4 title: Using Common Workflow Language
7 {% include 'what_is_cwl' %}
9 {% include 'tutorial_expectations' %}
11 h2. Preparing to work with Arvados CWL runner
13 h3. arvados-cwl-runner
15 The @arvados-cwl-runner@ client is installed by default on Arvados shell nodes.
17 However, if you do not have @arvados-cwl-runner@, you may install it using @pip@:
20 <pre><code>~$ <span class="userinput">virtualenv ~/venv</span>
21 ~$ <span class="userinput">. ~/venv/bin/activate</span>
22 ~$ <span class="userinput">pip install -U setuptools</span>
23 ~$ <span class="userinput">pip install arvados-cwl-runner</span>
27 h3. Check Docker access
29 Certain features of @arvados-cwl-runner@ require access to Docker.
31 You can determine if you have access to Docker by running @docker version@:
34 <pre><code>~$ <span class="userinput">docker version</span>
40 Built: Fri Nov 20 12:59:02 UTC 2015
48 Built: Fri Nov 20 12:59:02 UTC 2015
53 If this returns an error, contact the sysadmin of your cluster for assistance.
55 h3. Get the example files
57 The tutorial files are located in the documentation section of the Arvados source repository:
60 <pre><code>~$ <span class="userinput">git clone https://github.com/curoverse/arvados</span>
61 ~$ <span class="userinput">cd arvados/doc/user/cwl/bwa-mem</span>
65 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).
68 <pre><code>~$ <span class="userinput">arv-copy --src qr1hi --dst settings 2463fa9efeb75e099685528b3b9071e0+438</span>
69 ~$ <span class="userinput">arv-copy --src qr1hi --dst settings ae480c5099b81e17267b7445e35b4bc7+180</span>
73 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:
75 "https://cloud.curoverse.com/collections/2463fa9efeb75e099685528b3b9071e0+438":https://cloud.curoverse.com/collections/2463fa9efeb75e099685528b3b9071e0+438
77 "https://cloud.curoverse.com/collections/ae480c5099b81e17267b7445e35b4bc7+180":https://cloud.curoverse.com/collections/ae480c5099b81e17267b7445e35b4bc7+180
79 h2. Submitting a workflow to an Arvados cluster
81 {% include 'arvados_cwl_runner' %}
85 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@.
89 When running a workflow on an Arvados cluster, the input files must be stored in Keep. There are several ways this can happen.
91 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@.
93 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.
95 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.
97 h2. Registering a workflow to use in Workbench
99 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.
101 {% include 'register_cwl_workflow' %}
103 h2. Making workflows directly executable
105 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:
108 <pre><code>#!/usr/bin/env cwl-runner
113 <pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">./bwa-mem.cwl bwa-mem-input.yml</span>
114 arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
115 2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Upload local files: "bwa-mem.cwl"
116 2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Uploaded to qr1hi-4zz18-h7ljh5u76760ww2
117 2016-06-30 14:56:40 arvados.cwl-runner[27002] INFO: Submitted job qr1hi-8i9sb-fm2n3b1w0l6bskg
118 2016-06-30 14:56:41 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-fm2n3b1w0l6bskg) is Running
119 2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-fm2n3b1w0l6bskg) is Complete
120 2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Overall process status is success
123 "path": "keep:54325254b226664960de07b3b9482349+154/HWI-ST1027_129_D0THKACXX.1_1.sam",
124 "checksum": "sha1$0dc46a3126d0b5d4ce213b5f0e86e2d05a54755a",
132 You can even make an input file directly executable the same way with the following two lines at the top:
135 <pre><code>#!/usr/bin/env cwl-runner
136 cwl:tool: <span class="userinput">bwa-mem.cwl</span>
141 <pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">./bwa-mem-input.yml</span>
142 arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
143 2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Upload local files: "bwa-mem.cwl"
144 2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Uploaded to qr1hi-4zz18-h7ljh5u76760ww2
145 2016-06-30 14:56:40 arvados.cwl-runner[27002] INFO: Submitted job qr1hi-8i9sb-fm2n3b1w0l6bskg
146 2016-06-30 14:56:41 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-fm2n3b1w0l6bskg) is Running
147 2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-fm2n3b1w0l6bskg) is Complete
148 2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Overall process status is success
151 "path": "keep:54325254b226664960de07b3b9482349+154/HWI-ST1027_129_D0THKACXX.1_1.sam",
152 "checksum": "sha1$0dc46a3126d0b5d4ce213b5f0e86e2d05a54755a",
160 h2. Developing workflows
162 For an introduction and and detailed documentation about writing CWL, see the "CWL User Guide":http://commonwl.org/v1.0/UserGuide.html and the "CWL Specification":http://commonwl.org/v1.0 .
164 To run on Arvados, a workflow should provide a @DockerRequirement@ in the @hints@ section.
166 When developing a workflow, it is often helpful to run it on the local host to avoid the overhead of submitting to the cluster. To execute a workflow only on the local host (without submitting jobs to an Arvados cluster) you can use the @cwltool@ command. Note that you must also have the input data accessible on the local host. You can use @arv-get@ to fetch the data from Keep.
169 <pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arv-get 2463fa9efeb75e099685528b3b9071e0+438/ .</span>
170 156 MiB / 156 MiB 100.0%
171 ~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arv-get ae480c5099b81e17267b7445e35b4bc7+180/ .</span>
172 23 MiB / 23 MiB 100.0%
173 ~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">cwltool bwa-mem-input.yml bwa-mem-input-local.yml</span>
174 cwltool 1.0.20160629140624
175 [job bwa-mem.cwl] /home/example/arvados/doc/user/cwl/bwa-mem$ docker \
178 --volume=/home/example/arvados/doc/user/cwl/bwa-mem/19.fasta.ann:/var/lib/cwl/job979368791_bwa-mem/19.fasta.ann:ro \
179 --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 \
180 --volume=/home/example/arvados/doc/user/cwl/bwa-mem/19.fasta.sa:/var/lib/cwl/job979368791_bwa-mem/19.fasta.sa:ro \
181 --volume=/home/example/arvados/doc/user/cwl/bwa-mem/19.fasta.amb:/var/lib/cwl/job979368791_bwa-mem/19.fasta.amb:ro \
182 --volume=/home/example/arvados/doc/user/cwl/bwa-mem/19.fasta.pac:/var/lib/cwl/job979368791_bwa-mem/19.fasta.pac:ro \
183 --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 \
184 --volume=/home/example/arvados/doc/user/cwl/bwa-mem/19.fasta.bwt:/var/lib/cwl/job979368791_bwa-mem/19.fasta.bwt:ro \
185 --volume=/home/example/arvados/doc/user/cwl/bwa-mem:/var/spool/cwl:rw \
186 --volume=/tmp/tmpgzyou9:/tmp:rw \
187 --workdir=/var/spool/cwl \
193 --env=HOME=/var/spool/cwl \
200 '@RG ID:arvados_tutorial PL:illumina SM:HWI-ST1027_129' \
201 /var/lib/cwl/job979368791_bwa-mem/19.fasta \
202 /var/lib/cwl/job979368791_bwa-mem/HWI-ST1027_129_D0THKACXX.1_1.fastq \
203 /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
204 [M::bwa_idx_load_from_disk] read 0 ALT contigs
205 [M::process] read 100000 sequences (10000000 bp)...
206 [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 4745, 1, 0)
207 [M::mem_pestat] skip orientation FF as there are not enough pairs
208 [M::mem_pestat] analyzing insert size distribution for orientation FR...
209 [M::mem_pestat] (25, 50, 75) percentile: (154, 181, 214)
210 [M::mem_pestat] low and high boundaries for computing mean and std.dev: (34, 334)
211 [M::mem_pestat] mean and std.dev: (185.63, 44.88)
212 [M::mem_pestat] low and high boundaries for proper pairs: (1, 394)
213 [M::mem_pestat] skip orientation RF as there are not enough pairs
214 [M::mem_pestat] skip orientation RR as there are not enough pairs
215 [M::mem_process_seqs] Processed 100000 reads in 9.848 CPU sec, 9.864 real sec
216 [main] Version: 0.7.12-r1039
217 [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
218 [main] Real time: 10.061 sec; CPU: 10.032 sec
219 Final process status is success
223 "path": "/home/example/arvados/doc/user/cwl/bwa-mem/HWI-ST1027_129_D0THKACXX.1_1.sam",
224 "checksum": "sha1$0c668cca45fef02397bb5302880526d300ee4dac",
231 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.