X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/e4f96fc61cd9c85f91bdb0020bc365f2f4825ffb..b9d52229719c49e13aa8dfaae69da88a23fbfe44:/doc/user/tutorials/tutorial-keep.html.textile.liquid?ds=sidebyside diff --git a/doc/user/tutorials/tutorial-keep.html.textile.liquid b/doc/user/tutorials/tutorial-keep.html.textile.liquid index 6a797c001a..85d7dcc174 100644 --- a/doc/user/tutorials/tutorial-keep.html.textile.liquid +++ b/doc/user/tutorials/tutorial-keep.html.textile.liquid @@ -1,166 +1,56 @@ --- layout: default navsection: userguide -title: "Storing and Retrieving data using Keep" +title: "Uploading data" ... -This tutorial introduces you to the Arvados file storage system. +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 +notextile.
you
with your user id.
-
-First, log into the Arvados VM instance and set up the staging area:
-
-notextile. ~$ mkdir /scratch/you
-
-Next, download the file:
-
+# 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
~$ 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
/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
-
-/scratch/you$ arv keep ls c1bad4b39ca5a924e481008009d94e32+210
-var-GS000016015-ASM.tsv.bz2
-
-
-/scratch/you$ arv keep ls 887cd41e9c613463eab2f0d885c6dd96+83
-alice.txt
-bob.txt
-carol.txt
-
-/scratch/you$ arv keep ls -s c1bad4b39ca5a924e481008009d94e32+210
-221887 var-GS000016015-ASM.tsv.bz2
-
-/scratch/you$ arv keep get c1bad4b39ca5a924e481008009d94e32+210/ .
-
-/scratch/you$ arv keep get 887cd41e9c613463eab2f0d885c6dd96+83/alice.txt .
-
-/scratch/you$ md5sum var-GS000016015-ASM.tsv.bz2
-44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
-
-/scratch/you$ mkdir mnt
-/scratch/you$ arv-mount --collection c1bad4b39ca5a924e481008009d94e32+210 mnt &
-/scratch/you$ cd mnt
-/scratch/you/mnt$ ls
-var-GS000016015-ASM.tsv.bz2
-/scratch/you/mnt$ md5sum var-GS000016015-ASM.tsv.bz2
-44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
-/scratch/you/mnt$ cd ..
-/scratch/you$ fusermount -u mnt
-
-/scratch/you$ mkdir mnt
-/scratch/you$ arv-mount mnt &
-/scratch/you$ cd mnt/c1bad4b39ca5a924e481008009d94e32+210
-/scratch/you/mnt/c1bad4b39ca5a924e481008009d94e32+210$ ls
-var-GS000016015-ASM.tsv.bz2
-/scratch/you/mnt/c1bad4b39ca5a924e481008009d94e32+210$ md5sum var-GS000016015-ASM.tsv.bz2
-44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2
-/scratch/you/mnt/c1bad4b39ca5a924e481008009d94e32+210$ cd ../..
-/scratch/you$ fusermount -u mnt
+~$ mkdir tmp
+~$ echo "hello alice" > tmp/alice.txt
+~$ echo "hello bob" > tmp/bob.txt
+~$ echo "hello carol" > tmp/carol.txt
+~$ arv-put tmp
+0M / 0M 100.0%
+Collection saved as ...
+qr1hi-4zz18-yyyyyyyyyyyyyyy