How to install pygomodo locally

To install pygomodo locally you need:

Step 1 - Install all python packages from the environment.yml file.

conda env create -f environment.yml

Step 2 - Install hh-suite

Download and install:

https://github.com/soedinglab/hh-suite

or

conda install -c bioconda hhsuite

Step 3 - Install rdock

Download and install:

https://github.com/CBDD/rDock

⚠️ Warning: Do not run make install! Instead, make a copy of ALL rDock built binaries to your custom directory.

Step 4 - Install pdbx

Download and install:

https://github.com/soedinglab/pdbx

or

conda install -c conda-forge mmcif_pdbx

Step 5 - install modeller

Download and install:

https://salilab.org/modeller/download_installation.html

or

conda install -c salilab modeller

Step 6 - Decompress the pygomodo databases

Go to the directory pygomodo/databases and:

tar -xf GPCR_profiles_db.xz

Go to the directory pygomodo/databases/GPCR_templates and:

tar -xf hmm_profiles.xz

tar -xf pdb_clean_structures.xz

Step 7 - Copy the pygomodo code to python site-packages

cp -r pygomodo <your python path>/site_packages