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
sftp geoftp@sftp-private.ncbi.nlm.nih.gov
password: <PASSWORD>

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