Installation

For non-programmers and those unfamiliar with Anaconda or GitHub, see the programing basics page for information on how to set up your computer environment to run evSeq.

Installing from GitHub with the conda environment

The recommended way to install evSeq involves cloning the repository from GitHub and then creating the conda environment from the included evSeq.yml file. Open a terminal window (see here for instructions on opening a terminal window in Mac and Windows – Windows users must use Git Bash) and navigate to the folder where you want to install evSeq (using the cd command to change directories as needed), then, in a terminal window, enter the following:

git clone https://github.com/fhalab/evSeq.git
cd evSeq
conda env create -f envs/evSeq.yml

This will create an environment with the correct dependencies and versions.

Using the evSeq environment

This environment can subsequently be activated any time you want to run evSeq from the command line with:

conda activate evSeq

and deactivated with

conda deactivate

Standard pip Install and Dependencies

Advanced users: If you would rather not use the evSeq environment described above and run in a custom environment (or, if you’re a brave soul, your base environment), below are the evSeq dependencies, most of which are available through conda (only ninetysix and pyshortcuts require pip, but they are small packages with few dependencies).

The evSeq dependencies are explicitly listed all of the environment files and setup.py requirements:

- python>=3.7
- numpy
- pandas
- openpyxl
- biopython>=1.78
- scipy
- tqdm
- holoviews
- bokeh
- colorcet
- gooey
- pyshortcuts
- ninetysix

Jupyter installs are not listed here or in the setup.py requirements as they are not necessary if you do not plan to use any of the additional data visualization tools.

Releases of evSeq are hosted on the Python Package Index (PyPI), and thus can be pip installed in the standard way. From any location, run

pip install evSeq

Confirming your installation

Once evSeq is installed and your environment is suitable, you should confirm your installation.

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Next page: Running evSeq.

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Updating

By default, evSeq is installed in non-dev mode. This means that changes to the code base on your computer will not be reflected come run-time. If you want an editable version of evSeq, install with the evSeq_dev environment (note, however, that this environment does not set exact versions of dependencies like evSeq). We recommend installing in non-dev mode (i.e., using the evSeq environment). To update evSeq when installed in a non-dev environment, the environment must be recreated. The below commands will update evSeq. First, navigate the evSeq repository folder via command line and enter the below commands:

git pull
conda remove -n evSeq --all
conda env create -f envs/evSeq.yml