Download AppResults files at once

[Mariko T]

Hi all,

I ran 12 samples on MiSeq and performed the TruSeq Amplicon analysis on BaseSpace.

I'd like to download all the data under this folder using "bs" command in CLI.

~/BaseSpace/Projects/(my project)/AppResults/(sample1-12)/Files/ 

Specifically, I'd like to download *.bam *.bai *.gz data. 

What commands should I use?

I tried this command, but those data were not included.

".\bs run download /id (my project ID) /o ./Rundata

Thank you!

Mariko

[José Ferrão]

Hi, Mariko,

Please confirm exactly where the files are located. If they are in the project folder, maybe you can try:

bs project download --name "name_of_the_project" -o "output_dir"

and you can use additional options to select the files by extension, with --exclude and --include, e.g.:

bs project download --name "name_of_the_project" -o "output_dir" --exclude '*' --include '*.bam' --include '*.bai' --include '*.gz'

This command can also be useful:

bs list runs

Regards,

José

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José Ferrão

[Mariko T]

Hi  José,

Thank you for your response! It's really helpful.

Mariko

[Patricia Oliveira]

Hi!

Can you also download only specific files from an analysis within a project?

Cheers

Pat