Merge pull request #37 from athbaltzis/new_branch

Update ebi blast perl rest api
cbcrg · Oct 15, 2020 · 5becd5d · 5becd5d
2 parents 0818d8a + e03a1c7
commit 5becd5d
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diff --git a/lib/perl/lib/scripts/tc_generic_method.pl b/lib/perl/lib/scripts/tc_generic_method.pl
@@ -2611,7 +2611,7 @@ sub run_blast
 	    else
 	      {
 		if ( $cl_method =~/psiblast/){$cl_method ="blastp $psiJFlag";}
-		$command="t_coffee -other_pg ncbiblast_lwp.pl --email $EMAIL -D $db1 -p $cl_method --outfile $outfile --align 5 --stype protein $infile>/dev/null 2>$error_log";
+		$command="t_coffee -other_pg ncbiblast_lwp.pl --email $EMAIL --database $db1 --program $cl_method --outfile $outfile --alignments 5 --stype protein $infile>/dev/null 2>$error_log";
 		#DEBUG
 		#$command="t_coffee -other_pg ncbiblast_lwp.pl --email $EMAIL -D $db1 -p $cl_method --outfile $outfile --align 5 --stype protein $infile";