[ARVADOS] updated: 9c5dc2759edaa0f3c7bde4aa086971ffa54cbb42

[git at public.curoverse.com]

Summary of changes:
 .../pipeline_templates/gatk-exome-fq-snp.json      |    9 ++++++++-
 sdk/cli/bin/crunch-job                             |    2 +-
 2 files changed, 9 insertions(+), 2 deletions(-)

       via  9c5dc2759edaa0f3c7bde4aa086971ffa54cbb42 (commit)
       via  71f1843d04d596d7912bfa068f64717e5347afc5 (commit)
      from  ad0944aa970bf52bcc2387ac57e12cb69ae54d66 (commit)

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commit 9c5dc2759edaa0f3c7bde4aa086971ffa54cbb42
Author: Tom Clegg <tom at curoverse.com>
Date:   Mon Mar 31 23:29:16 2014 -0400

    Move keep mount point outside TASK_WORK directory to prevent conflict
    with arvados.util.clear_tmp().

diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job
index 567769b..6b96937 100755
--- a/sdk/cli/bin/crunch-job
+++ b/sdk/cli/bin/crunch-job
@@ -583,7 +583,7 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
     $ENV{"TASK_SLOT_NODE"} = $slot[$childslot]->{node}->{name};
     $ENV{"TASK_SLOT_NUMBER"} = $slot[$childslot]->{cpu};
     $ENV{"TASK_WORK"} = $ENV{"JOB_WORK"}."/$id.$$";
-    $ENV{"TASK_KEEPMOUNT"} = $ENV{"TASK_WORK"}."/keep";
+    $ENV{"TASK_KEEPMOUNT"} = $ENV{"TASK_WORK"}.".keep";
     $ENV{"TASK_TMPDIR"} = $ENV{"TASK_WORK"}; # deprecated
     $ENV{"CRUNCH_NODE_SLOTS"} = $slot[$childslot]->{node}->{ncpus};
     $ENV{"PATH"} = $ENV{"CRUNCH_INSTALL"} . "/bin:" . $ENV{"PATH"};

commit 71f1843d04d596d7912bfa068f64717e5347afc5
Author: Tom Clegg <tom at curoverse.com>
Date:   Mon Mar 31 23:28:13 2014 -0400

    Add repository=arvados now required by jobs.create.

diff --git a/doc/examples/pipeline_templates/gatk-exome-fq-snp.json b/doc/examples/pipeline_templates/gatk-exome-fq-snp.json
index f84ad3f..f8c08d1 100644
--- a/doc/examples/pipeline_templates/gatk-exome-fq-snp.json
+++ b/doc/examples/pipeline_templates/gatk-exome-fq-snp.json
@@ -2,6 +2,8 @@
  "name":"GATK / exome PE fastq to snp",
  "components":{
   "extract-reference":{
+   "repository":"arvados",
+   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"file-select",
    "script_parameters":{
     "names":[
@@ -11,10 +13,10 @@
     ],
     "input":"d237a90bae3870b3b033aea1e99de4a9+10820+K at qr1hi"
    },
-   "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "output_is_persistent":false
   },
   "bwa-index":{
+   "repository":"arvados",
    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"bwa-index",
    "script_parameters":{
@@ -29,6 +31,7 @@
    "output_is_persistent":false
   },
   "bwa-aln":{
+   "repository":"arvados",
    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"bwa-aln",
    "script_parameters":{
@@ -54,6 +57,7 @@
    "output_is_persistent":false
   },
   "picard-gatk2-prep":{
+   "repository":"arvados",
    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"picard-gatk2-prep",
    "script_parameters":{
@@ -74,6 +78,7 @@
    "output_is_persistent":false
   },
   "GATK2-realign":{
+   "repository":"arvados",
    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"GATK2-realign",
    "script_parameters":{
@@ -105,6 +110,7 @@
    "output_is_persistent":false
   },
   "GATK2-bqsr":{
+   "repository":"arvados",
    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"GATK2-bqsr",
    "script_parameters":{
@@ -127,6 +133,7 @@
    "output_is_persistent":false
   },
   "GATK2-merge-call":{
+   "repository":"arvados",
    "script_version":"e820bd1c6890f93ea1a84ffd5730bbf0e3d8e153",
    "script":"GATK2-merge-call",
    "script_parameters":{

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