Merge pull request #20 from mhalagan-nmdp/v1.0.5

V1.0.5
nmdp-bioinformatics · Nov 30, 2016 · 360abe7 · 360abe7
2 parents 198ec32 + 33fdbf2
commit 360abe7
Show file tree

Hide file tree

Showing 17 changed files with 714 additions and 283 deletions.
diff --git a/GFE_Submission/Makefile.PL b/GFE_Submission/Makefile.PL
@@ -68,7 +68,8 @@ WriteMakefile(
         'IO::Socket::SSL' => 0,
         'REST::Client' => 0,
         'Math::Round' => 0,
-        'File::Spec' => 0
+        'File::Spec' => 0,
+        'XML::DOM' => 0
     },
     dist                => { COMPRESS => 'gzip -9f', SUFFIX => 'gz', },
     clean               => { FILES => 'GFE_Submission-*' },

diff --git a/GFE_Submission/bin/app.pl b/GFE_Submission/bin/app.pl
@@ -38,7 +38,7 @@ =head1 LICENSE
 set 'logger'       => 'console';
 set 'session'      => 'Simple';
 set 'log'          => 'debug';
-set 'serializer'   => 'JSON'; 
+
 set 'show_errors'  => 1;
 set 'startup_info' => 1;
 set 'warnings'     => 1;

diff --git a/GFE_Submission/bin/fasta2gfe b/GFE_Submission/bin/fasta2gfe
@@ -80,10 +80,7 @@ use Cwd;
 our($s_subject_id) = (undef);
 &GetOptions('subject|i=s' => \$s_subject_id );
 
-my $o_gfe = GFE->new();
 
-$o_gfe->verbose(1);
-$o_gfe->return_structure(0);
 
 my %h_seqs;
 my $s_header;
@@ -115,6 +112,7 @@ foreach my $s_typing (keys %h_seqs){
     my $s_locus = $1;
     $s_locus =~ s/\|//g;
     next if(!defined $s_locus || $s_locus !~ /\S/);
+    my $o_gfe = GFE->new();
     my $rh_gfe = $o_gfe->getGfe($s_locus,$h_seqs{$s_typing});
     my $s_gfe  = defined $$rh_gfe{gfe} ? $$rh_gfe{gfe} : '';
     next if !defined $s_gfe || $s_gfe !~ /\S/;

diff --git a/GFE_Submission/bin/gfe_test.pl b/GFE_Submission/bin/gfe_test.pl
@@ -65,10 +65,10 @@ =head1 SUBROUTINES
 $o_gfe->verbose(1);
 $o_gfe->return_structure(0);
 
-my $s_path = `echo \$PATH`;chomp($s_path);
-foreach my $s_p (split(/:/,$s_path)){
-    print STDERR "PATH: ".$s_p,"\n";
-}
+# my $s_path = `echo \$PATH`;chomp($s_path);
+# foreach my $s_p (split(/:/,$s_path)){
+#     print STDERR "PATH: ".$s_p,"\n";
+# }
 
 my $s_hml   = "$FindBin::Bin/../t/resources/hmltest1.HML";
 my $rh_gfe  = $o_gfe->getGfeHmlNextflow($s_hml);