ms4_pipeline/workflow_notes.txt at master · JadhavLab/ms4_pipeline · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
                  _       __           __   ______
                 | |     / /___  _____/ /__/ __/ /___ _      __
                 | | /| / / __ \/ ___/ //_/ /_/ / __ \ | /| / /
                 | |/ |/ / /_/ / /  / ,< / __/ / /_/ / |/ |/ /
                 |__/|__/\____/_/  /_/|_/_/ /_/\____/|__/|__/

--------------------------------------------------------------------------------
Installation:
    - Get Mountainlab
    - Set ML_TEMPORTARY_DIRECTORY in mountainlab.env to be on the same drive as data
    - Install processors: qt-mountainview mountainlab mountainlab_pytools ml_ephys ml_ms4alg ml_ms3 ml_pyms
    - Get franklab custom processors:
        - pyms.add_curation_tags
        - pyms.anneal_segments

- ms_rn_filesetup: load preprocess data and export mda if mda does not exist. delete EMG spikes and mda files

- Create results directory expDir/dataDir/Mountain/animID_day_date.mountain/
- make subdir for each tetrode (tetList override): resDir/animID_dat_date.nt#/
- make prv referencing orig mda: raw.mda.prv
- make params file
- filter_mask_whiten
- sort_on_segs
- Add curation tags?
- export marks?
- import to matlab FF


Helper functions needed:
- mkTree
- create_prv
- ml_run_process
- import to matlab
- compare_ms_to_matclust
- setupMountainlab.sh
    - install conda if missing
    - install mountainlab
    - create env file
    - install processors