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Docker giving error while reading python dictionary


(Iaarya) #1

Hi all,

I am trying to run this program code (https://github.com/CAIsr/volgenmodel-nipype/blob/master/volgenmodel.py) in docker.

This program code already contains a docker file to execute it .

I also have the original program code on my workstation and have executed it several times without any problem.
Now I am trying to execute the same code within a docker environment. I was able to build the docker images after running the docker file. With build successful, you are trying to run in windows environment and may not have all read-write permissions.

Next I try to implement the run command, as also provided in the read-me file of the program code.
I have observed that the program code is executed for only the first iteration (iterative stages are given as fit_stages=lin,1,3 where lin is a linear fit while 1 and 3 are nonlinear fit under opt)
When the program has to run a nonlinear fit, where it is supposed to read the default_conf file; given as python dictionary lists, it runs into error,

Stating: String found where operator expected at (eval 8) line 6, near "u’step’ => 8, u’"
and Error reading config from /scratch/volgenmodel-fast-example/workflow/write_conf_01/fit_stage_01.conf (fix it!)_

I observe that this is a perl script error asking to check at the syntax of code for discrepancies; I have checked the code the syntax is all correct. But I dont understand how I can resolve this error.(note: that there is some perl conversion involved in the code, but the default option doesnt implement it)

I have installed docker for windows 10 and run it on windows powershell.
The docker file installs , python 2.7 and other necessary software toolbox and FROM UBUNTU.

In short: I am getting a perl script error, when docker is running a code written in python. The same code outside docker on a linux workstation runs fine.

Can some one help me fix this issue. Should I include perl installation in my docker file

Kind regards.
IA