---
layout: default
navsection: userguide
-title: Using Common Workflow Language
+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' %}
-h2. Preparing to work with Arvados cwl runner
+This tutorial will demonstrate how to submit a workflow at the command line using @arvados-cwl-runner@.
-h3. arvados-cwl-runner
+# "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 @arvados-cwl-runner@ client is installed by default on Arvados shell nodes.
+h2(#get-files). Get the tutorial files
-However, if you do not have @arvados-cwl-runner@, you may install it using @pip@:
+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
<notextile>
-<pre><code>~$ <span class="userinput">virtualenv ~/venv</span>
-~$ <span class="userinput">. ~/venv/bin/activate</span>
-~$ <span class="userinput">pip install -U setuptools</span>
-~$ <span class="userinput">pip install arvados-cwl-runner</span>
+<pre><code>~$ <span class="userinput">git clone https://git.arvados.org/arvados.git</span>
+~$ <span class="userinput">cd arvados/doc/user/cwl/bwa-mem</span>
</code></pre>
</notextile>
-h3. Check Docker access
-
-Certain features of @arvados-cwl-runner@ require access to Docker.
-
-You can determine if you have access to Docker by running @docker version@:
+The tutorial data is hosted on "https://playground.arvados.org":https://playground.arvados.org (also referred to by the identifier *pirca*). If you are using a different Arvados instance, you may need to copy the data to your own instance. One way to do this is with "arv-copy":{{site.baseurl}}/user/topics/arv-copy.html (this requires signing up for a free playground.arvados.org account).
<notextile>
-<pre><code>~$ <span class="userinput">docker version</span>
-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
+<pre><code>~$ <span class="userinput">arv-copy --src pirca --dst settings 2463fa9efeb75e099685528b3b9071e0+438</span>
+~$ <span class="userinput">arv-copy --src pirca --dst settings ae480c5099b81e17267b7445e35b4bc7+180</span>
</code></pre>
</notextile>
-If this returns an error, contact the sysadmin of your cluster for assistance.
+If you do not wish to create an account on "https://playground.arvados.org":https://playground.arvados.org, you may download the files anonymously and upload them to your local Arvados instance:
-h3. Get the example files
+"https://collections.pirca.arvadosapi.com/c=2463fa9efeb75e099685528b3b9071e0+438/":https://collections.pirca.arvadosapi.com/c=2463fa9efeb75e099685528b3b9071e0+438/
-The tutorial files are located in the documentation section of the Arvados source repository:
+"https://collections.pirca.arvadosapi.com/c=ae480c5099b81e17267b7445e35b4bc7+180/":https://collections.pirca.arvadosapi.com/c=ae480c5099b81e17267b7445e35b4bc7+180/
-<notextile>
-<pre><code>~$ <span class="userinput">git clone https://github.com/curoverse/arvados</span>
-~$ <span class="userinput">cd arvados/doc/user/cwl/bwa-mem</span>
-</code></pre>
-</notextile>
+h2(#submitting). Submitting a workflow to an Arvados cluster
-The tutorial data is hosted on "https://cloud.curoverse.com":https://cloud.curoverse.com (also referred to by the identifier *qr1hi*). If you are using a different Arvados instance, you may need to copy the data to your own instance. The easiest way to do this is with "arv-copy":{{site.baseurl}}/user/topics/arv-copy.html (this requires signing up for a free cloud.curoverse.com account).
+h3. Submit a workflow and wait for results
+
+Use @arvados-cwl-runner@ to submit CWL workflows to Arvados. After submitting the job, it will wait for the workflow to complete and print out the final result to standard output.
+
+*Note:* Once submitted, the workflow runs entirely on Arvados, so even if you log out, the workflow will continue to run. However, if you interrupt @arvados-cwl-runner@ with control-C it will cancel the workflow.
<notextile>
-<pre><code>~$ <span class="userinput">arv-copy --src qr1hi --dst settings 2463fa9efeb75e099685528b3b9071e0+438</span>
-~$ <span class="userinput">arv-copy --src qr1hi --dst settings ae480c5099b81e17267b7445e35b4bc7+180</span>
+<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner bwa-mem.cwl bwa-mem-input.yml</span>
+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": {
+ "location": "keep:54325254b226664960de07b3b9482349+154/HWI-ST1027_129_D0THKACXX.1_1.sam",
+ "checksum": "sha1$0dc46a3126d0b5d4ce213b5f0e86e2d05a54755a",
+ "class": "File",
+ "size": 30738986
+ }
+}
</code></pre>
</notextile>
-If you do not wish to create an account on "https://cloud.curoverse.com":https://cloud.curoverse.com, you may download the files anonymously and upload them to your local Arvados instance:
+h3. Referencing files
-"https://cloud.curoverse.com/collections/2463fa9efeb75e099685528b3b9071e0+438":https://cloud.curoverse.com/collections/2463fa9efeb75e099685528b3b9071e0+438
+When running a workflow on an Arvados cluster, the input files must be stored in Keep. There are several ways this can happen.
-"https://cloud.curoverse.com/collections/ae480c5099b81e17267b7445e35b4bc7+180":https://cloud.curoverse.com/collections/ae480c5099b81e17267b7445e35b4bc7+180
+A URI reference to Keep uses the @keep:@ scheme followed by either the portable data hash or UUID of the collection and then the location of the file inside the collection. For example, @keep:2463fa9efeb75e099685528b3b9071e0+438/19.fasta.bwt@ or @keep:zzzzz-4zz18-zzzzzzzzzzzzzzz/19.fasta.bwt@.
-h2. Submitting a workflow to an Arvados cluster
+If you reference a file in "arv-mount":{{site.baseurl}}/user/tutorials/tutorial-keep-mount-gnu-linux.html, such as @/home/example/keep/by_id/2463fa9efeb75e099685528b3b9071e0+438/19.fasta.bwt@, then @arvados-cwl-runner@ will automatically determine the appropriate Keep URI reference.
-{% include 'arvados_cwl_runner' %}
+If you reference a local file which is not in @arv-mount@, then @arvados-cwl-runner@ will upload the file to Keep and use the Keep URI reference from the upload.
-h2. Work reuse
+You can also execute CWL files that have been uploaded Keep:
+
+<notextile>
+<pre><code>
+~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arv-put --portable-data-hash --name "bwa-mem.cwl" bwa-mem.cwl</span>
+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$ <span class="userinput">arvados-cwl-runner keep:f141fc27e7cfa7f7b6d208df5e0ee01b+59/bwa-mem.cwl bwa-mem-input.yml</span>
+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 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
+ }
+}
+</code></pre>
+</notextile>
+
+Note: uploading a workflow file to Keep is _not_ the same as registering the workflow for use in Workbench. See "Registering a workflow to use in Workbench":#registering below.
+
+h3. Work reuse
Workflows submitted with @arvados-cwl-runner@ will take advantage of Arvados job reuse. If you submit a workflow which is identical to one that has run before, it will short cut the execution and return the result of the previous run. This also applies to individual workflow steps. For example, a two step workflow where the first step has run before will reuse results for first step and only execute the new second step. You can disable this behavior with @--disable-reuse@.
-h2. Referencing files
+h3. Command line options
-When running a workflow on an Arvados cluster, the input files must be stored in Keep. There are several ways this can happen.
+See "arvados-cwl-runner options":{{site.baseurl}}/user/cwl/cwl-run-options.html
-A URI reference to Keep uses the @keep:@ scheme followed by the portable data hash, collection size, and path to the file inside the collection. For example, @keep:2463fa9efeb75e099685528b3b9071e0+438/19.fasta.bwt@.
+h2(#registering). Registering a workflow to use in Workbench
-If you reference a file in "arv-mount":{{site.baseurl}}/user/tutorials/tutorial-keep-mount.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.
+Use @--create-workflow@ to register a CWL workflow with Arvados. This enables you to share workflows with other Arvados users, and run them by clicking the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a process...</span> button on the Workbench Dashboard and on the command line by UUID.
-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.
+<notextile>
+<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --create-workflow bwa-mem.cwl</span>
+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
+</code></pre>
+</notextile>
-h2. Registering a workflow to use in Workbench
+You can provide a partial input file to set default values for the workflow input parameters. You can also use the @--name@ option to set the name of the workflow:
-Use @--create-workflow@ to register a CWL workflow with Arvados. This enables you to share workflows with other Arvados users, and run them by clicking the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a process...</span> button on the Workbench Dashboard.
+<notextile>
+<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --name "My workflow with defaults" --create-workflow bwa-mem.cwl bwa-mem-template.yml</span>
+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
+</code></pre>
+</notextile>
-{% include 'register_cwl_workflow' %}
+h3. Running registered workflows at the command line
-h2. Making workflows directly executable
+You can run a registered workflow at the command line by its UUID:
+
+<notextile>
+<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner pirca-7fd4e-3nqbw08vtjl8ybz --help</span>
+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
+</code></pre>
+</notextile>
+
+h2(#executable). Make a workflow file directly executable
You can make a workflow file directly executable (@cwl-runner@ should be an alias to @arvados-cwl-runner@) by adding the following line to the top of the file:
<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">./bwa-mem.cwl bwa-mem-input.yml</span>
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": {
<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">./bwa-mem-input.yml</span>
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": {
</code></pre>
</notextile>
-h2. Developing workflows
-
-For an introduction and and detailed documentation about writing CWL, see the "CWL User Guide":http://commonwl.org/v1.0/UserGuide.html and the "CWL Specification":http://commonwl.org/v1.0 .
-
-To run on Arvados, a workflow should provide a @DockerRequirement@ in the @hints@ section.
-
-When developing a workflow, it is often helpful to run it on the local host to avoid the overhead of submitting to the cluster. To execute a workflow only on the local host (without submitting jobs to an Arvados cluster) you can use the @cwltool@ command. Note that you must also have the input data accessible on the local host. You can use @arv-get@ to fetch the data from Keep.
-
-<notextile>
-<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arv-get 2463fa9efeb75e099685528b3b9071e0+438/ .</span>
-156 MiB / 156 MiB 100.0%
-~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arv-get ae480c5099b81e17267b7445e35b4bc7+180/ .</span>
-23 MiB / 23 MiB 100.0%
-~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">cwltool bwa-mem-input.yml bwa-mem-input-local.yml</span>
-cwltool 1.0.20160629140624
-[job bwa-mem.cwl] /home/example/arvados/doc/user/cwl/bwa-mem$ docker \
- run \
- -i \
- --volume=/home/example/arvados/doc/user/cwl/bwa-mem/19.fasta.ann:/var/lib/cwl/job979368791_bwa-mem/19.fasta.ann:ro \
- --volume=/home/example/arvados/doc/user/cwl/bwa-mem/HWI-ST1027_129_D0THKACXX.1_1.fastq:/var/lib/cwl/job979368791_bwa-mem/HWI-ST1027_129_D0THKACXX.1_1.fastq:ro \
- --volume=/home/example/arvados/doc/user/cwl/bwa-mem/19.fasta.sa:/var/lib/cwl/job979368791_bwa-mem/19.fasta.sa:ro \
- --volume=/home/example/arvados/doc/user/cwl/bwa-mem/19.fasta.amb:/var/lib/cwl/job979368791_bwa-mem/19.fasta.amb:ro \
- --volume=/home/example/arvados/doc/user/cwl/bwa-mem/19.fasta.pac:/var/lib/cwl/job979368791_bwa-mem/19.fasta.pac:ro \
- --volume=/home/example/arvados/doc/user/cwl/bwa-mem/HWI-ST1027_129_D0THKACXX.1_2.fastq:/var/lib/cwl/job979368791_bwa-mem/HWI-ST1027_129_D0THKACXX.1_2.fastq:ro \
- --volume=/home/example/arvados/doc/user/cwl/bwa-mem/19.fasta.bwt:/var/lib/cwl/job979368791_bwa-mem/19.fasta.bwt:ro \
- --volume=/home/example/arvados/doc/user/cwl/bwa-mem:/var/spool/cwl:rw \
- --volume=/tmp/tmpgzyou9:/tmp:rw \
- --workdir=/var/spool/cwl \
- --read-only=true \
- --log-driver=none \
- --user=1001 \
- --rm \
- --env=TMPDIR=/tmp \
- --env=HOME=/var/spool/cwl \
- biodckr/bwa \
- bwa \
- mem \
- -t \
- 1 \
- -R \
- '@RG ID:arvados_tutorial PL:illumina SM:HWI-ST1027_129' \
- /var/lib/cwl/job979368791_bwa-mem/19.fasta \
- /var/lib/cwl/job979368791_bwa-mem/HWI-ST1027_129_D0THKACXX.1_1.fastq \
- /var/lib/cwl/job979368791_bwa-mem/HWI-ST1027_129_D0THKACXX.1_2.fastq > /home/example/arvados/doc/user/cwl/bwa-mem/HWI-ST1027_129_D0THKACXX.1_1.sam
-[M::bwa_idx_load_from_disk] read 0 ALT contigs
-[M::process] read 100000 sequences (10000000 bp)...
-[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 4745, 1, 0)
-[M::mem_pestat] skip orientation FF as there are not enough pairs
-[M::mem_pestat] analyzing insert size distribution for orientation FR...
-[M::mem_pestat] (25, 50, 75) percentile: (154, 181, 214)
-[M::mem_pestat] low and high boundaries for computing mean and std.dev: (34, 334)
-[M::mem_pestat] mean and std.dev: (185.63, 44.88)
-[M::mem_pestat] low and high boundaries for proper pairs: (1, 394)
-[M::mem_pestat] skip orientation RF as there are not enough pairs
-[M::mem_pestat] skip orientation RR as there are not enough pairs
-[M::mem_process_seqs] Processed 100000 reads in 9.848 CPU sec, 9.864 real sec
-[main] Version: 0.7.12-r1039
-[main] CMD: bwa mem -t 1 -R @RG ID:arvados_tutorial PL:illumina SM:HWI-ST1027_129 /var/lib/cwl/job979368791_bwa-mem/19.fasta /var/lib/cwl/job979368791_bwa-mem/HWI-ST1027_129_D0THKACXX.1_1.fastq /var/lib/cwl/job979368791_bwa-mem/HWI-ST1027_129_D0THKACXX.1_2.fastq
-[main] Real time: 10.061 sec; CPU: 10.032 sec
-Final process status is success
-{
- "aligned_sam": {
- "size": 30738959,
- "path": "/home/example/arvados/doc/user/cwl/bwa-mem/HWI-ST1027_129_D0THKACXX.1_1.sam",
- "checksum": "sha1$0c668cca45fef02397bb5302880526d300ee4dac",
- "class": "File"
- }
-}
-</code></pre>
-</notextile>
+h2(#setup). Setting up arvados-cwl-runner
-If you get the error @JavascriptException: Long-running script killed after 20 seconds.@ this may be due to the Dockerized Node.js engine taking too long to start. You may address this by installing Node.js locally (run @apt-get install nodejs@ on Debian or Ubuntu) or by specifying a longer timeout with the @--eval-timeout@ option. For example, run the workflow with @cwltool --eval-timeout=40@ for a 40-second timeout.
+See "Arvados CWL Runner":{{site.baseurl}}/sdk/python/arvados-cwl-runner.html
projects / arvados.git / blobdiff