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Welcome to the csa-atrophy wiki!

How to release

• go to "release"
• create new tag, e.g. rYYYYMMDD
• from master
• click "release"

Run on compute canada

First you must connect to compute canada with command ssh [email protected], then make sure you have the right python version installed

• module avail python

for example you can choose (python>3.6) ex: module load python/3.7.4

Once you have installed all requirements for csa-atrophy with command pip install -e ., you are ready to submit jobs to compute canada with command:

• run_all -config config_sct_run_batch.yml -job-template job_template.sh -n 32 (make sure to update job_template.sh)

You can check the status of your submitted jobs with command squeue -u userID

Once processing is finished, you can compress the files you want to transfer locally with command:

• tar -czvf results_t2_AAAAMMJJ.tar.gz log qc results process_data.sh

then to copy locally use command:

• scp -r [email protected]:/home/userID/scratch/results_csa_t2/results_t2_AAAAMMJJ.tar.gz /home/user/Github/results_t2_AAAAMMJJ

Initialize a virtual environment

Create a target directory for the virtual environment

• virtualenv --no-download ~/venv

then activate the virtual environment with command

• source ~/venv/bin/activate

you can now install python packages with pip. ex:pip install num

to deactivate the virtual environment run

• deactivate