[ARVADOS] updated: db1aad98d37e1e5930618336b50111ec836ba5d7

[git at public.curoverse.com]

Summary of changes:
 .../pipeline_templates/gatk-exome-fq-snp.json      |   85 ++++++++++++-------
 sdk/cli/bin/arv-run-pipeline-instance              |    3 +-
 2 files changed, 56 insertions(+), 32 deletions(-)

       via  db1aad98d37e1e5930618336b50111ec836ba5d7 (commit)
       via  9bdde1c9f875bab4e0bfee5e2259cc40b315ce68 (commit)
      from  adea7dcb58e33e4667ae228845b6a4c1bfb920f0 (commit)

Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.


commit db1aad98d37e1e5930618336b50111ec836ba5d7
Author: Tom Clegg <tom at curoverse.com>
Date:   Tue Mar 11 16:29:18 2014 -0400

    Bump versions, change optional=false to required=true, set dataclass
    for bwa-aln input.

diff --git a/doc/examples/pipeline_templates/gatk-exome-fq-snp.json b/doc/examples/pipeline_templates/gatk-exome-fq-snp.json
index 42ba79d..3668f00 100644
--- a/doc/examples/pipeline_templates/gatk-exome-fq-snp.json
+++ b/doc/examples/pipeline_templates/gatk-exome-fq-snp.json
@@ -5,39 +5,45 @@
    "script":"file-select",
    "script_parameters":{
     "names":[
-     "human_g1k_v37.fasta.gz", "human_g1k_v37.fasta.fai.gz", "human_g1k_v37.dict.gz"
+     "human_g1k_v37.fasta.gz",
+     "human_g1k_v37.fasta.fai.gz",
+     "human_g1k_v37.dict.gz"
     ],
     "input":"d237a90bae3870b3b033aea1e99de4a9+10820+K at qr1hi"
    },
-   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d"
+   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153"
   },
   "bwa-index":{
-   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"bwa-index",
    "script_parameters":{
     "input":{
      "output_of":"extract-reference"
     },
     "bwa_tbz":{
-     "optional":false
+     "value":"8b6e2c4916133e1d859c9e812861ce13+70",
+     "required":true
     }
    }
   },
   "bwa-aln":{
-   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"bwa-aln",
    "script_parameters":{
     "input":{
-     "optional":"false"
+     "dataclass":"Collection",
+     "required":"true"
     },
     "reference_index":{
      "output_of":"bwa-index"
     },
     "samtools_tgz":{
-     "optional":false
+     "value":"c777e23cf13e5d5906abfdc08d84bfdb+74",
+     "required":true
     },
     "bwa_tbz":{
-     "optional":false
+     "value":"8b6e2c4916133e1d859c9e812861ce13+70",
+     "required":true
     }
    },
    "runtime_constraints":{
@@ -45,17 +51,18 @@
    }
   },
   "picard-gatk2-prep":{
-   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"picard-gatk2-prep",
    "script_parameters":{
     "input":{
-      "output_of":"bwa-aln"
+     "output_of":"bwa-aln"
     },
     "reference":{
      "output_of":"extract-reference"
     },
     "picard_zip":{
-     "optional":false
+     "value":"687f74675c6a0e925dec619cc2bec25f+77",
+     "required":true
     }
    },
    "runtime_constraints":{
@@ -63,26 +70,29 @@
    }
   },
   "GATK2-realign":{
-   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"GATK2-realign",
    "script_parameters":{
     "input":{
-      "output_of":"picard-gatk2-prep"
+     "output_of":"picard-gatk2-prep"
     },
     "gatk_bundle":{
-     "optional":false
+     "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K at qr1hi",
+     "required":true
     },
     "picard_zip":{
-     "optional":false
+     "value":"687f74675c6a0e925dec619cc2bec25f+77",
+     "required":true
     },
     "gatk_tbz":{
-     "optional":false
+     "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
+     "required":true
     },
     "regions":{
-     "optional":true
+     "value":"13b53dbe1ec032dfc495fd974aa5dd4a+87/S02972011_Covered_sort_merged.bed"
     },
     "region_padding":{
-     "optional":true
+     "value":10
     }
    },
    "runtime_constraints":{
@@ -90,47 +100,60 @@
    }
   },
   "GATK2-bqsr":{
-   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"GATK2-bqsr",
    "script_parameters":{
     "input":{
-      "output_of":"GATK2-realign"
+     "output_of":"GATK2-realign"
     },
     "gatk_bundle":{
-     "optional":false
+     "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K at qr1hi",
+     "required":true
     },
     "picard_zip":{
-     "optional":false
+     "value":"687f74675c6a0e925dec619cc2bec25f+77",
+     "required":true
     },
     "gatk_tbz":{
-     "optional":false
+     "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
+     "required":true
     }
    }
   },
   "GATK2-merge-call":{
-   "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"GATK2-merge-call",
    "script_parameters":{
     "input":{
-      "output_of":"GATK2-bqsr"
+     "output_of":"GATK2-bqsr"
     },
     "gatk_bundle":{
-     "optional":false
+     "value":"d237a90bae3870b3b033aea1e99de4a9+10820+K at qr1hi",
+     "required":true
     },
     "picard_zip":{
-     "optional":false
+     "value":"687f74675c6a0e925dec619cc2bec25f+77",
+     "required":true
     },
     "gatk_tbz":{
-     "optional":false
+     "value":"7e0a277d6d2353678a11f56bab3b13f2+87",
+     "required":true
     },
     "regions":{
-     "optional":true
+     "value":"13b53dbe1ec032dfc495fd974aa5dd4a+87/S02972011_Covered_sort_merged.bed"
     },
     "region_padding":{
-     "optional":true
+     "value":10
     },
     "GATK2_UnifiedGenotyper_args":{
-     "default":["-stand_call_conf","30.0","-stand_emit_conf","30.0","-dcov","200"]
+     "default":[
+      "-stand_call_conf",
+      "30.0",
+      "-stand_emit_conf",
+      "30.0",
+      "-dcov",
+      "200"
+     ]
     }
    }
   }

commit 9bdde1c9f875bab4e0bfee5e2259cc40b315ce68
Author: Tom Clegg <tom at curoverse.com>
Date:   Tue Mar 11 16:27:55 2014 -0400

    Fix giving up on a pipeline prematurely when a component is waiting
    for an output produced by a component later in the components.each()
    loop.

diff --git a/sdk/cli/bin/arv-run-pipeline-instance b/sdk/cli/bin/arv-run-pipeline-instance
index dd89ad5..91d7192 100755
--- a/sdk/cli/bin/arv-run-pipeline-instance
+++ b/sdk/cli/bin/arv-run-pipeline-instance
@@ -519,12 +519,13 @@ class WhRunPipelineInstance
                 if p.is_a? Hash and p[:output_of] == cname.to_s
                   debuglog "parameter #{c2name}::#{pname} == #{c[:job][:output]}"
                   c2[:script_parameters][pname] = c[:job][:output]
+                  moretodo = true
                 end
               end
             end
           elsif c[:job][:running] ||
               (!c[:job][:started_at] && !c[:job][:cancelled_at])
-            moretodo ||= true
+            moretodo = true
           elsif c[:job][:cancelled_at]
             debuglog "component #{cname} job #{c[:job][:uuid]} cancelled."
           end

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