Merge pull request #87 from wtsi-npg/devel

release 0.16.1
wtsi-npg · Mar 19, 2015 · c59e324 · c59e324
2 parents 2658486 + 113c57e
commit c59e324
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Showing 7 changed files with 29 additions and 13 deletions.
diff --git a/Changes b/Changes
@@ -1,6 +1,9 @@
 CHANGES LOG
 -----------
 
+release 0.16.1
+ - add tempdir parameter and verbose (-v) flag for teepot
+
 release 0.16
  - human split: new alignment_wtsi_stage2_humansplit_template.json, seqchksum_hs.json; addition of subst_params to alignment_common
  - seqchksum comparisons: merge bamseqchksum files for outputs for comparison with initial bam file in seqchksum.json

diff --git a/data/vtlib/alignment_common.json b/data/vtlib/alignment_common.json
@@ -85,6 +85,17 @@
 			],
 			"postproc":{"op":"concat", "pad":""}
 		}
+	},
+	{"id":"teepot_tempdir_value","required":"no","default":"."},
+	{
+		"id":"teepot_tempdir_flag",
+		"required":"no",
+		"subst_constructor":{
+			"vals":[
+				"-t",
+				{"subst":"teepot_tempdir_value"}
+			]
+		}
 	}
 ]
 }
diff --git a/data/vtlib/alignment_wtsi_stage2_humansplit_template.json b/data/vtlib/alignment_wtsi_stage2_humansplit_template.json
@@ -253,8 +253,8 @@
 		"type":"EXEC",
 		"use_STDIN": true,
 		"use_STDOUT": false,
-		"comment":"large wait (500 minutes) to avoid unnecessary spill to disk",
-		"cmd":["teepot", "-w", "30000", "-m", "1G", "__PHIX_ALN_OUT__", "__TGT_ALN_OUT__", "__HUMAN_SPLIT_OUT__" ]
+		"comment":"large wait (500 minutes) to avoid unnecessary spill to disk; specify parameter value teepot_tempdir_value to specify teepot tempdir",
+		"cmd":["teepot", "-v", {"subst":"teepot_tempdir_flag"}, "-w", "30000", "-m", "1G", "__PHIX_ALN_OUT__", "__TGT_ALN_OUT__", "__HUMAN_SPLIT_OUT__" ]
 	},
 	{
 		"id":"pre_alignment_target",
@@ -353,8 +353,8 @@
 		"orig_type":"EXEC",
 		"orig_use_STDIN": true,
 		"orig_use_STDOUT": false,
-		"orig_comment":"large wait (500 minutes) to avoid unnecessary spill to disk - temporarily reduced to 166.6 mins",
-		"orig_cmd":["teepot", "-vv", "-w", "30000", "-m", "1G", "__TGT_OUT__", "__HUMAN_SPLIT_OUT__" ]
+		"orig_comment":"large wait (500 minutes) to avoid unnecessary spill to disk; specify parameter value teepot_tempdir_value to specify teepot tempdir",
+		"orig_cmd":["teepot", {"subst":"teepot_tempdir_flag"}, "-vv", "-w", "30000", "-m", "1G", "__TGT_OUT__", "__HUMAN_SPLIT_OUT__" ]
 	},
 	{
 		"id":"alignment_filter",

diff --git a/data/vtlib/alignment_wtsi_stage2_template.json b/data/vtlib/alignment_wtsi_stage2_template.json
@@ -189,8 +189,8 @@
 		"type":"EXEC",
 		"use_STDIN": true,
 		"use_STDOUT": false,
-		"comment":"large wait (500 minutes) to avoid unnecessary spill to disk",
-		"cmd":["teepot", "-w", "30000", "-m", "1G", "__PHIX_ALN_OUT__", "__TGT_ALN_OUT__" ]
+		"comment":"large wait (500 minutes) to avoid unnecessary spill to disk; specify parameter value teepot_tempdir_value to specify teepot tempdir",
+		"cmd":["teepot", "-v", {"subst":"teepot_tempdir_flag"}, "-w", "30000", "-m", "1G", "__PHIX_ALN_OUT__", "__TGT_ALN_OUT__" ]
 	},
 	{
 		"id":"pre_alignment_target",

diff --git a/data/vtlib/final_output_prep.json b/data/vtlib/final_output_prep.json
@@ -427,7 +427,8 @@
 		"type":"EXEC",
 		"use_STDIN": true,
 		"use_STDOUT": false,
-		"cmd":["teepot", "-w", "300", "__SCRAMBLE_OUT__", "__BAMCHECK_OUT__", "__FLAGSTAT_OUT__", "__CALIBRATION_PU_OUT__", "__BAM_OUT__", "__SAMTOOLS_STATS_F0x900__", "__SAMTOOLS_STATS_F0xB00__", "__SEQCHKSUM_OUT__", "__SEQCHKSUM_EXTRAHASH_OUT__" ]
+		"comment":"specify parameter value teepot_tempdir_value to specify teepot tempdir",
+		"cmd":["teepot", "-v", {"subst":"teepot_tempdir_flag"}, "-w", "300", "__SCRAMBLE_OUT__", "__BAMCHECK_OUT__", "__FLAGSTAT_OUT__", "__CALIBRATION_PU_OUT__", "__BAM_OUT__", "__SAMTOOLS_STATS_F0x900__", "__SAMTOOLS_STATS_F0xB00__", "__SEQCHKSUM_OUT__", "__SEQCHKSUM_EXTRAHASH_OUT__" ]
 	},
 	{
 		"id":"scramble",
@@ -441,8 +442,8 @@
 		"type":"EXEC",
 		"use_STDIN": true,
 		"use_STDOUT": false,
-		"cmd":["teepot", "-w", "30000", "__CRAM_OUT__", "__CRAI_OUT__", "__MD5_OUT__", "__SEQCHKSUM_OUT__" ],
-		"comment":"allow a generous 500 minutes for the teepot timeout"
+		"cmd":["teepot", "-v", {"subst":"teepot_tempdir_flag"}, "-w", "30000", "__CRAM_OUT__", "__CRAI_OUT__", "__MD5_OUT__", "__SEQCHKSUM_OUT__" ],
+		"comment":"allow a generous 500 minutes for the teepot timeout;specify parameter value teepot_tempdir_value to specify teepot tempdir"
 	},
 	{
 		"id":"scramble_md5",

diff --git a/data/vtlib/post_alignment.json b/data/vtlib/post_alignment.json
@@ -52,8 +52,8 @@
 		"type":"EXEC",
 		"use_STDIN": true,
 		"use_STDOUT": false,
-		"cmd":["teepot", "-w", "300", "-m", "5M", "__HEADER_FIX_OUT__", "__FULL_BAM_OUT__"],
-		"comment":"get deadlock when tee used here"
+		"cmd":["teepot", "-v", {"subst":"teepot_tempdir_flag"}, "-w", "300", "-m", "5M", "__HEADER_FIX_OUT__", "__FULL_BAM_OUT__"],
+		"comment":"get deadlock when tee used here; specify parameter value teepot_tempdir_value to specify teepot tempdir"
 	},
 	{
 		"id":"sam_headerSQfix",
@@ -76,7 +76,7 @@
 		"type":"EXEC",
 		"use_STDIN": true,
 		"use_STDOUT": true,
-		"cmd":["teepot", "-m", "5M", "-"]
+		"cmd":["teepot", "-v", "-m", "5M", "-"]
 	},
 	{
 		"id":"reheader_headerSQfix",

diff --git a/data/vtlib/realignment_wtsi_template.json b/data/vtlib/realignment_wtsi_template.json
@@ -194,7 +194,8 @@
 		"type":"EXEC",
 		"use_STDIN": true,
 		"use_STDOUT": false,
-		"cmd":["teepot", "__PHIX_ALN_OUT__", "__TGT_ALN_OUT__"]
+		"cmd":["teepot", "-v", {"subst":"teepot_tempdir_flag"}, "__PHIX_ALN_OUT__", "__TGT_ALN_OUT__"],
+		"comment":"specify parameter value teepot_tempdir_value to specif teepot tempdir"
 	},
 	{
 		"id":"pre_alignment_target",