X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/8b873a9b3b8865a4d451263e48b49122b9c32759..9696c090dbf9dd777fc0a2c8925c67093503d5dc:/doc/user/cwl/cwl-run-options.html.textile.liquid?ds=sidebyside diff --git a/doc/user/cwl/cwl-run-options.html.textile.liquid b/doc/user/cwl/cwl-run-options.html.textile.liquid index 725528f44d..d331dad871 100644 --- a/doc/user/cwl/cwl-run-options.html.textile.liquid +++ b/doc/user/cwl/cwl-run-options.html.textile.liquid @@ -1,7 +1,7 @@ --- layout: default navsection: userguide -title: "Using arvados-cwl-runner" +title: "arvados-cwl-runner options" ... {% comment %} Copyright (C) The Arvados Authors. All rights reserved. @@ -47,19 +47,20 @@ table(table table-bordered table-condensed). |==--no-wait==| Submit workflow runner and exit.| |==--log-timestamps==| Prefix logging lines with timestamp| |==--no-log-timestamps==| No timestamp on logging lines| -|==--api== {containers}|Select work submission API. Only supports 'containers'| |==--compute-checksum==| Compute checksum of contents while collecting outputs| |==--submit-runner-ram== SUBMIT_RUNNER_RAM|RAM (in MiB) required for the workflow runner (default 1024)| |==--submit-runner-image== SUBMIT_RUNNER_IMAGE|Docker image for workflow runner| |==--always-submit-runner==|When invoked with --submit --wait, always submit a runner to manage the workflow, even when only running a single CommandLineTool| -|==--submit-request-uuid== UUID|Update and commit to supplied container request instead of creating a new one (containers API only).| -|==--submit-runner-cluster== CLUSTER_ID|Submit workflow runner to a remote cluster (containers API only)| +|==--match-submitter-images==|Where Arvados has more than one Docker image of the same name, use image from the Docker instance on the submitting node.| +|==--submit-request-uuid== UUID|Update and commit to supplied container request instead of creating a new one.| +|==--submit-runner-cluster== CLUSTER_ID|Submit workflow runner to a remote cluster| |==--name NAME==|Name to use for workflow execution instance.| |==--on-error== {stop,continue}|Desired workflow behavior when a step fails. One of 'stop' (do not submit any more steps) or 'continue' (may submit other steps that are not downstream from the error). Default is 'continue'.| |==--enable-dev==|Enable loading and running development versions of CWL spec.| -|==--storage-classes== STORAGE_CLASSES|Specify comma separated list of storage classes to be used when saving workflow output to Keep.| +|==--storage-classes== STORAGE_CLASSES|Specify comma separated list of storage classes to be used when saving the final workflow output to Keep.| +|==--intermediate-storage-classes== STORAGE_CLASSES|Specify comma separated list of storage classes to be used when intermediate workflow output to Keep.| |==--intermediate-output-ttl== N|If N > 0, intermediate output collections will be trashed N seconds after creation. Default is 0 (don't trash).| -|==--priority== PRIORITY|Workflow priority (range 1..1000, higher has precedence over lower, containers api only)| +|==--priority== PRIORITY|Workflow priority (range 1..1000, higher has precedence over lower)| |==--thread-count== THREAD_COUNT|Number of threads to use for container submit and output collection.| |==--http-timeout== HTTP_TIMEOUT|API request timeout in seconds. Default is 300 seconds (5 minutes).| |==--trash-intermediate==|Immediately trash intermediate outputs on workflow success.| @@ -74,10 +75,10 @@ Use the @--name@ and @--output-name@ options to specify the name of the workflow 
~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner --name "Example bwa run" --output-name "Example bwa output" bwa-mem.cwl bwa-mem-input.yml
 arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
 2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Upload local files: "bwa-mem.cwl"
-2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Uploaded to qr1hi-4zz18-h7ljh5u76760ww2
-2016-06-30 14:56:40 arvados.cwl-runner[27002] INFO: Submitted job qr1hi-8i9sb-fm2n3b1w0l6bskg
-2016-06-30 14:56:41 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-fm2n3b1w0l6bskg) is Running
-2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-fm2n3b1w0l6bskg) is Complete
+2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Uploaded to zzzzz-4zz18-h7ljh5u76760ww2
+2016-06-30 14:56:40 arvados.cwl-runner[27002] INFO: Submitted job zzzzz-8i9sb-fm2n3b1w0l6bskg
+2016-06-30 14:56:41 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (zzzzz-8i9sb-fm2n3b1w0l6bskg) is Running
+2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (zzzzz-8i9sb-fm2n3b1w0l6bskg) is Complete
 2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Overall process status is success
 {
     "aligned_sam": {
@@ -98,9 +99,9 @@ To submit a workflow and exit immediately, use the @--no-wait@ option.  This wil
 
~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner --no-wait bwa-mem.cwl bwa-mem-input.yml
 arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
 2016-06-30 15:07:52 arvados.arv-run[12480] INFO: Upload local files: "bwa-mem.cwl"
-2016-06-30 15:07:52 arvados.arv-run[12480] INFO: Uploaded to qr1hi-4zz18-eqnfwrow8aysa9q
-2016-06-30 15:07:52 arvados.cwl-runner[12480] INFO: Submitted job qr1hi-8i9sb-fm2n3b1w0l6bskg
-qr1hi-8i9sb-fm2n3b1w0l6bskg
+2016-06-30 15:07:52 arvados.arv-run[12480] INFO: Uploaded to zzzzz-4zz18-eqnfwrow8aysa9q
+2016-06-30 15:07:52 arvados.cwl-runner[12480] INFO: Submitted job zzzzz-8i9sb-fm2n3b1w0l6bskg
+zzzzz-8i9sb-fm2n3b1w0l6bskg
 

 
 
@@ -111,10 +112,10 @@ To run a workflow with local control, use @--local@.  This means that the host w
 
 
~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner --local bwa-mem.cwl bwa-mem-input.yml
 arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
-2016-07-01 10:05:19 arvados.cwl-runner[16290] INFO: Pipeline instance qr1hi-d1hrv-92wcu6ldtio74r4
-2016-07-01 10:05:28 arvados.cwl-runner[16290] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-2nzzfbuf9zjrj4g) is Queued
-2016-07-01 10:05:29 arvados.cwl-runner[16290] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-2nzzfbuf9zjrj4g) is Running
-2016-07-01 10:05:45 arvados.cwl-runner[16290] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-2nzzfbuf9zjrj4g) is Complete
+2016-07-01 10:05:19 arvados.cwl-runner[16290] INFO: Pipeline instance zzzzz-d1hrv-92wcu6ldtio74r4
+2016-07-01 10:05:28 arvados.cwl-runner[16290] INFO: Job bwa-mem.cwl (zzzzz-8i9sb-2nzzfbuf9zjrj4g) is Queued
+2016-07-01 10:05:29 arvados.cwl-runner[16290] INFO: Job bwa-mem.cwl (zzzzz-8i9sb-2nzzfbuf9zjrj4g) is Running
+2016-07-01 10:05:45 arvados.cwl-runner[16290] INFO: Job bwa-mem.cwl (zzzzz-8i9sb-2nzzfbuf9zjrj4g) is Complete
 2016-07-01 10:05:46 arvados.cwl-runner[16290] INFO: Overall process status is success
 {
     "aligned_sam": {