use Maasha::NCBI;
use Maasha::Match;
use Maasha::UCSC;
-use Maasha::Jbrowse;
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
$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';
$options = Maasha::Biopieces::parse_options(
[
Maasha::Filesys::dir_create_if_not_exists( "$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" )
{
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' };
}