Merge pull request #65 from wtsi-npg/devel

release 0.12

Changes

@@ -1,5 +1,22 @@
 CHANGES LOG
 -----------
 
+release 0.12
+  -viv.pl
+    read/write to/from stdin/stdout
+    exec failure of a node's command is now fatal (bug fix)
+
+  -vtfp.pl
+    updated to use new subst_params format in templates
+    multiple -keys/-values pairs on the command-line now produce an array on substitution into the template
+    when substition of nested parameters is done, array elements which are themselves arrays are flattened
+      (its elements are spliced into the position of the original array); net result is that top-level
+      parameter substitutions result in either strings or arrays of strings
+
+  -templates
+    new subst_params format for production templates
+    changes to final_output_prep template to add flexibility to this phase of analysis (e.g. y chrom. split)
+    output of seqchksum files for hash type sha512primesums512 added
+
 release 0.09
-  -install action should not remove lib directory at target
+  -install action should not remove lib directory at target

MANIFEST

@@ -2,9 +2,6 @@ bin/viv.pl
 bin/vtfp.pl
 Build.PL
 Changes
-data/bwamem_wtsi_stage2_template.vtf
-data/snap_sample_template.vtf
-data/tophat2_wtsi_stage2_template.vtf
 examples/bwa_aln_cfg.png
 examples/bwa_mem/bwa_mem_alignment.vtf
 examples/bwa_mem/generic_alignment_with_phix.vtf

bin/viv.pl

@@ -124,6 +124,7 @@
 $logger->($VLMAX, "EXEC nodes(post EXEC nodes preprocessing): ", Dumper(%exec_nodes), "\n");
 setpgrp; # create new processgroup so signals can be fired easily in suitable way later
 # kick off any unblocked EXEC nodes, noting their details for later release of any dependants
+$logger->($VLMED, qq[master process is $$\n]);
 my %pid2id = ();
 for my $node_id (keys %exec_nodes) {
 	my $wait_counter = $exec_nodes{$node_id}->{wait_counter};
@@ -205,7 +206,6 @@
 sub _get_node_info {
 	my ($edge_id, $all_nodes) = @_;
 
-	my $from = $edge_id;
 	my ($id, $port);
 	# slightly more concise regex usage might be good here
 	if($edge_id =~ /^([^:]*):(.*)$/) {
@@ -303,16 +303,20 @@ sub _fork_off {
 			$0 .= q{ (pending }.$node->{'id'}.qq{: $cmd)}; #rename process so fork can be easily identified whilst open waits on fifo
 			open STDERR, q(>), $node->{'id'}.q(.).$$.q(.err) or croak "Failed to reset STDERR, pid $$ with cmd: $cmd";
 			select(STDERR);$|=1;
-			$node->{'STDIN'} ||= '/dev/null';
-			open STDIN,  q(<), $node->{'STDIN'} or croak "Failed to reset STDIN, pid $$ with cmd: $cmd";
-			$node->{'STDOUT'} ||= '/dev/null';
-			open STDOUT, q(>), $node->{'STDOUT'} or croak "Failed to reset STDOUT, pid $$ with cmd: $cmd";
+			if(not $node->{use_STDIN}) { $node->{'STDIN'} ||= '/dev/null'; }
+			if($node->{'STDIN'}) {
+				open STDIN,  q(<), $node->{'STDIN'} or croak "Failed to reset STDIN, pid $$ with cmd: $cmd";
+			}
+			if(not $node->{use_STDOUT}) { $node->{'STDOUT'} ||= '/dev/null'; }
+			if($node->{'STDOUT'}) {
+				open STDOUT, q(>), $node->{'STDOUT'} or croak "Failed to reset STDOUT, pid $$ with cmd: $cmd";
+			}
 			print STDERR "Process $$ for cmd $cmd:\n";
-			print STDERR ' fileno(STDIN,'.(fileno STDIN).') reading from '.$node->{'STDIN'} ."\n";
-			print STDERR ' fileno(STDOUT,'.(fileno STDOUT).') writing to '.$node->{'STDOUT'}."\n";
+			print STDERR ' fileno(STDIN,'.(fileno STDIN).') reading from '.($node->{'STDIN'}?$node->{'STDIN'}:'stdin') ."\n";
+			print STDERR ' fileno(STDOUT,'.(fileno STDOUT).') writing to '.($node->{'STDOUT'}?$node->{'STDOUT'}:'stdout') ."\n";
 			print STDERR ' fileno(STDERR,'.(fileno STDERR).")\n";
 			print STDERR " execing....\n";
-			exec @cmd;
+			exec @cmd or croak qq[Failed to exec cmd: ], join " ", @cmd;
 		}
 		else {
 			$logger->($VLMED, q[child exec not switched on], "\n");