Merge branch 'release/2.0.8'

.gitignore

@@ -1,2 +1,3 @@
 vcf
 xml*
+metadata_upload.log

README.md

@@ -37,6 +37,10 @@ If you are using the Docker version everything will be setup for you.  If not, y
 Or on an Ubuntu 12.04 host you would install via:
 
     sudo apt-get install libxml-dom-perl libxml-xpath-perl libjson-perl libxml-libxml-perl time libdata-uuid-libuuid-perl libcarp-always-perl libipc-system-simple-perl
+
+On Ubuntu 14.04 you would install:
+
+    sudo apt-get install -y python-dev python-pip libxml-dom-perl libxml-xpath-perl libjson-perl libxml-libxml-perl time libdata-uuid-libuuid-perl libcarp-always-perl libipc-system-simple-perl libdata-uuid-perl curl vim samtools tabix
 
 Once these are installed you can execute the script with the command below. For workflows and VMs used in the project, these dependencies will be pre-installed on the VM running the variant calling workflows.
 

gnos_upload_vcf.pl

@@ -97,6 +97,7 @@
 my $help = 0;
 my $workflow_file_subset = "";
 my $related_file_subset_uuids = "";
+my $gto_only = 0;
 
 # TODO: check the argument counts here
 if ( scalar(@ARGV) == 0 ) {
@@ -146,6 +147,7 @@
     "help"                       => \$help,
     "workflow-file-subset=s"     => \$workflow_file_subset,
     "related-file-subset-uuids=s" => \$related_file_subset_uuids,
+    "gto-only"                   => \$gto_only
 );
 
 # if --help
@@ -307,6 +309,7 @@ sub get_usage {
      [--upload-archive <path_of_dir_to_copy_upload_to_and_make_tarball_uuid.tar.gz>]
      [--uuid <uuis_for_use_as_upload_analysis_id>]
      [--test]
+     [--gto-only Pass the --gto-only flag to gtupload. GTO file will be generated, but no upload will occur. Do NOT use this flag with --skip-validate.]
      \n"
 }
 
@@ -429,7 +432,6 @@ sub validate_submission {
 # TODO: need to standardize on the return values... 1 or 0!!
 sub upload_submission {
     my ($sub_path) = @_;
-
     my $cmd = "cgsubmit -s $upload_url -o metadata_upload.log -u $sub_path -vv -c $key";
     say "UPLOADING METADATA CMD: $cmd";
     if ( !$test && !$skip_upload ) {
@@ -440,11 +442,28 @@ sub upload_submission {
     # we need to hack the manifest.xml to drop any files that are inputs and I won't upload again
     modify_manifest_file( "$sub_path/manifest.xml", $sub_path ) unless ($test || $skip_upload);
 
-    unless ( $test || $skip_upload ) {
-        die "ABORT: No gtupload installed, aborting!" if ( system("which gtupload") );
-	return 1 if ( GNOS::Upload->run_upload($sub_path, $key, $retries, $cooldown, $k_timeout_min) );
+    # Need to add code here to check for --gto-only. If it's there, call cgsubmit to generate manifest.xml,
+    # then call `gtupload --gt-only...` and DO NOT call GNOS::Upload->run_upload().
+    if ( $gto_only && !$test )
+    {
+      say "GTO Only mode is set - GTO file will be generated, but no upload will be perfomed.";
+      my @now = localtime();
+      my $time_stamp = sprintf("%04d-%02d-%02d-%02d-%02d-%02d",
+                               $now[5]+1900, $now[4]+1, $now[3],
+                               $now[2],      $now[1],   $now[0]);
+      my $log_filepath = "gtupload-$time_stamp.log";
+      my $gto_only_cmd = "cd $sub_path ; gtupload --gto-only -l $log_filepath -v -c $key -u ./manifest.xml";
+      run($gto_only_cmd);
     }
+    else
+    {
+
+      unless ( $test || $skip_upload ) {
+          die "ABORT: No gtupload installed, aborting!" if ( system("which gtupload") );
 
+      return 1 if ( GNOS::Upload->run_upload($sub_path, $key, $retries, $cooldown, $k_timeout_min) );
+      }
+    }
     # now make an archive tarball if requested
     if ($upload_archive ne "") {
       return 1 if (run("mkdir -p $upload_archive/$uuid && rsync -Lrauv $sub_path/* $upload_archive/$uuid/ && cd $upload_archive && tar zcf $uuid.tar.gz $uuid"));
@@ -1119,6 +1138,7 @@ sub download_metadata {
         my $xml_path = download_url( $url,  "xml2/data_$i.xml", $file_path );
         $metad->{$url} = parse_metadata($xml_path);
     }
+    #TODO: Error handline: This should thrown an error if there's no metadata at the metadata URL!!
     return ($metad);
 }