navsection: userguide
title: "Uploading data"
...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
-This tutorial describes how to to upload new Arvados data collections using the command line tool @arv keep put@.
+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.
+
+# "*Upload using command line tool*":#upload-using-command
+# "*Upload using Workbench*":#upload-using-workbench
notextile. <div class="spaced-out">
-{% include 'tutorial_expectations' %}
+h2(#upload-using-command). Upload using command line tool
-h2. Upload using command prompt
+{% include 'tutorial_expectations' %}
To upload a file to Keep using @arv keep put@:
<notextile>
</code></pre>
</notextile>
+
The output value @qr1hi-4zz18-xxxxxxxxxxxxxxx@ is the uuid of the Arvados collection created.
-The file used in this example is 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), downloadable "here":https://warehouse.pgp-hms.org/warehouse/f815ec01d5d2f11cb12874ab2ed50daa+234+K@ant/var-GS000016015-ASM.tsv.bz2.
+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@:
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 locator 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 keep 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.
+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.
!{display: block;margin-left: 25px;margin-right: auto;}{{ site.baseurl }}/images/workbench-move-selected.png!
notextile. </div>
-h2. Upload using Workbench
+h2(#upload-using-workbench). Upload using Workbench
To upload using Workbench, visit the Workbench *Dashboard*. Click on *Projects*<span class="caret"></span> dropdown menu in the top navigation menu and select your *Home* project or any other project of your choosing. You will see the *Data collections* tab for this project, which lists the collections in this project.
-To upload a file, click on *Add data*<span class="caret"></span> dropdown menu and select *Upload files from my computer*.
+To upload files into a new collection, click on *Add data*<span class="caret"></span> dropdown menu and select *Upload files from my computer*.
!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/upload-using-workbench.png!
!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/upload-tab-in-new-collection.png!
-Click on the *Browse...* button and select the files you would like to upload. You can select multiple files. You will be able to click on the "Browse..." button multiple times and select files. After you are done selecting files to upload, click on the *<i class="fa fa-fw fa-play"></i> Start* button to start upload. This will start uploading files to Arvados and Workbench will show you the progress bar. When upload is completed, you will see an indication to that effect.
+Click on the *Browse...* button and select the files you would like to upload. Selected files will be added to a list of files to be uploaded. After you are done selecting files to upload, click on the *<i class="fa fa-fw fa-play"></i> Start* button to start upload. This will start uploading files to Arvados and Workbench will show you the progress bar. When upload is completed, you will see an indication to that effect.
!{display: block;margin-left: 25px;margin-right: auto;border:1px solid lightgray;}{{ site.baseurl }}/images/files-uploaded.png!
-*Note:* If you were to leave the collection page during the upload, the upload action will be aborted and you would need to upload again.
+*Note:* If you leave the collection page during the upload, the upload process will be aborted and you will need to upload the files again.
-*Note:* You will be able to use the *Add data*<span class="caret"></span> dropdown menu to add additional files to a previously collection as well.
+*Note:* You can also use the Upload tab to add additional files to an existing collection.
projects / arvados.git / blobdiff