Merge pull request #47 from wtsi-npg/devel

release 0.09
wtsi-npg · Oct 23, 2014 · 6b33edc · 6b33edc
2 parents 6565a0a + 1d543e4
commit 6b33edc
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Showing 16 changed files with 59 additions and 514 deletions.
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,6 @@
+Build*
+MYMETA*
+_build/
+blib/
+*~
+
diff --git a/Build.PL b/Build.PL
@@ -15,19 +15,9 @@ my $class = Module::Build->subclass(code => <<'EOF');
 
   sub process_data_files {
    `cp -av data blib`;
-
     return;
   }
 
-  sub ACTION_install {
-    my $self = shift;
-    $self->SUPER::ACTION_install;
-    my $lib = $self->install_base() .'/lib';
-    if (-d $lib) {
-      `rm -frv $lib`;
-    }
-  }
-
   sub ACTION_code {
     my $self = shift;
 
@@ -68,6 +58,12 @@ my $builder = $class->new(
     'ExtUtils::CBuilder'    => 0
   },
 
+  'build_requires' => {
+    'English'               => 0,
+    'Test::More'            => 0,
+    'Test::Compile'         => 0,
+  },
+
   'requires' => {
     'Carp'                  => 0,
     'Cwd'                   => 0,
@@ -80,11 +76,10 @@ my $builder = $class->new(
     'JSON'                  => 0,
     'List::MoreUtils'       => 0,
     'POSIX'                 => 0,
-    'Readonly'              => 0
-  },
-
-  'build_requires' => {
-    'ExtUtils::CBuilder'    => 0
+    'Readonly'              => 0,
+    'strict'                => 0,
+    'Storable'              => 0,
+    'warnings'              => 0,
   },
 
   'dist' => { COMPRESS => 'gzip', SUFFIX => 'gz', }

diff --git a/Changes b/Changes
@@ -0,0 +1,5 @@
+CHANGES LOG
+-----------
+
+release 0.09
+  -install action should not remove lib directory at target
diff --git a/MANIFEST b/MANIFEST
@@ -1,9 +1,9 @@
 bin/viv.pl
 bin/vtfp.pl
 Build.PL
+Changes
 data/bwamem_wtsi_stage2_template.vtf
 data/snap_sample_template.vtf
-data/tophat2_wtsi_realign_template.vtf
 data/tophat2_wtsi_stage2_template.vtf
 examples/bwa_aln_cfg.png
 examples/bwa_mem/bwa_mem_alignment.vtf
@@ -23,6 +23,7 @@ README
 README.vtfp
 t/data/simple_failing_pipeline.vtf
 t/data/simple_pipeline.vtf
+t/00-scripts_compile.t
 visualisation/bwa_aln.cfg
 visualisation/bwa_aln.json
 visualisation/config_view.html

diff --git a/bin/viv.pl b/bin/viv.pl
@@ -1,17 +1,14 @@
 #!/usr/bin/env perl
 
 use strict;
-
+use warnings;
+use Carp;
 use File::Slurp;
 use JSON;
-
 use POSIX;
 use File::Temp qw/ tempdir /;
 use Getopt::Std;
 use Readonly;
-
-use Carp;
-
 use Data::Dumper;
 
 our $VERSION = '0';

diff --git a/bin/vtfp.pl b/bin/vtfp.pl
@@ -7,18 +7,17 @@
 ########################################################################################################
 
 use strict;
-
+use warnings;
+use Carp;
+use Readonly;
 use Getopt::Long;
-use Data::Dumper;
 use File::Which qw(which);
 use List::MoreUtils qw(any);
 use Cwd qw(abs_path);
 use File::Slurp;
 use JSON;
-
 use Storable 'dclone';
-use Carp;
-use Readonly;
+
 
 our $VERSION = '0';
 
@@ -386,7 +385,6 @@ sub resolve_subst_to_string {
 		$attrib_name ||= "element $elem_index";
 		my $subst_param_name = $subst_param->{param_name};
 		my $parent_id = $subst_param->{parent_id};
-		my $parent_id = $subst_param->{parent_id};
 		$parent_id ||= q[NO_PARENT_ID];   # should be ARRAY?
 
 		if($subst_param->{required} and not $query_mode) { # required means "must be specified by the caller", so default value is disregarded

diff --git a/data/bcl2bam_phix_deplex_wtsi_stage1_template.vtf b/data/bcl2bam_phix_deplex_wtsi_stage1_template.vtf
@@ -9,7 +9,7 @@
 			"required":"yes",
 			"subst_constructor":{
 			"vals":[
-					{"subst_param_name":"java_cmd","required":"no","default":"/software/jdk1.7.0_25/bin/java"},
+					{"subst_param_name":"java_cmd","required":"no","default":"java"},
 					"-Xmx1024m",
 					"-jar",{"subst_param_name":"illumina2bam_jar","required":"no","default":"/software/npg/java_jars/Illumina2bam.jar"},
 					{"subst_param_name":"i2b_intensity_flag",
@@ -115,7 +115,7 @@
 			"required":"yes",
 			"subst_constructor":{
 			"vals":[
-					{"subst_param_name":"java_cmd","required":"no","default":"/software/jdk1.7.0_25/bin/java"},
+					{"subst_param_name":"java_cmd","required":"no","default":"java"},
 					"-Xmx1024m",
 					"-jar",{"subst_param_name":"bamindexdecoder_jar","required":"no","default":"/software/npg/java_jars/BamIndexDecoder.jar"},
 					"I=/dev/stdin",
@@ -141,7 +141,7 @@
 			"required":"yes",
 			"subst_constructor":{
 			"vals":[
-					{"subst_param_name":"splitter_cmd","required":"no","default":"/software/solexa/pkg/samtools/samtools-1.1/samtools"},
+					{"subst_param_name":"samtools_cmd","required":"no","default":"samtools"},
 					"split",
 					"-f",
 					{"subst_param_name":"split_format", "required":"no",

diff --git a/data/bwamem_wtsi_stage2_template.vtf b/data/bwamem_wtsi_stage2_template.vtf
@@ -494,7 +494,7 @@
 			"required":"yes",
 			"subst_constructor":{
 			"vals":[
-					{"subst_param_name":"java_cmd","required":"no","default":"/software/jdk1.7.0_25/bin/java"},
+					{"subst_param_name":"java_cmd","required":"no","default":"java"},
 					"-Xmx1000m",
 					"-jar", {"subst_param_name":"alignment_filter_jar","required":"no",
 						"subst_constructor":{
@@ -556,8 +556,8 @@
 			"required":"yes",
 			"subst_constructor":{
 				"vals":[
-					"bamstreamingmarkduplicates ",
-					"level=0 ",
+					{"subst_param_name":"bmd_cmd","required":"no","default":"bammarkduplicates2"},
+					" level=0 ",
 					"verbose=0 ",
 					"M=",
 					{"subst_param_name":"outdatadir","required":"no","default":"."},
@@ -627,8 +627,8 @@
 			"required":"yes",
 			"subst_constructor":{
 				"vals":[
-					"bamstreamingmarkduplicates ",
-					"level=0 ",
+					{"subst_param_name":"bmd_cmd","required":"no","default":"bammarkduplicates2"},
+					" level=0 ",
 					"verbose=0 ",
 					"M=",
 					{"subst_param_name":"outdatadir","required":"no","default":"."},