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Handy scripts

GEO submission

  1. Login to GEO using Google
  2. Login to danGPU and change path to where the files are located
  3. It's either ~/Brickman/projects/ or ~/ucph/ndir/SUN-RENEW-Brickman/
  4. Download and update GEO template.
  5. NOTE: always make sure you use the latest version
  6. Click Transfer files and copy the login information for the ftp
  7. Adjust the variable from above step

NOTE: before running the command below, make sure you are already in the folder and you see all the folder/files you want to upload. It will make the steps below simpler.

# we run tmux session in case we loose connection
tmux new -s geo

# this loges you to FTP
password: <PASSWORD>

cd uploads/<FOLDER>
mkdir <RNAseq>
cd <RNAseq>
mput *