DeepMetaPSICOV_Kebnekaise_setup

This repo should let you setup DeepMetaPSICOV (DMP) in Kebnekaise.

Steps:

1. Enter to your Kebnekaise's user.
2. Check if you have already created the ~/pfs soft link in your $HOME, otherwise you have to do it like this:

~$ ln -s /pfs/nobackup$HOME $HOME/pfs

3. Clone this repository to one of your user folder.
   Checking and creating if need it a possible user folder:

~$ mkdir -p ~/pfs/softwares/<YOUR-PATH>

Using HTTPS:

~$ git clone https://github.com/tinchogb/DeepMetaPSICOV_Kebnekaise_setup ~/pfs/softwares/<YOUR-PATH>

Or using SSH:

~$ git clone git@github.com:tinchogb/DeepMetaPSICOV_Kebnekaise_setup ~/pfs/softwares/<YOUR-PATH>

4. Clone DMP from the corresponded github-site here to one folder of your own ~/pfs. Cloud be ~/pfs/softwares/.

~$ git clone https://github.com/psipred/DeepMetaPSICOV ~/pfs/softwares/<YOUR-PATH>

5. Check if you already have the hidden folder ~/.lmod.d in your $HOME. If not, create it in your ~/pfs, otherwise move it from $HOME to ~/pfs. At the end, you should have this: ~/pfs/.lmod.d.

~$ if [[ -d ~/.lmod.d ]] ; then mv ~/.lmod.d ~/pfs/.lmod.d; else mkdir -p ~/pfs/.lmod.d; fi

5.1. Make sure to create a symlink from the ~/pfs/l.mod.d to your home directory. This ensures that the module collections can be read from the batch system.

~$ ln -s /pfs/nobackup$HOME/.lmod.d $HOME/

6. From this cloned repository, move the file:
   6.1. mgb-ml-DMP to ~/pfs/.lmod.d

~$ if [[ -ef ~/pfs/softwares/<YOUR-PATH>/DeepMetaPSICOV_Kebnekaise_setup/mgb-ml-DMP ]] ; then mv ~/pfs/softwares/<YOUR-PATH>/DeepMetaPSICOV_Kebnekaise_setup/mgb-ml-DMP ~/pfs/.lmod.d; else echo "Check if your file path is correct.."; fi

6.2. run_DMP-Kebnekaiser-installation.sh to DMP/ directory (defined in step 4)

~$ if [[ -ef ~/pfs/softwares/<YOUR-PATH>/DeepMetaPSICOV_Kebnekaise_setup/run_DMP-Kebnekaiser-installation.sh ]] ; then mv ~/pfs/softwares/<YOUR-PATH>/DeepMetaPSICOV_Kebnekaise_setup/run_DMP-Kebnekaiser-installation.sh ~/pfs/softwares/<YOUR-PATH>/DeepMetaPSICOV; else echo "Check if your file path is correct.."; fi

7. Purge your current modules at Kebnekaise and then load the module collection:
   7.1. Purge modules

~$ ml purge

7.2. Loading module collection

~$ ml restore mgb-ml-DMP

7.3. Check that all the modular are loaded

~$ ml restore mgb-ml-DMP

8. Go to your DMP/ directory and run run_DMP-Kebnekaiser-installation.sh:

• Basic run like this (MANDATORY positional parameters):
  ~$ ./run_DMP-Kebnekaiser-installation.sh hhsuite-database-path blast-database-path
• Full run like this (Optional positional parameters):
  ~$ ./run_DMP-Kebnekaiser-installation.sh hhsuite-database-path blast-database-path hhblits-threats psiblast-threats psicov-threats ccmpred-threats freecontact-threats ccmpred-time psicov-time

9. When you have run it, one file is created in that folder, called old_unmodify_run_DMP.sh. This is a copy from the real unmodify running script (run_DMP.sh). This old_unmodify_run_DMP.sh is just for backup if you missed something or you want to change other settings and run again step 8 (like change databases, threats, etc).
10. If you need further information, you can open run_DMP-Kebnekaiser-installation.sh and read the first lines.

Thanks to DMP's group for the software!

Feel free to improve everything!