conda environment installation issues #65
Description
Hello,
I want to use HERRO for its experimental R9.4.1 correction model, but I'm having issues running this command to set up the conda environment:
conda env create --file scripts/herro-env.yml
I get an error saying that some dependencies are not available from conda-forge and bioconda. I went into the .yml file and searched through the list of dependencies and version numbers and was able to find many of the missing ones in the intel, anaconda, cctbx202211, popiclab-dev channels. I assume I can add these to the "channels:" section and that would fix that issue.
I updated it in the file by adding (please ignore the github format change):
channels:
- conda-forge
- bioconda
- intel
- anaconda
- cctbx202211
- popiclab-dev
That said, there are still some dependencies that are no longer available with their listed version. These are:
- libsqlite=3.44.0 (version 3.45.0 is available in the mark.harfouche channel)
- openssl=3.1.4 (version 3.1.3 is available in the intel channel)
- python=3.10.13 (version 3.10.14 is available in the intel channel)
- seqkit=2.5.1 (version 2.8.2 is available in the bioconda channel)
- setuptools=68.2.2 (version 75.1.0 is available in the conda-forge channel)
I'm new to running singularity images, but if I'm understanding correctly, I will need this conda environment active for when I run this command:
singularity run --nv --bind <host_path>:<dest_path> herro.sif inference
Do you either have an updated herro-env.yml file or is it advisable for me to change the unavailable dependency versions to available ones (even though this may not have been tested) and try to finish installing the conda environment?
Thank you for any help you're able to provide on this