./crunch-run.txt
./stderr.txt
./stdout.txt
-~$ <span class="userinput">arv keep get <b>a01df2f7e5bc1c2ad59c60a837e90dc6+166</b>/stdout.txt</span>
+~$ <span class="userinput">arv-get <b>a01df2f7e5bc1c2ad59c60a837e90dc6+166</b>/stdout.txt</span>
2016-08-05T13:53:06.201011Z Hello, Crunch!
</code></pre>
</notextile>
h3(#arv-ws). arv ws
+This is a frontend to @arv-ws@.
+
@arv ws@ provides access to the websockets event stream.
<notextile>
h3(#arv-keep). arv keep
-@arv keep@ provides access to the Keep storage service.
+@arv keep@ commands for accessing the Keep storage service.
<notextile>
<pre>
h3(#arv-keep-ls). arv keep ls
+This is a frontend to @arv-ls@.
+
<notextile>
<pre>
$ <code class="userinput">arv keep ls --help</code>
h3(#arv-keep-get). arv keep get
+This is a frontend to @arv-get@.
+
<notextile>
<pre>
$ <code class="userinput">arv keep get --help</code>
h3(#arv-keep-put). arv keep put
+This is a frontend to @arv-put@.
+
<notextile>
<pre>
$ <code class="userinput">arv keep put --help</code>
h3(#arv-pipeline-run). arv pipeline run
+WARNING: this uses the obsolete "job" API. Don't use this. You should use @arvados-cwl-runner@ instead.
+
@arv pipeline run@ can be used to start a pipeline run from the command line.
The User Guide has a page with a bit more information on "using arv pipeline run":{{site.baseurl}}/user/topics/running-pipeline-command-line.html.
h3(#arv-run). arv run
+WARNING: this uses the obsolete "job" API. Don't use this. You should use @arvados-cwl-runner@ instead.
+
The @arv-run@ command creates Arvados pipelines at the command line that fan out to multiple concurrent tasks across Arvados compute nodes.
The User Guide has a page on "using arv-run":{{site.baseurl}}/user/topics/arv-run.html.
In order to reassemble the file, Keep stores a *collection* data block which lists in sequence the data blocks that make up the original file. A collection data block may store the information for multiple files, including a directory structure.
-In this example we will use @c1bad4b39ca5a924e481008009d94e32+210@, which we added to Keep in "how to upload data":{{ site.baseurl }}/user/tutorials/tutorial-keep.html. First let us examine the contents of this collection using @arv keep get@:
+In this example we will use @c1bad4b39ca5a924e481008009d94e32+210@, which we added to Keep in "how to upload data":{{ site.baseurl }}/user/tutorials/tutorial-keep.html. First let us examine the contents of this collection using @arv-get@:
<notextile>
-<pre><code>~$ <span class="userinput">arv keep get c1bad4b39ca5a924e481008009d94e32+210</span>
+<pre><code>~$ <span class="userinput">arv-get c1bad4b39ca5a924e481008009d94e32+210</span>
. 204e43b8a1185621ca55a94839582e6f+67108864 b9677abbac956bd3e86b1deb28dfac03+67108864 fc15aff2a762b13f521baf042140acec+67108864 323d2a3ce20370c4ca1d3462a344f8fd+25885655 0:227212247:var-GS000016015-ASM.tsv.bz2
</code></pre>
</notextile>
-The command @arv keep get@ fetches the contents of the collection @c1bad4b39ca5a924e481008009d94e32+210@. In this example, this collection includes a single file @var-GS000016015-ASM.tsv.bz2@ which is 227212247 bytes long, and is stored using four sequential data blocks, @204e43b8a1185621ca55a94839582e6f+67108864@, @b9677abbac956bd3e86b1deb28dfac03+67108864@, @fc15aff2a762b13f521baf042140acec+67108864@, and @323d2a3ce20370c4ca1d3462a344f8fd+25885655@.
+The command @arv-get@ fetches the contents of the collection @c1bad4b39ca5a924e481008009d94e32+210@. In this example, this collection includes a single file @var-GS000016015-ASM.tsv.bz2@ which is 227212247 bytes long, and is stored using four sequential data blocks, @204e43b8a1185621ca55a94839582e6f+67108864@, @b9677abbac956bd3e86b1deb28dfac03+67108864@, @fc15aff2a762b13f521baf042140acec+67108864@, and @323d2a3ce20370c4ca1d3462a344f8fd+25885655@.
-Let's use @arv keep get@ to download the first data block:
+Let's use @arv-get@ to download the first data block:
notextile. <pre><code>~$ <span class="userinput">cd /scratch/<b>you</b></span>
-/scratch/<b>you</b>$ <span class="userinput">arv keep get 204e43b8a1185621ca55a94839582e6f+67108864 > block1</span></code></pre>
+/scratch/<b>you</b>$ <span class="userinput">arv-get 204e43b8a1185621ca55a94839582e6f+67108864 > block1</span></code></pre>
{% include 'notebox_begin' %}
notextile. <pre><code>WARNING:root:API lookup failed for collection 204e43b8a1185621ca55a94839582e6f+67108864 (<class 'apiclient.errors.HttpError'>: <HttpError 404 when requesting https://qr1hi.arvadosapi.com/arvados/v1/collections/204e43b8a1185621ca55a94839582e6f%2B67108864?alt=json returned "Not Found">)</code></pre>
-This happens because @arv keep get@ tries to find a collection with this identifier. When that fails, it emits this warning, then looks for a datablock instead, which succeeds.
+This happens because @arv-get@ tries to find a collection with this identifier. When that fails, it emits this warning, then looks for a datablock instead, which succeeds.
{% include 'notebox_end' %}
Download the GATK binary tarball[1] -- e.g., @GenomeAnalysisTK-2.6-4.tar.bz2@ -- and "copy it to your Arvados VM":{{site.baseurl}}/user/tutorials/tutorial-keep.html.
<notextile>
-<pre><code>~$ <span class="userinput">arv keep put GenomeAnalysisTK-2.6-4.tar.bz2</span>
+<pre><code>~$ <span class="userinput">arv-put GenomeAnalysisTK-2.6-4.tar.bz2</span>
c905c8d8443a9c44274d98b7c6cfaa32+94
</code></pre>
</notextile>
</code></pre>
</notextile>
-This collection consists of the @md5sum.txt@ file. Use @arv keep get@ to show the contents of the @md5sum.txt@ file:
+This collection consists of the @md5sum.txt@ file. Use @arv-get@ to show the contents of the @md5sum.txt@ file:
<notextile>
-<pre><code>~$ <span class="userinput">arv keep get dd755dbc8d49a67f4fe7dc843e4f10a6+54/md5sum.txt</span>
+<pre><code>~$ <span class="userinput">arv-get dd755dbc8d49a67f4fe7dc843e4f10a6+54/md5sum.txt</span>
44b8ae3fde7a8a88d2f7ebd237625b4f ./var-GS000016015-ASM.tsv.bz2
</code></pre>
</notextile>
</code></pre>
</notextile>
-The log collection consists of one log file named with the job's UUID. You can access it using @arv keep get@:
+The log collection consists of one log file named with the job's UUID. You can access it using @arv-get@:
<notextile>
-<pre><code>~$ <span class="userinput">arv keep get xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx+91/qr1hi-8i9sb-xxxxxxxxxxxxxxx.log.txt</span>
+<pre><code>~$ <span class="userinput">arv-get xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx+91/qr1hi-8i9sb-xxxxxxxxxxxxxxx.log.txt</span>
2013-12-16_20:44:35 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 check slurm allocation
2013-12-16_20:44:35 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 node compute13 - 8 slots
2013-12-16_20:44:36 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 start
<notextile>
<pre><code>~/$USER/crunch_scripts$ <span class="userinput">arv keep ls e2ccd204bca37c77c0ba59fc470cd0f7+162</span>
./md5sum.txt
-~/$USER/crunch_scripts$ <span class="userinput">arv keep get e2ccd204bca37c77c0ba59fc470cd0f7+162/md5sum.txt</span>
+~/$USER/crunch_scripts$ <span class="userinput">arv-get e2ccd204bca37c77c0ba59fc470cd0f7+162/md5sum.txt</span>
0f1d6bcf55c34bed7f92a805d2d89bbf alice.txt
504938460ef369cd275e4ef58994cffe bob.txt
8f3b36aff310e06f3c5b9e95678ff77a carol.txt
SPDX-License-Identifier: CC-BY-SA-3.0
{% endcomment %}
-Arvados Data collections can be uploaded using either the @arv keep put@ command line tool or using Workbench.
+Arvados Data collections can be uploaded using either the @arv-put@ command line tool or using Workbench.
# "*Upload using command line tool*":#upload-using-command
# "*Upload using Workbench*":#upload-using-workbench
{% include 'tutorial_expectations' %}
-To upload a file to Keep using @arv keep put@:
+To upload a file to Keep using @arv-put@:
<notextile>
-<pre><code>~$ <span class="userinput">arv keep put var-GS000016015-ASM.tsv.bz2</span>
+<pre><code>~$ <span class="userinput">arv-put var-GS000016015-ASM.tsv.bz2</span>
216M / 216M 100.0%
Collection saved as ...
qr1hi-4zz18-xxxxxxxxxxxxxxx
Note: The file used in this example is a freely available TSV file containing variant annotations from the "Personal Genome Project (PGP)":http://www.pgp-hms.org participant "hu599905":https://my.pgp-hms.org/profile/hu599905), downloadable "here":https://warehouse.pgp-hms.org/warehouse/f815ec01d5d2f11cb12874ab2ed50daa+234+K@ant/var-GS000016015-ASM.tsv.bz2. Alternatively, you can replace @var-GS000016015-ASM.tsv.bz2@ with the name of any file you have locally, or you could get the TSV file by "downloading it from Keep.":{{site.baseurl}}/user/tutorials/tutorial-keep-get.html
-<notextile><a name="dir"></a></notextile>It is also possible to upload an entire directory with @arv keep put@:
+<notextile><a name="dir"></a></notextile>It is also possible to upload an entire directory with @arv-put@:
<notextile>
<pre><code>~$ <span class="userinput">mkdir tmp</span>
~$ <span class="userinput">echo "hello alice" > tmp/alice.txt</span>
~$ <span class="userinput">echo "hello bob" > tmp/bob.txt</span>
~$ <span class="userinput">echo "hello carol" > tmp/carol.txt</span>
-~$ <span class="userinput">arv keep put tmp</span>
+~$ <span class="userinput">arv-put tmp</span>
0M / 0M 100.0%
Collection saved as ...
qr1hi-4zz18-yyyyyyyyyyyyyyy
</code></pre>
</notextile>
-In both examples, the @arv keep put@ command created a collection. The first collection contains the single uploaded file. The second collection contains the entire uploaded directory.
+In both examples, the @arv-put@ command created a collection. The first collection contains the single uploaded file. The second collection contains the entire uploaded directory.
-@arv keep put@ accepts quite a few optional command line arguments, which are described on the "arv subcommands":{{site.baseurl}}/sdk/cli/subcommands.html#arv-keep-put page.
+@arv-put@ accepts quite a few optional command line arguments, which are described on the "arv subcommands":{{site.baseurl}}/sdk/cli/subcommands.html#arv-keep-put page.
h3. Locate your collection in Workbench
-Visit the Workbench *Dashboard*. Click on *Projects*<span class="caret"></span> dropdown menu in the top navigation menu, select your *Home* project. Your newly uploaded collection should appear near the top of the *Data collections* tab. The collection name printed by @arv keep put@ will appear under the *name* column.
+Visit the Workbench *Dashboard*. Click on *Projects*<span class="caret"></span> dropdown menu in the top navigation menu, select your *Home* project. Your newly uploaded collection should appear near the top of the *Data collections* tab. The collection name printed by @arv-put@ will appear under the *name* column.
To move the collection to a different project, check the box at the left of the collection row. Pull down the *Selection...*<span class="caret"></span> menu near the top of the page tab, and select *Move selected...* button. This will open a dialog box where you can select a destination project for the collection. Click a project, then finally the <span class="btn btn-sm btn-primary">Move</span> button.
projects / arvados.git / commitdiff