ReactionDecoder folder right location?

[smoretti]

Hi
I wonder where the ReactionDecoder/ folder should be.

According to ReactionDecoder/README.md I would install ReactionDecoder.jar in a ReactionDecoder folder within the ehreact package folder, e.g. in python3.9/site-packages/ehreact/ReactionDecoder/ReactionDecoder.jar

But according to ehreact/helpers/transition_state.py the path should be python3.9/site-packages/ReactionDecoder/ReactionDecoder.jar in my case.

Did I understand it wrongly?

(I installed ehreact with pip)

[hesther]

Hi @smoretti, as a quick fix, you can download and install the package, instead of directly installing via pip (and then place the jar file to ehreact/ReactionDecoder/ReactionDecoder.jar with ehreact being the downloaded folder from GitHub). When installing with pip, the dependencies to data files change (so simply copying to the respective directory won't do unfortunately) - I am not sure how to fix this without distributing the actual jar file with ehreact - let me do a bit of googling

[smoretti]

In the meantime I have installed ehreact with pip (within EasyBuild) and copy manually ReactionDecoder.jar in python3.9/site-packages/ReactionDecoder/ (next to python3.9/site-packages/ehreact/) to satisfy the ReactionDecoder.jar path.