-h1. Putting Data into Keep
+h2(#upload-using-command). Upload using command line tool
-We will start by downloading a freely available VCF file from "Personal Genome Project (PGP)":http://www.personalgenomes.org subject "hu599905":https://my.personalgenomes.org/profile/hu599905 to a staging directory on the VM, and adding it to Keep. In the following commands, replace *@you@* with your login name.
-
-First, log into your Arvados VM and set up the staging area:
-
-notextile.
~$ mkdir /scratch/you
-
-Next, download the file:
+{% include 'tutorial_expectations' %}
+To upload a file to Keep using @arv keep put@:
-~$ cd /scratch/you
-/scratch/you$ curl -o var-GS000016015-ASM.tsv.bz2 'https://warehouse.personalgenomes.org/warehouse/f815ec01d5d2f11cb12874ab2ed50daa+234+K@ant/var-GS000016015-ASM.tsv.bz2'
- % 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
+~$ arv keep put var-GS000016015-ASM.tsv.bz2
+216M / 216M 100.0%
+Collection saved as ...
+qr1hi-4zz18-xxxxxxxxxxxxxxx
-{% include 'notebox_begin' %}
-
-If you have your own data, for example @MyData.vcf@, you can use @scp@ or @rsync@ to copy from your local workstation to the shell VM (run this on your local workstation):
-
-notextile.
~$ scp MyData.vcf you@shell.arvados:/scratch/you/MyData.vcf
-
-{% include 'notebox_end' %}
-
-Now use @arv keep put@ to add your VCF data to Keep, then delete the local copy of the file:
-
-
-/scratch/you$ arv keep put var-GS000016015-ASM.tsv.bz2
-c1bad4b39ca5a924e481008009d94e32+210
-/scratch/you$ rm var-GS000016015-ASM.tsv.bz2
-
-
-The output value @c1bad4b39ca5a924e481008009d94e32+210@ from @arv keep put@ is the Keep locator. This enables you to access the file you just uploaded, and is explained in the next section.
+The output value @qr1hi-4zz18-xxxxxxxxxxxxxxx@ is the uuid of the Arvados collection created.
-h2(#dir). Putting a directory
+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
-You can also use @arv keep put@ to add an entire directory:
+
It is also possible to upload an entire directory with @arv keep put@:
-/scratch/you$ mkdir tmp
-/scratch/you$ echo "hello alice" > tmp/alice.txt
-/scratch/you$ echo "hello bob" > tmp/bob.txt
-/scratch/you$ echo "hello carol" > tmp/carol.txt
-/scratch/you$ arv keep put tmp
+~$ mkdir tmp
+~$ echo "hello alice" > tmp/alice.txt
+~$ echo "hello bob" > tmp/bob.txt
+~$ echo "hello carol" > tmp/carol.txt
+~$ arv keep put tmp
0M / 0M 100.0%
-887cd41e9c613463eab2f0d885c6dd96+83
+Collection saved as ...
+qr1hi-4zz18-yyyyyyyyyyyyyyy
-The locator @887cd41e9c613463eab2f0d885c6dd96+83@ represents a collection with multiple files.
+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.
-h1. Getting Data from Keep
+@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.
-h2. Using Workbench
+h3. Locate your collection in Workbench
-You may access collections through the "Collections section of Arvados Workbench":https://{{ site.arvados_workbench_host }}/collections at *Data* %(rarr)→% *Collections (data files)*. You can also access individual files within a collection. Some examples:
+Visit the Workbench *Dashboard*. Click on *Projects*
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.
-* "https://{{ site.arvados_workbench_host }}/collections/c1bad4b39ca5a924e481008009d94e32+210":https://{{ site.arvados_workbench_host }}/collections/c1bad4b39ca5a924e481008009d94e32+210
-* "https://{{ site.arvados_workbench_host }}/collections/887cd41e9c613463eab2f0d885c6dd96+83/alice.txt":https://{{ site.arvados_workbench_host }}/collections/887cd41e9c613463eab2f0d885c6dd96+83/alice.txt
+To move the collection to a different project, check the box at the left of the collection row. Pull down the *Selection...*
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
Move button.
-h2(#arv-get). Using the command line
+!{display: block;margin-left: 25px;margin-right: auto;}{{ site.baseurl }}/images/workbench-move-selected.png!
-You can view the contents of a collection using @arv keep ls@:
+Click on the *
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.
-
-/scratch/you$ arv keep ls c1bad4b39ca5a924e481008009d94e32+210
-var-GS000016015-ASM.tsv.bz2
-
+notextile.