MAVIS (Mini) Tutorial

This tutorial is based on the data included in the tests folder of MAVIS. The data files are very small and this tutorial is really only intended for testing a MAVIS install. The data here is simulated and results are not representitive of the typical events you would see reported from MAVIS. For a more complete tutorial with actual fusion gene examples, please see the full tutorial.

The first step is to clone or download a zip of the MAVIS repository (https://github.com/bcgsc/mavis). You will need the tests directory. The tag you check out should correspond to the MAVIS version you have installed

git clone https://github.com/bcgsc/mavis.git
git checkout v2.0.0
mv mavis/tests .
rm -r mavis

Now you should have a folder called tests in your current directory. You will need to specify the scheduler if you want to test one that is not the default. For example

export MAVIS_SCHEDULER=LOCAL

Since this is a trivial example, it can easily be run locally. By default MAVIS in local mode will run a maximum of 1 less than the current cpu count processes. If you are running other things on the same machine you may find it useful to set this directly.

export MAVIS_CONCURRENCY_LIMIT=2

The above will limit mavis to running 2 processes concurrently.

Now you are ready to run MAVIS itself. This can be done in two commands (since the config file we are going to use is already built). First set up the pipeline

mavis setup tests/data/pipeline_config.cfg -o output_dir

Now if you run the schedule step (without the submit flag, schedule acts as a checker) you should see something like

mavis schedule -o output_dir/

                        MAVIS: 1.8.4
                        hostname: gphost08.bcgsc.ca
[2018-06-01 12:19:31] arguments
                        command = 'schedule'
                        log = None
                        log_level = 'INFO'
                        output = 'output_dir/'
                        resubmit = False
                        submit = False
[2018-06-01 12:19:31] validate
                        MV_mock-A36971_batch-s4W2Go4tinn49nkhSuusrE-1 is NOT SUBMITTED
                        MV_mock-A36971_batch-s4W2Go4tinn49nkhSuusrE-2 is NOT SUBMITTED
                        MV_mock-A47933_batch-s4W2Go4tinn49nkhSuusrE-1 is NOT SUBMITTED
                        MV_mock-A47933_batch-s4W2Go4tinn49nkhSuusrE-2 is NOT SUBMITTED
                        MV_mock-A47933_batch-s4W2Go4tinn49nkhSuusrE-3 is NOT SUBMITTED
[2018-06-01 12:19:31] annotate
                        MA_mock-A36971_batch-s4W2Go4tinn49nkhSuusrE-1 is NOT SUBMITTED
                        MA_mock-A36971_batch-s4W2Go4tinn49nkhSuusrE-2 is NOT SUBMITTED
                        MA_mock-A47933_batch-s4W2Go4tinn49nkhSuusrE-1 is NOT SUBMITTED
                        MA_mock-A47933_batch-s4W2Go4tinn49nkhSuusrE-2 is NOT SUBMITTED
                        MA_mock-A47933_batch-s4W2Go4tinn49nkhSuusrE-3 is NOT SUBMITTED
[2018-06-01 12:19:31] pairing
                        MP_batch-s4W2Go4tinn49nkhSuusrE is NOT SUBMITTED
[2018-06-01 12:19:31] summary
                        MS_batch-s4W2Go4tinn49nkhSuusrE is NOT SUBMITTED
                        rewriting: output_dir/build.cfg

Adding the submit argument will start the pipeline

mavis schedule -o output_dir/ --submit

After this completes, run schedule without the submit flag again and you should see something like

                        MAVIS: 1.8.4
                        hostname: gphost08.bcgsc.ca
[2018-06-01 13:15:28] arguments
                        command = 'schedule'
                        log = None
                        log_level = 'INFO'
                        output = 'output_dir/'
                        resubmit = False
                        submit = False
[2018-06-01 13:15:28] validate
                        MV_mock-A36971_batch-s4W2Go4tinn49nkhSuusrE-1 (zQJYndSMimaoALwcSSiYwi) is COMPLETED
                        MV_mock-A36971_batch-s4W2Go4tinn49nkhSuusrE-2 (BHFVf3BmXVrDUA5X4GGSki) is COMPLETED
                        MV_mock-A47933_batch-s4W2Go4tinn49nkhSuusrE-1 (tUpx3iabCrpR9iKu9rJtES) is COMPLETED
                        MV_mock-A47933_batch-s4W2Go4tinn49nkhSuusrE-2 (hgmH7nqPXZ49a8yTsxSUWZ) is COMPLETED
                        MV_mock-A47933_batch-s4W2Go4tinn49nkhSuusrE-3 (cEoRN582An3eAGALaSKmpJ) is COMPLETED
[2018-06-01 13:15:28] annotate
                        MA_mock-A36971_batch-s4W2Go4tinn49nkhSuusrE-1 (tMHiVR8ueNokhBDnghXYo6) is COMPLETED
                        MA_mock-A36971_batch-s4W2Go4tinn49nkhSuusrE-2 (AsNpNdvUyhNtKmRZqRSPpR) is COMPLETED
                        MA_mock-A47933_batch-s4W2Go4tinn49nkhSuusrE-1 (k7qQiAzxfC2dnZwsGH7BzD) is COMPLETED
                        MA_mock-A47933_batch-s4W2Go4tinn49nkhSuusrE-2 (dqAuhhcVKejDvHGBXn22xb) is COMPLETED
                        MA_mock-A47933_batch-s4W2Go4tinn49nkhSuusrE-3 (eB69Ghed2xAdp2VRdaCJBf) is COMPLETED
[2018-06-01 13:15:28] pairing
                        MP_batch-s4W2Go4tinn49nkhSuusrE (6LfEgBtBsmGhQpLQp9rXmi) is COMPLETED
[2018-06-01 13:15:28] summary
                        MS_batch-s4W2Go4tinn49nkhSuusrE (HDJhXgKjRmseahcQ7mgNoD) is COMPLETED
                        rewriting: output_dir/build.cfg
                        run time (hh/mm/ss): 0:00:00
                        run time (s): 0

If you see the above, then MAVIS has completed correctly!