Add run.pl for manual run

run.pl

@@ -0,0 +1,86 @@
+#! /usr/bin/perl
+
+#Copyright (C) 2015 Feiyu Du <[email protected]>
+#              and Washington University The Genome Institute
+
+#This script is distributed in the hope that it will be useful, 
+#but WITHOUT ANY WARRANTY or the implied warranty of 
+#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the 
+#GNU General Public License for more details.
+
+
+use strict;
+use warnings;
+use File::Spec;
+use File::Basename;
+use IO::File;
+
+umask 002;
+
+die "Provide batch_name, index_mapping_tsv, instrument_data_id, flow_cell_id, lane_number, csf_raw_fastq_dir" unless @ARGV and @ARGV == 6;
+my ($name, $map_tsv, $instrument_id, $flow_cell_id, $lane_num, $fastq_dir) = @ARGV;
+
+unless (-d $fastq_dir) {
+    die "csq_fastq_dir $fastq_dir is not valid";
+}
+
+unless ($lane_num =~ /^\d+$/) {
+    die "lane_number $lane_num is not a number";
+}
+
+my $dir = '/gscmnt/gc13016/cle/54f8f7b915cb472aa183c721307369ab_scratch_space/myeloseq/RUN';
+my $out_dir = $dir . '/wdl_out';
+my $log_dir = $dir . '/log';
+my $wdl_path = $dir . '/Haloplex.wdl';
+my $template_json = $dir.'/template.json';
+my $conf_path = $dir . '/application.conf';
+
+my $run_dir = $out_dir . "/$name";
+unless (mkdir $run_dir) {
+    die "Failed to make directory $run_dir";
+}
+
+my $pu = join '.', $flow_cell_id, $lane_num;
+
+my $sample_index  = $run_dir . '/sample_index';
+my $json_file     = $run_dir . '/Haloplex.json';
+
+my $in_fh    = IO::File->new($map_tsv);
+my $index_fh = IO::File->new(">$sample_index");
+
+while (my $line = $in_fh->getline) {
+    chomp $line;
+    my ($index, $lib_name) = split /\t/, $line;
+    my ($sample) = $lib_name =~ /^(\S+?)\-lib\d+/;
+    my $rg_str = '@RG\tPU:'.$pu.'\tLB:'.$lib_name.'\tID:'.$instrument_id.'\tSM:'.$sample.'\tPL:ILLUMINA\tCN:WUGSC';
+    $index_fh->print(join "\t", $index, $lib_name, $rg_str);
+    $index_fh->print("\n");
+}
+$in_fh->close;
+$index_fh->close;
+
+my $template_json_fh = IO::File->new($template_json);
+my $json_fh  = IO::File->new(">$json_file");
+
+while (my $l = $template_json_fh->getline) {
+    if ($l =~ /SampleSheet/) {
+        $l =~ s/PATH/$sample_index/;
+    }
+    elsif ($l =~ /OutputDir/) {
+        $l =~ s/PATH/$run_dir/;
+    }
+    elsif ($l =~ /IlluminaDir/) {
+        $l =~ s/PATH/$fastq_dir/;
+    }
+    $json_fh->print($l);
+}
+$template_json_fh->close;
+$json_fh->close;
+
+my $out_log = File::Spec->join($dir, 'log', $name.'.out');
+my $err_log = File::Spec->join($dir, 'log', $name.'.err');
+
+`bsub -oo $out_log -eo $err_log -q compute-mgi-cle -R "select[mem>8000] rusage[mem=8000]" -M 8000000 -a "docker(sleongmgi/cromwell:develop-with-mysql)" /usr/bin/java -Dconfig.file=$conf_path -jar /cromwell/cromwell.jar run $wdl_path $json_file`;
+
+print "$name job submitted\n";
+