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anopheles-genomic-surveillance/selection-atlas

Domaine:

healthcare
Créateur:
ano
Hôte:
An atlas of recent positive selection in African malaria vectors # Malaria Vector Selection Atlas This repo contains the source code for the Malaria Vector Selection Atlas. This README contains information for developers and contributors to the selection atlas. ## Development docs The following documents capture early design work and implementation planning. These are mostly redundant now as the proposed work has been completed, and further work will be discussed via GitHub issues, but these may still be of some historical interest: - Implementation plan - UI design - Workflow design ## Conda environment management In order to develop or contribute to the selection atlas, you will need to create a conda environment on the system where you are working. Instructions below assume you have a recent version of conda and mamba installed. Alternatively you could use micromamba instead of conda and mamba. The file `workflow/common/envs/selection-atlas.yaml` has a fully pinned conda environment specification. This is the environment to use for development work and running workflows. To create and activate an environment on your own computer: ``` conda env remove --name selection-atlas mamba env create --file workflow/common/envs/selection-atlas.yaml conda activate selection-atlas pip install -e . # install local Python sources in editable mode ``` To create and activate an environment on datalab-bespin: ``` mamba env remove --prefix=${HOME}/envs/selection-atlas mamba env create --prefix=${HOME}/envs/selection-atlas --file workflow/common/envs/selection-atlas.yaml conda activate ${HOME}/envs/selection-atlas pip install -e . # install local Python sources in editable mode ``` If you are developing and need to add or upgrade a package, edit `workflow/common/envs/selection-atlas-requirements.yaml`. **Do not edit `workflow/common/envs/selection-atlas.yaml`**. Then re-solve the environment to regenerate `workflow/common/envs/selection-atlas.yaml` as follows: ``` mamba env create --file workflow/common/envs/selection-atl …

Visit

github.com

Languages

VunjoZimba

Licenses

MIT

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