X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/cc952178056bf6d29471f6986306fb673dcf394a..f0f77a857e065550a5ca07be127a5a120528e6ef:/doc/user/cwl/cwl-run-options.html.textile.liquid diff --git a/doc/user/cwl/cwl-run-options.html.textile.liquid b/doc/user/cwl/cwl-run-options.html.textile.liquid index 27970f440a..761d198ee4 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. @@ -32,25 +32,25 @@ table(table table-bordered table-condensed). |==--debug==| Print even more logging| |==--metrics==| Print timing metrics| |==--tool-help==| Print command line help for tool| -|==--enable-reuse==| Enable job or container reuse (default)| -|==--disable-reuse==| Disable job or container reuse| -|==--project-uuid UUID==| Project that will own the workflow jobs, if not provided, will go to home project.| +|==--enable-reuse==| Enable container reuse (default)| +|==--disable-reuse==| Disable container reuse| +|==--project-uuid UUID==| Project that will own the workflow containers, if not provided, will go to home project.| |==--output-name OUTPUT_NAME==|Name to use for collection that stores the final output.| |==--output-tags OUTPUT_TAGS==|Tags for the final output collection separated by commas, e.g., =='--output-tags tag0,tag1,tag2'==.| -|==--ignore-docker-for-reuse==|Ignore Docker image version when deciding whether to reuse past jobs.| +|==--ignore-docker-for-reuse==|Ignore Docker image version when deciding whether to reuse past containers.| |==--submit==| Submit workflow runner to Arvados to manage the workflow (default).| -|==--local==| Run workflow on local host (still submits jobs to Arvados).| +|==--local==| Run workflow on local host (still submits containers to Arvados).| |==--create-template==| (Deprecated) synonym for --create-workflow.| -|==--create-workflow==| Create an Arvados workflow (if using the 'containers' API) or pipeline template (if using the 'jobs' API). See --api.| +|==--create-workflow==| Register an Arvados workflow that can be run from Workbench| |==--update-workflow== UUID|Update an existing Arvados workflow or pipeline template with the given UUID.| -|==--wait==| After submitting workflow runner job, wait for completion.| -|==--no-wait==| Submit workflow runner job and exit.| +|==--wait==| After submitting workflow runner, wait for completion.| +|==--no-wait==| Submit workflow runner and exit.| |==--log-timestamps==| Prefix logging lines with timestamp| |==--no-log-timestamps==| No timestamp on logging lines| -|==--api== {jobs,containers}|Select work submission API. Default is 'jobs' if that API is available, otherwise 'containers'.| +|==--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 job (default 1024)| -|==--submit-runner-image== SUBMIT_RUNNER_IMAGE|Docker image for workflow runner job| +|==--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)| @@ -60,7 +60,7 @@ table(table table-bordered table-condensed). |==--storage-classes== STORAGE_CLASSES|Specify comma separated list of storage classes to be used when saving 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)| -|==--thread-count== THREAD_COUNT|Number of threads to use for job submit and output collection.| +|==--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.| |==--no-trash-intermediate==|Do not trash intermediate outputs (default).| @@ -74,10 +74,10 @@ 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": {
@@ -98,23 +98,23 @@ 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
 

 
 
 h3(#local). Control a workflow locally
 
-To run a workflow with local control, use @--local@.  This means that the host where you run @arvados-cwl-runner@ will be responsible for submitting jobs, however, the jobs themselves will still run on the Arvados cluster.  With @--local@, if you interrupt @arvados-cwl-runner@ or log out, the workflow will be terminated.
+To run a workflow with local control, use @--local@.  This means that the host where you run @arvados-cwl-runner@ will be responsible for submitting containers, however, the containers themselves will still run on the Arvados cluster.  With @--local@, if you interrupt @arvados-cwl-runner@ or log out, the workflow will be terminated.
 
 
 
~/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": {