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layout: default
navsection: userguide
title: "Uploading data"
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This tutorial describes how to to upload new Arvados data collections using the command line tool @arv-put@.  This example uses a freely available TSV file containing variant annotations from "Personal Genome Project (PGP)":http://www.pgp-hms.org participant "hu599905.":https://my.pgp-hms.org/profile/hu599905

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# Begin by installing the "Arvados Python SDK":{{site.baseurl}}/sdk/python/sdk-python.html on the system from which you will upload the data (such as your workstation, or a server containing data from your sequencer).  This will install the Arvados file upload tool, @arv-put@.  Alternately, you can log into an Arvados VM (instructions for "Unix":{{site.baseurl}}/user/getting_started/ssh-access-unix.html#login or "Windows":{{site.baseurl}}/user/getting_started/ssh-access-windows.html#login).
# On system from which you will upload data, configure the environment with the Arvados instance host name and authentication token as decribed in "Getting an API token.":{{site.baseurl}}/user/reference/api-tokens.html  (If you are logged into an Arvados VM, you can skip this step.)
# Download the following example file.  (If you are uploading your own data, you can skip this step.)
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<pre><code>~$ <span class="userinput">curl -o var-GS000016015-ASM.tsv.bz2 'https://warehouse.pgp-hms.org/warehouse/f815ec01d5d2f11cb12874ab2ed50daa+234+K@ant/var-GS000016015-ASM.tsv.bz2'</span>
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  216M  100  216M    0     0  10.0M      0  0:00:21  0:00:21 --:--:-- 9361k
</code></pre>
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# Now upload the file to Keep using @arv-put@:
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<pre><code>~$ <span class="userinput">arv-put var-GS000016015-ASM.tsv.bz2</span>
216M / 216M 100.0%
Collection saved as ...
qr1hi-4zz18-xxxxxxxxxxxxxxx
</code></pre>
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* The output value @qr1hi-4zz18-xxxxxxxxxxxxxxx@ is the uuid of the Arvados collection created.

Now 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 locator 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*. 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.

!{{ site.baseurl }}/images/workbench-move-selected.png!

Click on the *<i class="fa fa-fw fa-archive"></i> Show* button next to the collection's listing on a project page to go to the Workbench page for your collection.  On this page, you can see the collection's contents, download individual files, and set sharing options.

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h2(#dir). Putting a directory

If you give @arv-put@ a directory, it will recursively upload the entire directory:

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<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-put tmp</span>
0M / 0M 100.0%
Collection saved as ...
qr1hi-4zz18-yyyyyyyyyyyyyyy
</code></pre>
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