X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/488c69fb1049b5fff7fd544a1635e232ade001e3..d5ba0e97f8522ba3ce6ad36edf099c661a43f6b7:/doc/user/tutorials/tutorial-keep.textile diff --git a/doc/user/tutorials/tutorial-keep.textile b/doc/user/tutorials/tutorial-keep.textile index 825544079b..6683498e86 100644 --- a/doc/user/tutorials/tutorial-keep.textile +++ b/doc/user/tutorials/tutorial-keep.textile @@ -6,7 +6,7 @@ title: "Storing and Retrieving data using Arvados Keep" navorder: 11 --- -h1. Tutorial: Storing and Retrieving data using Arvados Keep +h1. Storing and Retrieving data using Arvados Keep This tutorial introduces you to the Arvados file storage system. @@ -21,29 +21,38 @@ The Arvados distributed file system is called *Keep*. Keep is a content-address h1. Putting Data into Keep -We will start with downloading a freely available VCF exome from the "Personal Genome Project (PGP)":http://www.personalgenomes.org subject "hu599905":https://my.personalgenomes.org/profile/hu599905 and add it to Keep. From an Arvados VM instance: +We will start with downloading a freely available VCF file from the "Personal Genome Project (PGP)":http://www.personalgenomes.org subject "hu599905":https://my.personalgenomes.org/profile/hu599905 to a staging directory on the VM, and then add it to Keep. + +First, log into the Arvados VM instance and set up the staging area: + +notextile.
$ mkdir /scratch/you
+
+Next, download the file:
$ curl -o var-GS000016015-ASM.tsv.bz2 'https://warehouse.personalgenomes.org/warehouse/f815ec01d5d2f11cb12874ab2ed50daa+234+K@ant/var-GS000016015-ASM.tsv.bz2'
+$ mkdir /scratch/you
+$ cd /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
$ rsync MyExome.vcf shell.qr1hi:MyExome.vcf
+notextile. $ scp MyData.vcf you@shell.arvados:/scratch/you/MyData.vcf
Now use @arv keep put@ to add your VCF data to Keep:
$ arv keep put var-GS000016015-ASM.tsv.bz2
-33a9f3842b01ea3fdf27cc582f5ea2af
+$ cd /scratch/you
+$ arv keep put var-GS000016015-ASM.tsv.bz2
+c1bad4b39ca5a924e481008009d94e32+210