Installation¶
We recommend installing pAPRika in a fresh conda
environment if possible. There are three ways to install this package:
Installing from Conda¶
To install the latest release of paprika from conda, run:
conda install -c conda-forge paprika
In order to use all features of paprika, you must either have AmberTools
(http://ambermd.org/AmberTools.php) in your $PATH or separately install AmberTools
with the command below if it is not already installed in your environment:
conda install -c conda-forge ambertools=22
Optional dependencies¶
If you want to run simulations with Plumed-based restraints (needed for running APR in GROMACS
) you can compile Plumed from source or install through conda:
conda install -c conda-forge plumed
Although GROMACS
is available in conda (Bioconda), a version that is patched with Plumed is currently not available. Therefore, if you want to run GROMACS
simulations in paprika you will need to compile from source manually (patched with Plumed).
Installing a stable version from source¶
To install the a stable version of paprika download the source code from Github.
Then, unzip the files and change to the paprika
directory:
tar -xvzf paprika-version.tgz
cd pAPRika-version/
Change the name
field in devtools/conda-envs/test_env.yaml
to be paprika
and create the environment:
conda env create -f devtools/conda-envs/test_env.yaml
Activate the environment:
conda activate paprika
and install paprika in the environment:
pip install .
Installing latest from source¶
To install paprika with the latest features, clone the repository from the master
branch on Github:
git clone https://github.com/GilsonLabUCSD/pAPRika.git
Change directory to the paprika
folder, change the name
field in devtools/conda-envs/test_env.yaml
to paprika
and create the conda environment:
conda env create -f devtools/conda-envs/test_env.yaml
Activate the environment:
conda activate paprika
and install paprika in the environment:
pip install .