X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/50a3cf5df8624618cc00308159fde643dd8d6f28..3aaefcb3c76ff470b475d950398d01255e87712a:/doc/user/cwl/cwl-runner.html.textile.liquid
diff --git a/doc/user/cwl/cwl-runner.html.textile.liquid b/doc/user/cwl/cwl-runner.html.textile.liquid
index dc1415ed17..442a60b04f 100644
--- a/doc/user/cwl/cwl-runner.html.textile.liquid
+++ b/doc/user/cwl/cwl-runner.html.textile.liquid
@@ -1,49 +1,50 @@
---
layout: default
navsection: userguide
-title: "Running an Arvados workflow"
+title: "Starting a Workflow at the Command Line"
...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
{% include 'what_is_cwl' %}
{% include 'tutorial_expectations' %}
-{% include 'notebox_begin' %}
-
-By default, the @arvados-cwl-runner@ is installed on Arvados shell nodes. If you want to submit jobs from somewhere else, such as your workstation, you may install "arvados-cwl-runner.":#setup
-
-{% include 'notebox_end' %}
-
This tutorial will demonstrate how to submit a workflow at the command line using @arvados-cwl-runner@.
-h3. Get the example files
+# "Get the tutorial files":#get-files
+# "Submitting a workflow to an Arvados cluster":#submitting
+# "Registering a workflow to use in Workbench":#registering
+# "Make a workflow file directly executable":#executable
-The tutorial files are located in the "documentation section of the Arvados source repository:":https://github.com/curoverse/arvados/tree/master/doc/user/cwl/bwa-mem
+h2(#get-files). Get the tutorial files
+
+The tutorial files are located in the documentation section of the Arvados source repository, which can be found on "git.arvados.org":https://git.arvados.org/arvados.git/tree/HEAD:/doc/user/cwl/bwa-mem or "github":https://github.com/arvados/arvados/tree/master/doc/user/cwl/bwa-mem
~$ git clone https://github.com/curoverse/arvados
+
~$ git clone https://git.arvados.org/arvados.git
~$ cd arvados/doc/user/cwl/bwa-mem
~$ arv-copy --src qr1hi --dst settings 2463fa9efeb75e099685528b3b9071e0+438
-~$ arv-copy --src qr1hi --dst settings ae480c5099b81e17267b7445e35b4bc7+180
-~$ arv-copy --src qr1hi --dst settings 655c6cd07550151b210961ed1d3852cf+57
+
~$ arv-copy --src pirca --dst settings 2463fa9efeb75e099685528b3b9071e0+438
+~$ arv-copy --src pirca --dst settings ae480c5099b81e17267b7445e35b4bc7+180
~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner 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": {
- "path": "keep:54325254b226664960de07b3b9482349+154/HWI-ST1027_129_D0THKACXX.1_1.sam",
+ "location": "keep:54325254b226664960de07b3b9482349+154/HWI-ST1027_129_D0THKACXX.1_1.sam",
"checksum": "sha1$0dc46a3126d0b5d4ce213b5f0e86e2d05a54755a",
"class": "File",
"size": 30738986
@@ -71,43 +72,123 @@ arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107,
-h3. Submit a workflow with no waiting
+h3. Referencing files
+
+When running a workflow on an Arvados cluster, the input files must be stored in Keep. There are several ways this can happen.
+
+A URI reference to Keep uses the @keep:@ scheme followed by either the portable data hash or UUID of the collection and then the location of the file inside the collection. For example, @keep:2463fa9efeb75e099685528b3b9071e0+438/19.fasta.bwt@ or @keep:zzzzz-4zz18-zzzzzzzzzzzzzzz/19.fasta.bwt@.
+
+If you reference a file in "arv-mount":{{site.baseurl}}/user/tutorials/tutorial-keep-mount-gnu-linux.html, such as @/home/example/keep/by_id/2463fa9efeb75e099685528b3b9071e0+438/19.fasta.bwt@, then @arvados-cwl-runner@ will automatically determine the appropriate Keep URI reference.
+
+If you reference a local file which is not in @arv-mount@, then @arvados-cwl-runner@ will upload the file to Keep and use the Keep URI reference from the upload.
-To submit a workflow and exit immediately, use the @--no-wait@ option. This will submit the workflow to Arvados, print out the UUID of the job that was submitted to standard output, and exit.
+You can also execute CWL files that have been uploaded Keep:
~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner --no-wait bwa-mem.cwl bwa-mem-input.yml
+
+~/arvados/doc/user/cwl/bwa-mem$ arv-put --portable-data-hash --name "bwa-mem.cwl" bwa-mem.cwl
+2020-08-20 13:40:02 arvados.arv_put[12976] INFO: Collection saved as 'bwa-mem.cwl'
+f141fc27e7cfa7f7b6d208df5e0ee01b+59
+~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner keep:f141fc27e7cfa7f7b6d208df5e0ee01b+59/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 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": {
+ "location": "keep:54325254b226664960de07b3b9482349+154/HWI-ST1027_129_D0THKACXX.1_1.sam",
+ "checksum": "sha1$0dc46a3126d0b5d4ce213b5f0e86e2d05a54755a",
+ "class": "File",
+ "size": 30738986
+ }
+}
~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner --create-workflow bwa-mem.cwl
+arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
+2016-07-01 12:21:01 arvados.arv-run[15796] INFO: Upload local files: "bwa-mem.cwl"
+2016-07-01 12:21:01 arvados.arv-run[15796] INFO: Uploaded to zzzzz-4zz18-7e0hedrmkuyoei3
+2016-07-01 12:21:01 arvados.cwl-runner[15796] INFO: Created template zzzzz-p5p6p-rjleou1dwr167v5
+zzzzz-p5p6p-rjleou1dwr167v5
+
+~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner --name "My workflow with defaults" --create-workflow bwa-mem.cwl bwa-mem-template.yml
+arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
+2016-07-01 14:09:50 arvados.arv-run[3730] INFO: Upload local files: "bwa-mem.cwl"
+2016-07-01 14:09:50 arvados.arv-run[3730] INFO: Uploaded to zzzzz-4zz18-0f91qkovk4ml18o
+2016-07-01 14:09:50 arvados.cwl-runner[3730] INFO: Created template zzzzz-p5p6p-0deqe6nuuyqns2i
+zzzzz-p5p6p-zuniv58hn8d0qd8
+
+~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner pirca-7fd4e-3nqbw08vtjl8ybz --help
+INFO /home/peter/work/scripts/venv3/bin/arvados-cwl-runner 2.1.0.dev20200814195416, arvados-python-client 2.1.0.dev20200814195416, cwltool 3.0.20200807132242
+INFO Resolved 'pirca-7fd4e-3nqbw08vtjl8ybz' to 'arvwf:pirca-7fd4e-3nqbw08vtjl8ybz#main'
+usage: pirca-7fd4e-3nqbw08vtjl8ybz [-h] [--PL PL] [--group_id GROUP_ID]
+ [--read_p1 READ_P1] [--read_p2 READ_P2]
+ [--reference REFERENCE]
+ [--sample_id SAMPLE_ID]
+ [job_order]
+
+positional arguments:
+ job_order Job input json file
+
+optional arguments:
+ -h, --help show this help message and exit
+ --PL PL
+ --group_id GROUP_ID
+ --read_p1 READ_P1 The reads, in fastq format.
+ --read_p2 READ_P2 For mate paired reads, the second file (optional).
+ --reference REFERENCE
+ The index files produced by `bwa index`
+ --sample_id SAMPLE_ID
+
+#!/usr/bin/env cwl-runner
+
+~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner keep:655c6cd07550151b210961ed1d3852cf+57/bwa-mem.cwl bwa-mem-input.yml
+~/arvados/doc/user/cwl/bwa-mem$ ./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: 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: Upload local files: "bwa-mem.cwl"
+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": {
@@ -120,42 +201,34 @@ arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107,
~$ virtualenv ~/venv
-~$ . ~/venv/bin/activate
-~$ pip install -U setuptools
-~$ pip install arvados-cwl-runner
+#!/usr/bin/env cwl-runner
+cwl:tool: bwa-mem.cwl
~$ docker version
-Client:
- Version: 1.9.1
- API version: 1.21
- Go version: go1.4.2
- Git commit: a34a1d5
- Built: Fri Nov 20 12:59:02 UTC 2015
- OS/Arch: linux/amd64
-
-Server:
- Version: 1.9.1
- API version: 1.21
- Go version: go1.4.2
- Git commit: a34a1d5
- Built: Fri Nov 20 12:59:02 UTC 2015
- OS/Arch: linux/amd64
+~/arvados/doc/user/cwl/bwa-mem$ ./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 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": {
+ "path": "keep:54325254b226664960de07b3b9482349+154/HWI-ST1027_129_D0THKACXX.1_1.sam",
+ "checksum": "sha1$0dc46a3126d0b5d4ce213b5f0e86e2d05a54755a",
+ "class": "File",
+ "size": 30738986
+ }
+}