X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fformat_genome;h=9b3e4fe81790b7ea159efaad477bb5d87922dbad;hb=5de6112b70b59420b245ce636a8b2e3c90acbe00;hp=36cc541a6bb064399f4e8f41752c80766b312b5d;hpb=24d3b192da2b4949e44971f01abcb0831d49b6e2;p=biopieces.git

diff --git a/bp_bin/format_genome b/bp_bin/format_genome
index 36cc541..9b3e4fe 100755
--- a/bp_bin/format_genome
+++ b/bp_bin/format_genome
@@ -35,7 +35,6 @@ use Maasha::BWA;
 use Maasha::NCBI;
 use Maasha::Match;
 use Maasha::UCSC;
-use Maasha::Jbrowse;
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
@@ -46,7 +45,7 @@ my ( $default, $formats, $options, $in, $out, $record, $data_out, $entry,
 
 $tmp_dir = Maasha::Biopieces::get_tmpdir();
 $default = $ENV{ 'BP_DATA' };
-$formats = 'fasta,blast,vmatch,bowtie,bwa,phastcons,jbrowse';
+$formats = 'fasta,blast,vmatch,bowtie,bwa,phastcons';
 
 $options = Maasha::Biopieces::parse_options(
     [
@@ -66,7 +65,7 @@ $genome = $options->{ 'genome' };
 Maasha::Filesys::dir_create_if_not_exists( "$dir/genomes" );
 Maasha::Filesys::dir_create_if_not_exists( "$dir/genomes/$genome" );
 
-if ( grep { $_ =~ /fasta|blast|vmatch|bowtie|bwa|jbrowse/i } @{ $options->{ "formats" } } )
+if ( grep { $_ =~ /fasta|blast|vmatch|bowtie|bwa/i } @{ $options->{ "formats" } } )
 {
     if ( -f "$dir/genomes/$genome/fasta/$genome.fna" )
     {
@@ -123,7 +122,6 @@ foreach $format ( @{ $options->{ 'formats' } } )
     elsif ( $format =~ /^bowtie$/i )    { Maasha::Bowtie::bowtie_index( "$fasta_dir/$genome.fna", "$dir/genomes/$genome/bowtie", $genome, $options->{ 'verbose' } ) }
     elsif ( $format =~ /^bwa$/i )       { Maasha::BWA::bwa_index( "$fasta_dir/$genome.fna", "$dir/genomes/$genome/bwa", $genome, $options->{ 'verbose' } ) }
     elsif ( $format =~ /^phastcons$/i ) { Maasha::UCSC::phastcons_index( "$genome.pp", $phastcons_dir ) }
-    elsif ( $format =~ /^jbrowse$/i )   { Maasha::Jbrowse::install_seq( "$fasta_dir/$genome.fna", "$dir/genomes/$genome/jbrowse", $genome ) }
 
     print STDERR qq(done.\n) if $options->{ 'verbose' };
 }