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Owl (& Gannet?) servers access for Sarah Tanja #1974

Closed sarahtanja closed 1 month ago

sarahtanja commented 1 month ago

I need access to owl (and maybe gannet?) servers:

stanja@uw.edu

Currently trying to follow NGS Data Management Plan from the Roberts Lab Handbook to put new M. capitata NGS raw RNA-seq files on owl ... but I currently only have access to raven

I have my code directory already on raven, but looking for advice on which server I can be operating on this quarter (gannet?)

Is it ok to have raw files on owl and run my code in raven?

kubu4 commented 1 month ago

Data backup - You should submit your RNA-seq data to NCBI. This should be the first step. Then, your data will have full metadata info and will be securely backed up.

Raven - Raven is designed for analysis and temporary storage. Work that you do on Raven should be backed up to another computer/website whenever some analysis is complete. GitHub is ideal, but if you have large files, that won't work. So, using another computer/server is the next option.

If you'd like to backup your work on one of our servers, I'll go ahead and get you set up. Use it as you see fit. Keep an eye on your email for an automated message from Gannet in a few mins...

kubu4 commented 1 month ago

Alrighty, you should get an email to log in to Gannet to change your password.

Your data directory can be viewed here: https://gannet.fish.washington.edu/stanja/

To access your directory via command line (ssh/rsync):

/volume2/web/stanja

sarahtanja commented 1 month ago

Thank you @kubu4 ! For migrating & backing up NGS files, I'm following the Azenta command line instructions, and plan to do this within gannet. Is that OK?

kubu4 commented 1 month ago

Certainly.

Don't forget to verify checksums after downloading.

sarahtanja commented 1 month ago

This is going to be a silly question... but how do I open terminal in gannet? I've gotten it figured out for raven (and followed along with some troubleshooting from an old issue by grace 1460, but can't even find the terminal application in gannet....

sarahtanja commented 1 month ago

Also, should I still copy files to owl/nightingale like the handbook directs too?

kubu4 commented 1 month ago

but how do I open terminal in gannet?

You need to ssh into Gannet from your own computer. Then, you can go from there.

Also, should I still copy files to owl/nightingale like the handbook directs too?

No. That location is limited to Roberts Lab projects. Thanks for checking.