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If you want to perform “omics”-like analyses you probably need to upload data (resources). By default Armadillo supports file uploads up to 500MB. If you need to upload larger resources, please contact molgenis-support@umcg.nl.
There are 2 roles you can assume using the package. The datamanager role and the researcher role.
The datamanager needs to make the data available to the researchers. Besides this you need to create the resources to access the data.
The researcher can call DataSHIELD analysis methods on the data uploaded by the datamanager.
As a datamanager you need to access the Armadillo webinterface to be able to access the resource.
omics
.ewas
.A second option to upload data (resources) is using Rstudio. As
datamanager you first need to login to Armadillo (as
superuser
)
armadillo.login("https://armadillo-demo.molgenis.net/")
#> [1] "We're opening a browser so you can log in with code 8N8MHJ"
If you want to install a package on the Armadillo Rserver you can
execute the following. The selected profile is always
default
if none is specified. If your profile doesn’t have
the resourcer
package installed, install it:
In order to be able to assign the data uploaded in the armadillo you
need to create the resources as well. The data files you uploaded to
armadillo, can be retrieved via the following URL:
yoururl + /storage/projects/{project name}/objects/{folder name}%2F{filename}
an example is:
https://armadillo-demo.molgenis.net/storage/projects/omics/objects/ewas%2Fgse66351_1.rda
.
Here the URL is https://armadillo-demo.molgenis.net/
, the
project name is omics
, the folder is ewas
and
the name of the data file is gse66351_1.rda
.
resGSE1 <- resourcer::newResource(
name = "GSE66351_1",
url = "https://armadillo-demo.molgenis.net/storage/projects/omics/objects/ewas%2Fgse66351_1.rda",
format = "ExpressionSet"
)
resGSE2 <- resourcer::newResource(
name = "GSE66351_1",
url = "https://armadillo-demo.molgenis.net/storage/projects/omics/objects/ewas%2Fgse66351_1.rda",
format = "ExpressionSet"
)
armadillo.upload_resource(project="omics", folder="ewas", resource = resGSE1, name = "GSE66351_1")
#> Compressing...
#> Uploaded ewas/GSE66351_1
armadillo.upload_resource(project="omics", folder="ewas", resource = resGSE2, name = "GSE66351_2")
#> Compressing...
#> Uploaded ewas/GSE66351_2
The data is now available for researcher to assign.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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