -0400
+From: "Aaron M. Ucko" <ucko at debian.org>
+Origin: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=956848#20
+Description: See origin
+
+--- a/example/tc_generic_method.pl
++++ b/example/tc_generic_method.pl
+@@ -1183,7 +1183,7 @@ sub pg_is_installed
+ 	if ($r eq ""){$r=0;}
+ 	else {$r=1;}
+ 
+-	if ($r==0 && is_blast_package ($p)){return pg_is_installed ("legacy_blast.pl");}
++	if ($r==0 && is_blast_package ($p)){return pg_is_installed ("blastn");}
+ 	else {return $r;}
+       }
+   }
+@@ -2611,26 +2611,20 @@ sub run_blast
+ 			$cl_db=$db;
+ 	    }
+ 
+-        ##
+ 		## BLAST+ provide different binaries names and CLI options
+-		## Use the 'legacy_blast.pl' to keep compatibility with old blast commands
+-		##
+-		$path=`which legacy_blast.pl 2>/dev/null`;  
+-		$path=`dirname $path`; 
+-		chomp($path);
+ 	    if ($method eq "blastp"){
+-			&check_configuration("legacy_blast.pl");
+-			$command="legacy_blast.pl blastpgp --path $path -d $cl_db -i $infile -o $outfile -m7 -j1";
++			&check_configuration("psiblast");
++			$command="psiblast -db $cl_db -query $infile -num_iterations 1 -out $outfile -outfmt 5";
+ 	    }
+ 	    elsif ($method eq "psiblast")
+ 	      {
+-		&check_configuration("legacy_blast.pl");
+-		$command="legacy_blast.pl blastpgp --path $path -d $cl_db -i $infile -o $outfile -m7 -j5";
++		&check_configuration("psiblast");
++		$command="psiblast -db $cl_db -query $infile -num_iterations 5 -out $outfile -outfmt 5";
+ 	      }
+ 	    elsif ($method eq "blastn")
+ 	      {
+-		&check_configuration("legacy_blast.pl");
+-		$command="legacy_blast.pl blastall --path $path -p blastn -d $cl_db -i $infile -o $outfile -m7 -W6";
++		&check_configuration("blastn");
++		$command="blastn -task blastn -db $cl_db -query $infile -word_size 6 -out $outfile -outfmt 5";
+ 	      }
+ 	    print "$command\n";
+ 	    &safe_system ($command);


=====================================
debian/patches/probconsrna.patch
=====================================
@@ -3,8 +3,8 @@ Description: Debian-specific adjustment.
 Forwarded: not-needed
 Last-Update: Sat, 16 Aug 2014 00:19:42 +0200
 
---- T-COFFEE_distribution_Version_11.00.8cbe486.orig/t_coffee_source/data_headers/programmes_define.h
-+++ T-COFFEE_distribution_Version_11.00.8cbe486/t_coffee_source/data_headers/programmes_define.h
+--- a/t_coffee_source/data_headers/programmes_define.h
++++ b/t_coffee_source/data_headers/programmes_define.h
 @@ -68,7 +68,7 @@
  #define POA_FILE1 "blosum80.mat"
  


=====================================
debian/patches/series
=====================================
@@ -1,5 +1,6 @@
 probconsrna.patch
-ncbi-blast++_has_dropped_pl_extension.patch
+# ncbi-blast++_has_dropped_pl_extension.patch
+bypass_legacy_blast.patch
 use_debian_packaged_TMalign.patch
 hardening.patch
 set_proper_dir_permissions.patch



View it on GitLab: https://salsa.debian.org/med-team/t-coffee/-/commit/773699b71310396b4dc03d964cd117c84ee4ed22

-- 
View it on GitLab: https://salsa.debian.org/med-team/t-coffee/-/commit/773699b71310396b4dc03d964cd117c84ee4ed22
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