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 <[email protected]> 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" <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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