Installation¶
Tested on: Mac OSX Mojave and Ubuntu 20.04
Requirements¶
We strongly recommend installing within a python environment as there are many dependencies that you may not want polluting your regular python environment. Make sure you are using python 3.
An environment can be created with using the conda package manager:
$ conda create --name <env>
$ conda activate <env>
Which you can deactivate with:
$ conda deactivate
Or using virtualenv:
$ python -m virtualenv /path/to/venv/
$ source /path/to/venv/bin/activate
This will download all of your packages under /path/to/venv
and then activate it.
Deactivate using
$ deactivate
You will also need to make sure you have a recent version of pip. In your local environment, run:
$ pip install --upgrade pip
Or using pyenv with pyenv-virtualenv:
$ pyenv install 3.7.9
$ pyenv virtualenv 3.7.9 aliby
$ pyenv local aliby
Pipeline installation¶
Pip version¶
Once you have created your local environment, run:
$ cd aliby
$ pip install -e ./
Git version¶
We use poetry for dependency management.
In case you want to have local versions (usually for development) the main three aliby dependencies you must install them in a specific order:
$ git clone git@git.ecdf.ed.ac.uk:swain-lab/aliby/aliby.git
$ git clone git@git.ecdf.ed.ac.uk:swain-lab/aliby/postprocessor.git
$ git clone git@git.ecdf.ed.ac.uk:swain-lab/aliby/agora.git
$ cd aliby && poetry install
$ cd ../postprocessor && poetry install
$ cd ../agora && poetry install
And that should install all three main dependencies in an editable mode. The same process can be used for BABY