A couple of questions about epitome

[aigoyal]

Hi Joseph,

1. Everytime one generates a pipeline using epitome check, this creates an instance of a pipeline in the user's home directory. But, this copy of pipeline in the user's home directory is not referenced when the the pipeline is generated or executed ... correct?

2. I wanted to skip the T1 processing in freesurfer, so tried to add a module called init_t1-basic that is listed in the list of modules while one is building the pipeline. Pipeline generation immediately crashes with the following error:

   option #: 9
   Traceback (most recent call last):
   File "/srv/CODE/epitome/bin/epitome", line 764, in
   run_epitome()
   File "/srv/CODE/epitome/bin/epitome", line 665, in run_epitome
   line, output = eval(command)
   File "", line 1, in
   AttributeError: 'module' object has no attribute 'init_t1'

Any thoughts?

[josephdviviano]

Hi Aman,

1. Pipelines are created using epitome run, not epitome check.
2. Every time the master script is executed (the thing generated by epitome run), it regenerates the proclist and cmd files using the modules in the /home directory.
3. Yes, that module (and a few others) don't have command.py modules yet, so they won't work via epitome run (though you could manually edit a master script to get them to work at the moment.