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
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.
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!