updated BLAST to faster, smaller ncbi-blast-2.14.0+ binaries, also up…

…dated bin.tgz v3.6

CHANGES.txt

@@ -406,3 +406,5 @@
 22032023: annotate_cluster.pl -u produces unaligned complete sequences, flipped if required to facilitate multiple alignments
 28032023: added more dependencies required for compiling R packages in install_R_deps.R
 05052023: check that download_genomes_ncbi.pl still works with sample_genome.list
+15052023: updated BLAST to faster, smaller ncbi-blast-2.14.0+ binaries
+15052022: update install.pl and updated bin.tgz (v3.6)

install.pl

@@ -2,7 +2,7 @@
 
 # Script that checks/compiles software required by get_homologues[-est] and 
 # checks dependencies for first-time users.
-# last checked Apr2022
+# last checked May2023
 
 use strict;
 use warnings;
@@ -20,8 +20,8 @@
 my $DOWNLOADEXE = 'wget'; # add path if required, curl in MacOS
 my $BINTGZFILE = 'bin.tgz';
 my $BINOSXTGZFILE = 'binosx.tgz';
-my $BINURL = "https://github.com/eead-csic-compbio/get_homologues/releases/download/v3.5/$BINTGZFILE";
-my $BINOSXURL = "https://github.com/eead-csic-compbio/get_homologues/releases/download/v3.5/$BINOSXTGZFILE";
+my $BINURL = "https://github.com/eead-csic-compbio/get_homologues/releases/download/v3.6/$BINTGZFILE";
+my $BINOSXURL = "https://github.com/eead-csic-compbio/get_homologues/releases/download/v3.6/$BINOSXTGZFILE";
 
 my $PFAMSERVERURL   = 'ftp.ebi.ac.uk';
 my $PFAMFOLDER      = 'pub/databases/Pfam/current_release/';
@@ -40,7 +40,7 @@
   'GD'=>['libgd-gd2-perl','perl-GD','perl-GD','gd']
   );
 
-my $nonCOGS = 'diamond-0.8.25 hmmer-3.1b2 mcl-14-137 ncbi-blast-2.8.1+ phylip-3.695';
+my $nonCOGS = 'diamond-0.8.25 hmmer-3.1b2 mcl-14-137 ncbi-blast-2.14.0+ phylip-3.695';
 
 my ($SOguess,$output,$command,$cwd) = ('','','',getcwd());
 my ($downloadOK,$force_unsupervised,$noDBs) = (0,0,0);
@@ -244,7 +244,7 @@
   print "## Checking blast (lib/phyTools: \$ENV{'EXE_BLASTP'})\n";
 
   if($downloadOK){
-      $ENV{'EXE_BLASTP'} = $ENV{'MARFIL'}."/bin/ncbi-blast-2.8.1+/bin/blastp"
+      $ENV{'EXE_BLASTP'} = $ENV{'MARFIL'}."/bin/ncbi-blast-2.14.0+/bin/blastp"
   }
 
   $output = `$ENV{'EXE_BLASTP'} 2>&1`;

lib/phyTools.pm

@@ -1,5 +1,5 @@
 # Bruno Contreras-Moreira, Pablo Vinuesa
-# 2005-22 CCG/UNAM, Mexico, EEAD/CSIC, Zaragoza, Spain
+# 2005-23 CCG/UNAM, Mexico, EEAD/CSIC, Zaragoza, Spain
 # This is a collection of subroutines used in our projects,
 # including primers4clades and get_homologues
 
@@ -87,7 +87,7 @@ sub set_phyTools_env
 
   # BLAST
   if( ! defined($ENV{'BLAST_PATH'}) ){ 
-    $ENV{'BLAST_PATH'} = $ENV{'MARFIL'}.'bin/ncbi-blast-2.8.1+/bin/'; 
+    $ENV{'BLAST_PATH'} = $ENV{'MARFIL'}.'bin/ncbi-blast-2.14.0+/bin/'; 
     if(!-e $ENV{'BLAST_PATH'}){ 
       $ENV{'BLAST_PATH'} = ''; # should work if in PATH
     }