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WarpToolsWrapper

A light wrapper around warp/M

Description

The aim of this wrapper is to be a light layer over WarpTools (and assoc. programs) command line arguments. The options to the different subprograms is intended to be provided via a config (e.g.movie_preprocessing.ini) file. Think of the config files as recipes that you use to run WarpTools on your linux box (cluster). While it is possible to run through the entire processing pipeline by concatenating all the commands into a single bash file, it is hoped that by providing different config files for different sub-routines, the user will be in a slightly better position to track their actions and allow them to be more exploratory with the data in their lab.

Installation

Since it is meant to be a light wrapper there arent many significant dependencies. However, typer is required. To install -

git clone git@github.com:shahpnmlab/WarpToolsWrapper.git
cd WarpToolsWrapper
pip install -e .

If you want to update the program, navigate to the WarpToolsWrapper directory on your computer and run

git pull

Running

Once installed you can call the program with warper

One can call the program in several ways -

  1. warper -c <recipe>.ini -> This will generate a script file with the following name warpTools_<HHMMSS>_<YYMMDD>.sh
  2. warper -c <recipe>.ini -o <a_unique_name>.sh -> This will generate a script file a user provided file name.
  3. warper -c <recipe>.ini -s <a_submission_script>.sh -> This will generate a submission script based on the user provided template.

    Note: Sucesssive calls -s will result in a submission script with accumulated bash commands. It is up to the user to review the submission script before submitting it.

Recipe file construction

The construction of the recipes has the following format

[<warp_main_cmd>:<sub_routine_within_cmd>]
option1 = <value1>
option2 = <value2>
option3 = <value3>

You can see example config files in the examples directory of the repo.