how to get data from basespace

Question

[polangxin]

I need to get data from basespace, on command line mode (linux, putty).

Is there any scripts/apps do this work?

Thanks!

Answer 1

[IV]

I think that the easiest way has been recently introduced by Illumina with Basemount: http://blog.basespace.illumina.com/2015/07/23/basemount-a-linux-command-line-interface-for-basespace/

It still needs a bit of work but at last they have noticed that there is a (vast) Linux userspace in NGS.

[Dan D]

I second BaseMount. I use it every day and while it doesn't overcome some of the problems with the core BaseSpace philosophy of organizing projects and runs, it's a huge improvement over the old solutions for retrieving data.

Answer 2

[Dan D]

Yes, there is a way:

https://support.basespace.illumina.com/knowledgebase/articles/403618-python-run-downloader

[polangxin]

Great! Thanks a lot!

I'm not familiar with api, but this script works, and I'll learn more with it!

[jurgnjn]

Here's a modified version of Illumina's BaseSpace Python Run Downloader. It takes the project name (instead of the run id) and downloads base calls as fastq files (instead of getting the image/intensity data). It also checks that the sizes of the downloaded files match with what's reported by the BaseSpace REST API, and has rudimentary support for resuming interrupted downloads.

[Konrad]

Unfortunately this requires getting an API token and the description you link to is outdated — the “My Apps” link simply leads to the BaseSpace dashboard.

Answer 3

[dariober]

This is a solution using R with library BaseSpaceR (see also this post on SeqAnswers):

library(BaseSpaceR)
ACCESS_TOKEN<- 'dd9...mytoken...43'
PROJECT_ID<- '123456'  ## Get proj ID from url of the project

aAuth<- AppAuth(access_token = ACCESS_TOKEN)
selProj <- Projects(aAuth, id = PROJECT_ID, simplify = TRUE) 
sampl <- listSamples(selProj, limit= 1000)
inSample <- Samples(aAuth, id = Id(sampl), simplify = TRUE)
for(s in inSample){ 
    f <- listFiles(s, Extensions = ".gz")
    print(Name(f))
    getFiles(aAuth, id= Id(f), destDir = 'outdir/', verbose = TRUE)
}