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Welcome to the scMultipleX Wiki!

Installation

Create new conda environment with python 3.8+:

conda create -n scmpx python=3.8

Activate the conda environment:

conda activate scmpx

Install scMultipleX:

pip install git+https://github.com/fmi-basel/gliberal-scMultipleX.git

Demo Run of scMultipleX

1. SSH into [email protected]:

ssh [email protected]

Note to Windows users: use power shell, or Putty.

2. Create an output directory (ex. username/scMultiplex-demo-test)

mkdir /tungstenfs/scratch/gliberal/Users/MY_SAVE_DIR

3. Copy demo config file (demo.ini) to own user folder

cp -t /tungstenfs/scratch/gliberal/Users/MY_SAVE_DIR /tungstenfs/scratch/gliberal/Code/Common/Repositories/gliberal-scMultipleX/resources/scMultipleX_testdata/demo.ini

4. Check that demo.ini it is copied over: ls /tungstenfs/scratch/gliberal/Users/MY_SAVE_DIR

You should see the demo.ini file listed in directory

5. Edit this config file:

• Remote into favorite virtual machine
• Navigate to demo.ini and open it in favorite text editor (e.g. Notepad++)
• Change base_dir_save to MY_SAVE_DIR path, save.

6. This step needs to be performed only once per machine and user Make symlink in user home bin directory that points to run_scmultiplex executable:

• cd $HOME
• mkdir -p bin
• `ln -s -t bin /tungstenfs/scratch/gliberal/Code/Common/Repositories/gliberal-scMultipleX/run_scmultiplex``
• ls -l bin

7. Run scMultipleX on test dataset

run_scmultiplex --help

run_scmultiplex --cpus 12 --config /tungstenfs/scratch/gliberal/Users/MY_SAVE_DIR/demo.ini --tasks 0 1 2 3 4 5 6 7

8. Check output folder!

Configuring scMultipleX

Running scMultipleX

scMultipleX is installed on tungsten at: scratch/gliberal/Code/Common/Repositories/gliberal-scMultipleX

and can be run on any machine.

To run on CPU cluster, configure the clusterme.sh file From vcl1043, navigate to folder containing clusterme.sh and run:

sbatch clusterme.sh