/usr/bin/scan_gbrowse is in gbrowse 2.54+dfsg-2build1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 | #!/usr/bin/perl
eval 'exec /usr/bin/perl -S $0 ${1+"$@"}'
if 0; # not running under some shell
#$Id: scan_gbrowse.pl,v 1.1 2009-03-05 23:02:59 lstein Exp $
# This script scans the gbrowse at the indicated URL and returns track
# configuration stanzas for all tracks that are marked "discoverable."
# If the --cache <cachetime> argument is present, then results will be
# cached for <cachetime> seconds.
use strict;
use warnings;
use Getopt::Long;
use File::Spec;
use File::Basename 'basename';
use LWP::Simple;
use constant SECS_PER_DAY => 60*60*24;
my $cache_time = 0;
my $USAGE = <<USAGE;
Usage: $0 <gbrowse_url>
Scan the gbrowse2 instance at <gbrowse_url> for discoverable tracks
and create appropriate remote track configuration stanzas suitable for
incorporation into the local gbrowse2 config file.
Options:
--cache <cachetime> Cache the results in a temporary file
for cachetime seconds.
USAGE
;
GetOptions('cache=i' => \$cache_time) or die $USAGE;
my $url = shift or die $USAGE;
my $tmpdir = File::Spec->catfile(File::Spec->tmpdir,'gbrowse_scanner'.'_'.(getpwuid($<))[0]);
unless (-e $tmpdir && -d _) {
mkdir $tmpdir or die "Couldn't create $tmpdir: $!";
}
(my $fname = $url) =~ s!/!_!g;
my $cache_file = File::Spec->catfile($tmpdir,"$fname.cache");
my $dest_file = File::Spec->catfile($tmpdir,"$fname.dest");
build_cache($url,$dest_file,$cache_file)
unless -e $cache_file && ((-M $cache_file) * SECS_PER_DAY)<$cache_time;
open my $fh,'<',$cache_file or die "Couldn't open cache file $cache_file: $!";
print while <$fh>;
close $fh;
exit 0;
sub build_cache {
my ($url,$dest,$cache) = @_;
$url =~ s/\?.+//; # get rid of any CGI args there already
my $source = basename($url);
$url .= '/' unless $url =~ /\/$/;
my $response = mirror("$url?gbgff=scan",$dest);
if (is_error($response)) {
die "Could not scan $url. Status code was $response";
}
open my $fh,'<',$dest or die "Could not open $dest: $!";
open my $out,'>',$cache or die "Could not open $cache for writing: $!";
my ($hostname) = $url =~ /^\w+:\/\/([^\/]+)/;
(my $colon_escape = $url) =~ s/:/\\:/g;
# paragraph mode to read stanzas
local $/ = '';
while (<$fh>) {
my ($label,$rest) = /\[([^\]]+)\]\s+(.+)/s;
my $remote = "$url?gbgff=1;s=1;t=$label;segment=\$segment";
chomp($rest);
print $out <<END;
[${hostname}_${source}_${label}]
remote feature = $remote
category = Tracks from $colon_escape
$rest
END
;
}
close $out;
close $fh;
}
__END__
|