Installation¶
Dependencies¶
The current version of GADMA (greater than 2.0.0) supports Python3 only. Older versions supported Python 2 as well but not any more.
Below we hightlight GADMA dependencies. All of them could be easily installed using requirements files which are specified in the brackets before lists. To install dependencies from requerement file run:
$ pip -r requirements_file
GADMA requires the following dependencies (requirements/minimal.txt):
- Python3
- NumPy (>= 1.2.0)
- Scipy (>= 0.6.0)
- ruamel.yaml
dadi
(>= 1.7.0)moments
(>= 1.0.0)momi
moments.LD
(manual installation ofmoments
with –ld-extension flag)- nlopt (for
dadi
) - Cython (for
moments
) - mpmath (for
moments
)
To draw demographic models one should also install the following packages (requirements/minimal.txt):
- matplotlib (>= 0.98.1)
- Pillow (>= 4.2.1) - optional
moments
(>= 1.0.0)
To use demes
engine to draw models (requirements/engines.txt):
- demes
- demesdraw
To calculate confidence intervals one should install (requirements/minimal.txt):
- pandas
To run Bayesian optimization smac of specified version is requered (requirements/bayes_opt.txt):
- scikit-optimize
- configspace
- smac (==0.13.1)
Note
momi
package sometimes is not installed correctly for Windows and MacOS. If momi
is not available please install it manually following the installation instructions in momi’s manual.
Note
momentsLD
- the extension of moments
, should be installed manually following the installation instructions in moments’s manual.
Getting help for engine installation¶
If there are some troubles installing the engine, please, first of all check the table below for the ability to install this engine on your system. You are always welcome to open an issue on GitHub for getting help.
GADMA has automatic tests on GitHUb for engines on different systems (Linux, Windows, MacOS). The following table indicates (according to our tests) if engine could be installed on specified system:
Feature | dadi |
moments |
momi |
momentsLD |
---|---|---|---|---|
Linux | ✅ | ✅ | ✅ | ✅ |
Windows | ✅ | ✅ | ❌ | ✅ |
MacOS | ✅ | ✅ | ✅ | ✅ |
Installing the latest release¶
The latest release of GADMA is easily installed via pip
or conda
(bioconda
):
$ pip install gadma
or
$ conda install -c bioconda gadma
Warning
Installation via pip
and conda
will not install the moments
library. To install it one should run:
$ pip install git+https://github.com/MomentsLD/moments.git
or
$ conda install -c bioconda moments
Manual installation¶
Some features are added to the GADMA project but are not released yet. One can install GADMA directly from the repository.
First clone the repository:
$ git clone https://github.com/ctlab/GADMA.git $ cd GADMA
Dependencies could be installed either automatically or manually.
Full-manual mode¶
Install dependencies manually:
- NumPy
$ pip install numpy
- Scipy
$ pip install scipy
- ruamel.yaml
$ pip install ruamel.yaml
dadi
, nlopt $ pip install dadi
moments
, mpmath, Cython $ pip install --upgrade Cython $ pip install mpmath $ pip install git+https://github.com/MomentsLD/moments.git
momi
$ pip install momi
- matplotlib
$ pip install matplotlib
- Pillow
$ pip install Pillow
- pandas
$ pip install pandas
- Install GADMA
$ pip install .
Verifying installation¶
To verify the installation, run:
$ gadma --test
If the installation was successful, one will find the following information at the end:
--Finish pipeline--
--Test passed correctly--
Thank you for using GADMA!