A couple of questions about epitome
aigoyal opened this issue · 1 comments
Hi Joseph,
-
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? -
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?
Hi Aman,
- Pipelines are created using
epitome run
, notepitome check
. - Every time the
master
script is executed (the thing generated byepitome run
), it regenerates theproclist
andcmd
files using the modules in the/home
directory. - Yes, that module (and a few others) don't have
command.py
modules yet, so they won't work viaepitome run
(though you could manually edit amaster
script to get them to work at the moment.