Installation
PYPI
We have posted wgd v2
on PYPI so the easiest way of installing is via pip:
$ pip install wgd
The version can be specified by replaceing “wgd” with, for instance “wgd==2.0.19”.
Source
Another recommended way is to install from the source. The example code is below:
$ git clone https://github.com/heche-psb/wgd
$ cd wgd
$ virtualenv -p=python3 ENV (or python3 -m venv ENV)
$ source ENV/bin/activate
(ENV) $ python setup.py install (or python -m pip install -r requirements.txt)
(ENV) $ pip install .
Note
We suggest setting a separate virtual environment in case that the dependency of wgd v2
messes up the original package environment. When met with permission problem in the pip install .
step, please try adding the option -e
. If multiply versions of wgd
were installed in the system, please make sure setting the one (either wgd v1
or wgd v2
) desired ahead in the environment variables. The version of numpy
is important and often the dependency of other packages, for instance fastcluster
. We found that some build errors come from the incompatibility of numpy
version required by other packages. So far, the numpy
version 1.19.0 works in our test. Since the pip
can not always decide the best compatible package and the existing packages that match the requirement will not be redownloaded again. If users met some installation issues, it’s suggested to pre-install the numpy
version 1.19.0 before installing the wgd v2
package and try again.
Conda
We also posted wgd v2
on bioconda. With an activated Bioconda channel, install with:
$ conda install wgd
Docker
The docker container is another possible option for installation.
$ docker pull quay.io/biocontainers/wgd:<tag>