diff bin/downloaddb.pl @ 1:adc0f7765d85 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/downloaddb.pl	Thu Sep 07 15:06:58 2017 -0400
@@ -0,0 +1,54 @@
+use strict;
+use Cwd;
+
+my %flags=(
+	"hg18"=>0,
+	"mm9"=>0,
+	"rn4"=>0,
+);
+my $PROG = $0;
+my $PROG_ABS_PATH = Cwd::abs_path($PROG);
+$PROG_ABS_PATH = `dirname $PROG_ABS_PATH`;
+chomp($PROG_ABS_PATH);
+print "\n\tPrepare to download databases from CSHL...\n";
+
+print "\tWhich database(s) do you want to download?\n";
+print "\tChoose from\t ";
+foreach my $key (keys %flags)
+{
+	print $key,"/";
+}
+print "ALL \n\n\tseparated by blank...don't enter anything if you don't want to download!\n\nPlease enter:[NONE]";
+
+my @dbnames = split(/\s+/,<>);
+for (my $i=0;$i<@dbnames;$i++)
+{
+	if (uc($dbnames[$i]) eq "ALL" )
+	{
+	foreach my $key (keys %flags)
+	{
+		$flags{$key}=1;
+	}
+	last;
+	}
+	
+	if( exists $flags{$dbnames[$i]})
+	{
+		$flags{$dbnames[$i]} = 1;
+	}
+	#system ("wget http://rulai.cshl.edu/splicetrap/db/")		
+}
+
+foreach my $key (keys %flags)
+{
+	if ($flags{$key} ==1)
+	{
+		system ("wget http://rulai.cshl.edu/splicetrap/db/".$key.".tar.gz");
+		print "untar the database file for $key...please wait...";
+		system ("tar -ixzf $key.tar.gz");
+		system ("rm $key.tar.gz");
+		mkdir "$key/parallel";
+		print "creating files for parallel computing...\n";
+		system("bash $PROG_ABS_PATH/splitdb.sh $key/parallel")
+	}
+}