+# 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 the 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.)
-~$ 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'
+~$ curl -o var-GS000016015-ASM.tsv.bz2 'https://warehouse.pgp-hms.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
-
-{% 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:
-
+# Now upload the file to Keep using @arv-put@:
-/scratch/you$ arv keep put var-GS000016015-ASM.tsv.bz2
-c1bad4b39ca5a924e481008009d94e32+210
-/scratch/you$ rm var-GS000016015-ASM.tsv.bz2
+~$ arv-put var-GS000016015-ASM.tsv.bz2
+216M / 216M 100.0%
+Collection saved as ...
+qr1hi-4zz18-xxxxxxxxxxxxxxx
-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. Putting a directory
+Now 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 locator printed by @arv-put@ will appear under the *name* column.
-You can also use @arv keep put@ to add an entire directory:
+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*. This will open a dialog box where you can select a destination project for the collection. Click a project, then finally the
Move button.
-
-/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
-0M / 0M 100.0%
-887cd41e9c613463eab2f0d885c6dd96+83
-
-
+!{{ site.baseurl }}/images/workbench-move-selected.png!
-h1. Getting Data from Keep
+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.
-In Keep, information is stored in *data blocks*. Data blocks are normally between 1 byte and 64 megabytes in size. If a file exceeds the maximum size of a single data block, the file will be split across multiple data blocks until the entire file can be stored. These data blocks may be stored and replicated across multiple disks, servers, or clusters. Each data block has its own identifier for the contents of that specific data block.
+notextile.