I need to get data from basespace, on command line mode (linux, putty).
Is there any scripts/apps do this work?
Thanks!
I need to get data from basespace, on command line mode (linux, putty).
Is there any scripts/apps do this work?
Thanks!
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.
Yes, there is a way:
https://support.basespace.illumina.com/knowledgebase/articles/403618-python-run-downloader
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.
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)
}
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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.