[ARVADOS] updated: 50a3cf5df8624618cc00308159fde643dd8d6f28
Git user
git at public.curoverse.com
Tue Dec 13 10:33:21 EST 2016
Summary of changes:
doc/_config.yml | 3 +-
doc/_includes/_register_cwl_workflow.liquid | 21 ---
doc/user/cwl/cwl-extensions.html.textile.liquid | 21 ++-
doc/user/cwl/cwl-runner.html.textile.liquid | 154 +++++++++++++++++-
...nning-workflow-command-line.html.textile.liquid | 155 ------------------
.../writing-cwl-workflow.html.textile.liquid | 176 +++++++++++++--------
6 files changed, 279 insertions(+), 251 deletions(-)
delete mode 100644 doc/_includes/_register_cwl_workflow.liquid
via 50a3cf5df8624618cc00308159fde643dd8d6f28 (commit)
from 8e8b3d8dd81e4fd9c910e6739c74998f3b6ed288 (commit)
Those revisions listed above that are new to this repository have
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commit 50a3cf5df8624618cc00308159fde643dd8d6f28
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Tue Dec 13 10:33:18 2016 -0500
10576: Integrate CWL extensions page, reorganize running and developing docs.
diff --git a/doc/_config.yml b/doc/_config.yml
index 3b60ee1..fbe95fa 100644
--- a/doc/_config.yml
+++ b/doc/_config.yml
@@ -44,7 +44,7 @@ navbar:
- user/topics/keep.html.textile.liquid
- user/topics/arv-copy.html.textile.liquid
- Running workflows at the command line:
- - user/topics/running-workflow-command-line.html.textile.liquid
+ - user/cwl/cwl-runner.html.textile.liquid
- user/topics/running-pipeline-command-line.html.textile.liquid
- user/topics/arv-run.html.textile.liquid
- Working with git repositories:
@@ -54,6 +54,7 @@ navbar:
- user/tutorials/intro-crunch.html.textile.liquid
- user/tutorials/writing-cwl-workflow.html.textile.liquid
- user/cwl/cwl-style.html.textile.liquid
+ - user/cwl/cwl-extensions.html.textile.liquid
- user/tutorials/running-external-program.html.textile.liquid
- user/topics/crunch-tools-overview.html.textile.liquid
- user/tutorials/tutorial-firstscript.html.textile.liquid
diff --git a/doc/_includes/_register_cwl_workflow.liquid b/doc/_includes/_register_cwl_workflow.liquid
deleted file mode 100644
index 438115b..0000000
--- a/doc/_includes/_register_cwl_workflow.liquid
+++ /dev/null
@@ -1,21 +0,0 @@
-<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 qr1hi-4zz18-7e0hedrmkuyoei3
-2016-07-01 12:21:01 arvados.cwl-runner[15796] INFO: Created template qr1hi-p5p6p-rjleou1dwr167v5
-qr1hi-p5p6p-rjleou1dwr167v5
-</code></pre>
-</notextile>
-
-You can provide a partial input file to set default values for the workflow input parameters:
-
-<notextile>
-<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --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 qr1hi-4zz18-0f91qkovk4ml18o
-2016-07-01 14:09:50 arvados.cwl-runner[3730] INFO: Created template qr1hi-p5p6p-0deqe6nuuyqns2i
-qr1hi-p5p6p-0deqe6nuuyqns2i
-</code></pre>
-</notextile>
diff --git a/doc/user/cwl/cwl-extensions.html.textile.liquid b/doc/user/cwl/cwl-extensions.html.textile.liquid
index 5fb5370..cd7037a 100644
--- a/doc/user/cwl/cwl-extensions.html.textile.liquid
+++ b/doc/user/cwl/cwl-extensions.html.textile.liquid
@@ -4,9 +4,16 @@ navsection: userguide
title: Arvados CWL Extensions
...
+To use Arvados CWL extensions, add the following section at the top of your CWL file:
+
<pre>
$namespaces:
arv: "http://arvados.org/cwl#"
+</pre>
+
+Arvados extensions should go into the @hints@ section, for example:
+
+<pre>
hints:
arv:RunInSingleContainer: {}
arv:RuntimeConstraints:
@@ -25,21 +32,23 @@ h2. arv:RuntimeConstraints
Set Arvados-specific runtime hints.
-|field|type|description|
+table(table table-bordered table-condensed).
+|_. Field |_. Type |_. Description |
|keep_cache|int|Size of file data buffer for Keep mount in MiB. Default is 256 MiB. Increase this to reduce cache thrashing in situations such as accessing multiple large (64+ MiB) files at the same time, or performing random access on a large file.|
-|outputDirType|enum|Preferred backing store for output staging. If not specified, the system may choose which one to use.
+|outputDirType|enum|Preferred backing store for output staging. If not specified, the system may choose which one to use. One of *local_output_dir* or *keep_output_dir*|
-local_output_dir: Use regular file system local to the compute node. There must be sufficient local scratch space to store entire output; specify this with `outdirMin` of `ResourceRequirement`. Files are batch uploaded to Keep when the process completes. Most compatible, but upload step can be time consuming for very large files.
+*local_output_dir*: Use regular file system local to the compute node. There must be sufficient local scratch space to store entire output; specify this with `outdirMin` of `ResourceRequirement`. Files are batch uploaded to Keep when the process completes. Most compatible, but upload step can be time consuming for very large files.
-keep_output_dir: Use writable Keep mount. Files are streamed to Keep as they are written. Does not consume local scratch space, but does consume RAM for output buffers (up to 192 MiB per file simultaneously open for writing.) Best suited to processes which produce sequential output of large files (non-sequential writes may produced fragmented file manifests). Supports regular files and directories, does not support special files such as symlinks, hard links, named pipes, named sockets, or device nodes.|
+*keep_output_dir*: Use writable Keep mount. Files are streamed to Keep as they are written. Does not consume local scratch space, but does consume RAM for output buffers (up to 192 MiB per file simultaneously open for writing.) Best suited to processes which produce sequential output of large files (non-sequential writes may produced fragmented file manifests). Supports regular files and directories, does not support special files such as symlinks, hard links, named pipes, named sockets, or device nodes.|
h2. arv:PartitionRequirement
Select preferred compute partitions on which to run jobs.
-|field|type|description|
+table(table table-bordered table-condensed).
+|_. Field |_. Type |_. Description |
|partition|string or array of string||
h2. arv:APIRequirement
-Indicates that process wants to access to the Arvados API. Will be granted limited network access and have ARVADOS_API_HOST and ARVADOS_API_TOKEN set in the environment.
+Indicates that process wants to access to the Arvados API. Will be granted limited network access and have @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ set in the environment.
diff --git a/doc/user/cwl/cwl-runner.html.textile.liquid b/doc/user/cwl/cwl-runner.html.textile.liquid
index bb7c82a..dc1415e 100644
--- a/doc/user/cwl/cwl-runner.html.textile.liquid
+++ b/doc/user/cwl/cwl-runner.html.textile.liquid
@@ -1,9 +1,161 @@
---
layout: default
navsection: userguide
-title: Running Common Workflow Language
+title: "Running an Arvados workflow"
...
{% 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 at .
+
+h3. Get the example files
+
+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
+
+<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>
+
+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).
+
+<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>
+~$ <span class="userinput">arv-copy --src qr1hi --dst settings 655c6cd07550151b210961ed1d3852cf+57</span>
+</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:
+
+"https://cloud.curoverse.com/collections/2463fa9efeb75e099685528b3b9071e0+438":https://cloud.curoverse.com/collections/2463fa9efeb75e099685528b3b9071e0+438
+
+"https://cloud.curoverse.com/collections/ae480c5099b81e17267b7445e35b4bc7+180":https://cloud.curoverse.com/collections/ae480c5099b81e17267b7445e35b4bc7+180
+
+"https://cloud.curoverse.com/collections/655c6cd07550151b210961ed1d3852cf+57":https://cloud.curoverse.com/collections/655c6cd07550151b210961ed1d3852cf+57
+
+h2. Submitting a workflow to an Arvados cluster
+
+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>~/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 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 14:57:12 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$0dc46a3126d0b5d4ce213b5f0e86e2d05a54755a",
+ "class": "File",
+ "size": 30738986
+ }
+}
+</code></pre>
+</notextile>
+
+h3. Submit a workflow with no waiting
+
+To submit a workflow and exit immediately, use the @--no-wait@ option. This will submit the workflow to Arvados, print out the UUID of the job that was submitted to standard output, and exit.
+
+<notextile>
+<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --no-wait 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 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
+</code></pre>
+</notextile>
+
+h2. 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 at .
+
+h2. 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 the portable data hash, collection size, and path to the file inside the collection. For example, @keep:2463fa9efeb75e099685528b3b9071e0+438/19.fasta.bwt at .
+
+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.
+
+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.
+
+You can also execute CWL files directly from Keep:
+
+<notextile>
+<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner keep:655c6cd07550151b210961ed1d3852cf+57/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 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 14:57:12 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$0dc46a3126d0b5d4ce213b5f0e86e2d05a54755a",
+ "class": "File",
+ "size": 30738986
+ }
+}
+</code></pre>
+</notextile>
+
+h2(#setup). Setting up arvados-cwl-runner
+
+By default, the @arvados-cwl-runner@ is installed on Arvados shell nodes. If you want to submit jobs from somewhere else, such as your workstation, you may install @arvados-cwl-runner@ using @pip@:
+
+<notextile>
+<pre><code>~$ <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>
+</code></pre>
+</notextile>
+
+h3. Check Docker access
+
+In order to pull and upload Docker images, @arvados-cwl-runner@ requires access to Docker. You do not need Docker if the Docker images you intend to use are already available in Aravdos.
+
+You can determine if you have access to Docker by running @docker version@:
+
+<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
+</code></pre>
+</notextile>
+
+If this returns an error, contact the sysadmin of your cluster for assistance.
diff --git a/doc/user/topics/running-workflow-command-line.html.textile.liquid b/doc/user/topics/running-workflow-command-line.html.textile.liquid
index 905aa12..e69de29 100644
--- a/doc/user/topics/running-workflow-command-line.html.textile.liquid
+++ b/doc/user/topics/running-workflow-command-line.html.textile.liquid
@@ -1,155 +0,0 @@
----
-layout: default
-navsection: userguide
-title: "Running an Arvados workflow"
-...
-
-{% include 'what_is_cwl' %}
-
-{% include 'tutorial_expectations' %}
-
-h2. arvados-cwl-runner
-
-Use the @arvados-cwl-runner@ tool to submit workflows to Arvados cluster at the command prompt. 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@ using @pip@:
-
-<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>
-</code></pre>
-</notextile>
-
-h3. Check Docker access
-
-In order to pull and upload Docker images, @arvados-cwl-runner@ requires access to Docker. You do not need Docker if the Docker images you intend to use are already available in Aravdos.
-
-You can determine if you have access to Docker by running @docker version@:
-
-<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
-</code></pre>
-</notextile>
-
-If this returns an error, contact the sysadmin of your cluster for assistance.
-
-h3. Get the example files
-
-The tutorial files are located in the documentation section of the Arvados source repository:
-
-<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>
-
-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).
-
-<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>
-~$ <span class="userinput">arv-copy --src qr1hi --dst settings 655c6cd07550151b210961ed1d3852cf+57</span>
-</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:
-
-"https://cloud.curoverse.com/collections/2463fa9efeb75e099685528b3b9071e0+438":https://cloud.curoverse.com/collections/2463fa9efeb75e099685528b3b9071e0+438
-
-"https://cloud.curoverse.com/collections/ae480c5099b81e17267b7445e35b4bc7+180":https://cloud.curoverse.com/collections/ae480c5099b81e17267b7445e35b4bc7+180
-
-"https://cloud.curoverse.com/collections/655c6cd07550151b210961ed1d3852cf+57":https://cloud.curoverse.com/collections/655c6cd07550151b210961ed1d3852cf+57
-
-h2. Submitting a workflow to an Arvados cluster
-
-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 attempt to cancel the workflow.
-
-<notextile>
-<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner keep:655c6cd07550151b210961ed1d3852cf+57/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 14:57:12 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$0dc46a3126d0b5d4ce213b5f0e86e2d05a54755a",
- "class": "File",
- "size": 30738986
- }
-}
-</code></pre>
-</notextile>
-
-h3. Submit a workflow with no waiting
-
-To submit a workflow and exit immediately, use the @--no-wait@ option. This will submit the workflow to Arvados, print out the UUID of the job that was submitted to standard output, and exit.
-
-<notextile>
-<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --no-wait 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 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
-</code></pre>
-</notextile>
-
-h3. Run a workflow locally
-
-To run a workflow with local control, use @--local at . This means that the host where you run @arvados-cwl-runner@ will be responsible for submitting jobs. With @--local@, if you interrupt @arvados-cwl-runner@ or log out, the workflow will be terminated.
-
-<notextile>
-<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --local bwa-mem.cwl bwa-mem-input.yml</span>
-arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
-2016-07-01 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 10:05:46 arvados.cwl-runner[16290] INFO: Overall process status is success
-{
- "aligned_sam": {
- "size": 30738986,
- "path": "keep:15f56bad0aaa7364819bf14ca2a27c63+88/HWI-ST1027_129_D0THKACXX.1_1.sam",
- "checksum": "sha1$0dc46a3126d0b5d4ce213b5f0e86e2d05a54755a",
- "class": "File"
- }
-}
-</code></pre>
-</notextile>
-
-h2. 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 at .
-
-h2. 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 the portable data hash, collection size, and path to the file inside the collection. For example, @keep:2463fa9efeb75e099685528b3b9071e0+438/19.fasta.bwt at .
-
-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.
-
-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.
diff --git a/doc/user/tutorials/writing-cwl-workflow.html.textile.liquid b/doc/user/tutorials/writing-cwl-workflow.html.textile.liquid
index 335e9ce..258b024 100644
--- a/doc/user/tutorials/writing-cwl-workflow.html.textile.liquid
+++ b/doc/user/tutorials/writing-cwl-workflow.html.textile.liquid
@@ -8,69 +8,6 @@ title: "Writing a CWL workflow"
{% include 'tutorial_expectations' %}
-h2. Registering a workflow to use in Workbench
-
-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.
-
-{% include 'register_cwl_workflow' %}
-
-h2. Making workflows 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:
-
-<notextile>
-<pre><code>#!/usr/bin/env cwl-runner
-</code></pre>
-</notextile>
-
-<notextile>
-<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 14:57:12 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$0dc46a3126d0b5d4ce213b5f0e86e2d05a54755a",
- "class": "File",
- "size": 30738986
- }
-}
-</code></pre>
-</notextile>
-
-You can even make an input file directly executable the same way with the following two lines at the top:
-
-<notextile>
-<pre><code>#!/usr/bin/env cwl-runner
-cwl:tool: <span class="userinput">bwa-mem.cwl</span>
-</code></pre>
-</notextile>
-
-<notextile>
-<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <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 14:57:12 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$0dc46a3126d0b5d4ce213b5f0e86e2d05a54755a",
- "class": "File",
- "size": 30738986
- }
-}
-</code></pre>
-</notextile>
-
h2. Developing workflows
For an introduction and and detailed documentation about writing CWL, see the "CWL User Guide":http://commonwl.org/v1.0/UserGuide.html and the "CWL Specification":http://commonwl.org/v1.0 .
@@ -144,12 +81,117 @@ Final process status is success
If you get the error @JavascriptException: Long-running script killed after 20 seconds.@ this may be due to the Dockerized Node.js engine taking too long to start. You may address this by installing Node.js locally (run @apt-get install nodejs@ on Debian or Ubuntu) or by specifying a longer timeout with the @--eval-timeout@ option. For example, run the workflow with @cwltool --eval-timeout=40@ for a 40-second timeout.
-h2. Running a CWL workflow
+h2. Registering a workflow to use in Workbench
+
+Use @--create-workflow@ to register a CWL workflow with Arvados. This enables you to share workflows with other Arvados users, and run them by clicking the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a process...</span> button on the Workbench Dashboard.
+
+<notextile>
+<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --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 qr1hi-4zz18-7e0hedrmkuyoei3
+2016-07-01 12:21:01 arvados.cwl-runner[15796] INFO: Created template qr1hi-p5p6p-rjleou1dwr167v5
+qr1hi-p5p6p-rjleou1dwr167v5
+</code></pre>
+</notextile>
-h3. Running a workflow at command prompt
+You can provide a partial input file to set default values for the workflow input parameters:
+<notextile>
+<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --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 qr1hi-4zz18-0f91qkovk4ml18o
+2016-07-01 14:09:50 arvados.cwl-runner[3730] INFO: Created template qr1hi-p5p6p-0deqe6nuuyqns2i
+qr1hi-p5p6p-0deqe6nuuyqns2i
+</code></pre>
+</notextile>
+h2. Running registered workflows at the command line
-h3. Running a workflow using Workbench
+You can run a registered workflow at the command line by its UUID:
-The workflow can also be executed using Workbench. Go to the Workbench Dashboard and click the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a process...</span> button and select the desired workflow.
+<notextile>
+<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner 962eh-7fd4e-660fw86nz0w77mk bwa-mem-input.yml</span>
+</code></pre>
+</notextile>
+
+h2. Making workflows 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:
+
+<notextile>
+<pre><code>#!/usr/bin/env cwl-runner
+</code></pre>
+</notextile>
+
+<notextile>
+<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 14:57:12 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$0dc46a3126d0b5d4ce213b5f0e86e2d05a54755a",
+ "class": "File",
+ "size": 30738986
+ }
+}
+</code></pre>
+</notextile>
+
+You can even make an input file directly executable the same way with the following two lines at the top:
+
+<notextile>
+<pre><code>#!/usr/bin/env cwl-runner
+cwl:tool: <span class="userinput">bwa-mem.cwl</span>
+</code></pre>
+</notextile>
+
+<notextile>
+<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <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 14:57:12 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$0dc46a3126d0b5d4ce213b5f0e86e2d05a54755a",
+ "class": "File",
+ "size": 30738986
+ }
+}
+</code></pre>
+</notextile>
+
+h3. Control a workflow locally
+
+To run a workflow with local control, use @--local at . This means that the host where you run @arvados-cwl-runner@ will be responsible for submitting jobs, however, the jobs themselves will still run on the Arvados cluster. With @--local@, if you interrupt @arvados-cwl-runner@ or log out, the workflow will be terminated.
+
+<notextile>
+<pre><code>~/arvados/doc/user/cwl/bwa-mem$ <span class="userinput">arvados-cwl-runner --local bwa-mem.cwl bwa-mem-input.yml</span>
+arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
+2016-07-01 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 10:05:46 arvados.cwl-runner[16290] INFO: Overall process status is success
+{
+ "aligned_sam": {
+ "size": 30738986,
+ "path": "keep:15f56bad0aaa7364819bf14ca2a27c63+88/HWI-ST1027_129_D0THKACXX.1_1.sam",
+ "checksum": "sha1$0dc46a3126d0b5d4ce213b5f0e86e2d05a54755a",
+ "class": "File"
+ }
+}
+</code></pre>
+</notextile>
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