Merge pull request #34 from wtsi-npg/devel

pull request from wtsi devel to master - release 0.07

MANIFEST

@@ -0,0 +1,31 @@
+bin/viv.pl
+bin/vtfp.pl
+Build.PL
+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
+examples/bwa_mem/generic_alignment_with_phix.vtf
+examples/bwa_mem/post_alignment.vtf
+examples/bwa_mem/post_alignment_filter.vtf
+examples/bwa_mem/README.bwa_mem
+examples/bwa_mem/seqchksum.vtf
+examples/example_01.cfg
+examples/example_02.cfg
+examples/example_03.cfg
+examples/example_04.cfg
+examples/README.examples
+examples/tophat2_cfg.png
+MANIFEST			This list of files
+README
+README.vtfp
+t/data/simple_failing_pipeline.vtf
+t/data/simple_pipeline.vtf
+visualisation/bwa_aln.cfg
+visualisation/bwa_aln.json
+visualisation/config_view.html
+visualisation/README.visualisation
+visualisation/tophat2.cfg
+visualisation/tophat2.json

data/bwamem_wtsi_stage2_template.vtf

@@ -5,43 +5,43 @@
 		"id":"bmd_phix_tee0",
 		"type":"EXEC",
 		"use_STDIN": true,
-		"use_STDOUT": true,
-		"cmd":"tee __pFIFO0__"
+		"use_STDOUT": false,
+		"cmd":"teepot -w 300 __OUT1__ __OUT2__"
 	},
 	{
 		"id":"bmd_tee1",
 		"type":"EXEC",
 		"use_STDIN": true,
-		"use_STDOUT": true,
-		"cmd":"tee __FIFO1__"
+		"use_STDOUT": false,
+		"cmd":"teepot -w 300 __OUT1__ __OUT2__"
 	},
 	{
 		"id":"bmd_tee2",
 		"type":"EXEC",
 		"use_STDIN": true,
-		"use_STDOUT": true,
-		"cmd":"tee __FIFO2__"
+		"use_STDOUT": false,
+		"cmd":"teepot -w 300 __OUT1__ __OUT2__"
 	},
 	{
 		"id":"bmd_tee3",
 		"type":"EXEC",
 		"use_STDIN": true,
-		"use_STDOUT": true,
-		"cmd":"tee __FIFO3__"
+		"use_STDOUT": false,
+		"cmd":"teepot -w 300 __OUT1__ __OUT2__"
 	},
 	{
 		"id":"bmd_phix_tee1",
 		"type":"EXEC",
 		"use_STDIN": true,
-		"use_STDOUT": true,
-		"cmd":"tee __pFIFO1__"
+		"use_STDOUT": false,
+		"cmd":"teepot -w 300 __OUT1__ __OUT2__"
 	},
 	{
 		"id":"bmd_phix_tee2",
 		"type":"EXEC",
 		"use_STDIN": true,
-		"use_STDOUT": true,
-		"cmd":"tee __pFIFO2__"
+		"use_STDOUT": false,
+		"cmd":"teepot -w 300 __OUT1__ __OUT2__"
 	},
 	{
 		"id":"scramble",
@@ -284,7 +284,7 @@
 		"type":"EXEC",
 		"use_STDIN": true,
 		"use_STDOUT": false,
-		"cmd":"mbuffer -f -q -m 1G -o __OUT1__ -o __OUT2__"
+		"cmd":"teepot -w 300 -m 1G __OUT1__ __OUT2__"
 	},
 	{
 		"id":"bamrecompress_input",
@@ -383,8 +383,8 @@
 		"id":"tee_headerSQfix",
 		"type":"EXEC",
 		"use_STDIN": true,
-		"use_STDOUT": true,
-		"cmd":"mbuffer -f -q -m 5M -o - -o __OUT1__",
+		"use_STDOUT": false,
+		"cmd":"teepot -w 300 -m 5M __OUT2__ __OUT1__",
 		"comment":"get deadlock when tee used here"
 	},
 	{
@@ -408,7 +408,7 @@
 		"type":"EXEC",
 		"use_STDIN": true,
 		"use_STDOUT": true,
-		"cmd":"mbuffer -f -q -m 5M"
+		"cmd":"teepot -w 300 -m 5M /dev/stdout"
 	},
 	{
 		"id":"reheader_headerSQfix",
@@ -707,7 +707,7 @@
 	},
 	{   
 		"id":"bmd_phix_tee0_to_bmd_phix_tee0",
-		"from":"bmd_phix_tee0:__pFIFO0__",
+		"from":"bmd_phix_tee0:__OUT2__",
 		"to":"bmd_phix_tee1"
 	},
 	{   
@@ -717,47 +717,47 @@
 	},
 	{   
 		"id":"tee_to_scramble_phix",
-		"from":"bmd_phix_tee1:__pFIFO1__",
+		"from":"bmd_phix_tee1:__OUT2__",
 		"to":"scramble_phix"
 	},
 	{   
 		"id":"tee_to_scramble",
-		"from":"bmd_tee1:__FIFO1__",
+		"from":"bmd_tee1:__OUT2__",
 		"to":"scramble"
 	},
 	{   
 		"id":"bmd_phix_tee1_to_bmd_phix_tee2",
-		"from":"bmd_phix_tee1",
+		"from":"bmd_phix_tee1:__OUT1__",
 		"to":"bmd_phix_tee2"
 	},
 	{   
 		"id":"bmd_tee1_to_bmd_tee2",
-		"from":"bmd_tee1",
+		"from":"bmd_tee1:__OUT1__",
 		"to":"bmd_tee2"
 	},
 	{
 		"id":"tee_phix_to_bamcheck_phix",
-		"from":"bmd_phix_tee2",
+		"from":"bmd_phix_tee2:__OUT1__",
 		"to":"bamcheck_phix"
 	},
 	{
 		"id":"tee_to_bamcheck",
-		"from":"bmd_tee2:__FIFO2__",
+		"from":"bmd_tee2:__OUT2__",
 		"to":"bamcheck"
 	},
 	{
 		"id":"bmd_tee2_to_bmd_tee3",
-		"from":"bmd_tee2",
+		"from":"bmd_tee2:__OUT1__",
 		"to":"bmd_tee3"
 	},
 	{
 		"id":"bmd_tee2_phix_to_flagstat",
-		"from":"bmd_phix_tee2:__pFIFO2__",
+		"from":"bmd_phix_tee2:__OUT2__",
 		"to":"flagstat_phix"
 	},
 	{
 		"id":"bmd_tee3_to_flagstat_filter",
-		"from":"bmd_tee3:__FIFO3__",
+		"from":"bmd_tee3:__OUT2__",
 		"to":"flagstat_filter"
 	},
 	{
@@ -877,7 +877,7 @@
 	},
 	{
 		"id":"tee_headerSQfix_to_mbuffer",
-		"from":"tee_headerSQfix",
+		"from":"tee_headerSQfix:__OUT2__",
 		"to":"mbuffer_headerSQfix"
 	},
 	{
@@ -948,7 +948,7 @@
 	},
 	{
 		"id":"bmd_phix_tee0_to_bamrecompress_phix",
-		"from":"bmd_phix_tee0",
+		"from":"bmd_phix_tee0:__OUT1__",
 		"to":"bamrecompress_phix"
 	},
 	{
@@ -971,7 +971,7 @@
 	},
 	{
 		"id":"bmd_to_bamrecompress",
-		"from":"bmd_tee3",
+		"from":"bmd_tee3:__OUT1__",
 		"to":"bamrecompress_target"
 	},
 	{