Installation & Updates¶
How to install OMMProtocol¶
First method: Standalone installer¶
If you haven’t used Anaconda or Miniconda before (a Python distribution with a cool package manager), your best bet is to simply download the installer for the latest release, which includes everything you need.
- Go to the OMMProtocol releases page and download the latest installer for your platform.
- Run the installer and follow the instructions!
- In Linux, open the terminal and run
bash ~/Downloads/ommprotocol*.sh
or whatever path the file got saved. - In Windows, double click on the downloaded
ommprotocol*.exe
.
- In Linux, open the terminal and run
- The installer will create, by default, a new directory called
ommprotocol
in your$HOME
. Underommprotocol/bin``(Linux) or ``ommprotocol/Scripts
(Windows) you will find theommprotocol
executable.
Second method: Conda package¶
OMMProtocol is also distributed as a separate conda
package. If you already have Anaconda/Miniconda installed, you won’t probably want to download a separate Python distribution. In that case, skip to step 2.
- Download and install Miniconda, a tiny Python distribution with a cool package manager and installer. Check its webpage for more info.
For Linux:
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3*.sh
For Windows, download the EXE installer:
https://repo.continuum.io/miniconda/Miniconda3-latest-Windows-x86_64.exe
- Install it in the default environment…
conda install -c omnia -c insilichem ommprotocol
- … or use a new, separate environment (optional):
conda create -n ommprotocol -c omnia -c insilichem ommprotocol
conda activate ommprotocol
- If everything is OK, these sould run correctly.
ommprotocol -h
ommanalyze -h
Third method: From source¶
If there’s no package for your platform, install the dependencies with conda
and then install ommprotocol
from pip or source.
conda create -n ommprotocol -c omnia openmm ruamel_yaml parmed openmoltools mdtraj netcdf4 jinja2 pdbfixer
conda activate ommprotocol
# stable version
pip install ommprotocol
# dev version
pip install https://github.com/insilichem/ommprotocol/archive/master.zip
Updating OMMProtocol¶
Depending on the installation method, updating OMMProtocol involves different steps.
First method: Standalone installer¶
Just download the installer for the new version and run it. In Linux/MacOS you will need to append the -u
flag to the installer. In Windows, just follow the wizard.
Second method: Conda package¶
Within the activated environment, run conda update -c insilichem -c omnia ommprotocol
. That’s it.
Third method: From source¶
Simply pass the -U
flag to pip: pip install -U ommprotocol
or, for development version, pip install -U https://github.com/insilichem/ommprotocol/archive/master.zip
.