HOWTO: install Surface Morphometrics Pipeline on CentOS 7.X

Another boring post about computing stuff. A brief description of what is Surface Morphometrics Pipeline (copied from the GitHub page, from where I took the image also): it’s a pipeline of tools to generate robust open mesh surfaces from voxel segmentations of biological membranes. My installation story is below:

Clone the git repository: git clone https://github.com/grotjahnlab/surface_morphometrics.git

Install the conda environment

> conda env create -f environment.yml
Channels: 
- defaults 
- conda-forge 
Platform: linux-64 
Collecting package metadata (repodata.json): done 
Solving environment: done 

Downloading and Extracting Packages: 

Preparing transaction: done 
Verifying transaction: done 
Executing transaction: | 
| 
/ 
done 
# 
# To activate this environment, use 
# 
# $ conda activate morphometrics 
# 
# To deactivate an active environment, use 
# 
# $ conda deactivate 

Now we activate it, and install the requirements (this step was quite slow)

$ > conda activate morphometrics 
(morphometrics) user@computer $ > pip install -r pip_requirements.txt 
Collecting git+https://github.com/vladanl/Pyto.git 
(from -r pip_requirements.txt (line 1))
 ... some stuff here (donwload and install)
Successfully built pyto pycurv

Installing collected packages: zipp, tifffile, pyyaml, 
pymeshlab, ppft, pox, pluggy, nibabel, networkx, mrcfile,
 lazy_loader, iniconfig, imageio, future, exceptiongroup,
 dill, cloudpickle, click, scikit-image, pytest, multiprocess,
 importlib-metadata, vtk, pyto, pathos, doit, pycurv

Successfully installed click-8.1.7 cloudpickle-3.0.0 
dill-0.3.8 doit-0.36.0 exceptiongroup-1.2.0 
future-1.0.0 imageio-2.34.0 importlib-metadata-7.0.1 
iniconfig-2.0.0 lazy_loader-0.3 mrcfile-1.5.0 
multiprocess-0.70.16 networkx-3.2.1 nibabel-5.2.1 
pathos-0.3.2 pluggy-1.4.0 pox-0.3.4 ppft-1.7.6.8 
pycurv-2.0.0 pymeshlab-2022.2.post3 pytest-8.0.2 
pyto-1.7 pyyaml-6.0.1 scikit-image-0.22.0 
tifffile-2024.2.12 vtk-9.3.0 zipp-3.17.0

That’s it. I didn’t get any errors whatsoever. If only, it took quite some time to finish the install. The problem will come the moment we start using it, probably. I will update this entry if needed.