Docker instructions missing path

[danjgale]

Hi, thanks for making this package!

I successfully installed macapype via Docker and tried to run it using the instructions provided here.

Unfortunately, /opt/packages/macapype/workflows/ used in the commands does not exist in the container. I am aware that the segment_pnh command can be used instead (see n.b. here), however, params_segment_pnh_ants_based.json cannot be found. I don't know if I'm missing something or if there is an error in the instructions. Any guidance here would be helpful! Thanks

[davidmeunier79]

Hi @danjgale , many thanks for your feedback.

Sorry the documentation has been fully updated according to the latest developments.

Indeed, it is not possible to call python workflows/segment_pnh.py directly from the docker image. The command has now changed and the default params.json are now called with the -species parameter in the command (in can take values macaque, marmo and baboon so far) and it will take defaut json parameters that are located in workflows, depending on -soft and -species (not all combinations are possible). If you want to specify your own user defined params it has be callable from outsite the image (i.e. with proper bindings).