diff --git a/docs/_config.yml b/docs/_config.yml index 5d25e6fc..b3f92d07 100644 --- a/docs/_config.yml +++ b/docs/_config.yml @@ -2,6 +2,8 @@ theme: jekyll-theme-cayman show_downloads: false nav: + - title: Home + url: / - title: Data url: data.html - title: FAQ diff --git a/docs/_layouts/default.html b/docs/_layouts/default.html index 81ae146a..e1afc98d 100644 --- a/docs/_layouts/default.html +++ b/docs/_layouts/default.html @@ -20,7 +20,6 @@ - diff --git a/docs/faq.md b/docs/faq.md index d0dd1859..cb9afc81 100644 --- a/docs/faq.md +++ b/docs/faq.md @@ -48,6 +48,26 @@ We use a [Welch's _t_-test](https://en.wikipedia.org/wiki/Welch%27s_t-test) impl # Problems, errors, & bugs +#### How do I create a Python 3.6 environment for _cellxgene_? + +If you use conda and want to create a [conda environment](https://conda.io/docs/user-guide/tasks/manage-environments.html) for _cellxgene_ you can use the following commands + +``` +conda create --yes -n cellxgene python=3.6 +conda activate cellxgene +pip install cellxgene +``` + +Or you can create a virtual environment by using + +``` +ENV_NAME=cellxgene +python3.6 -m venv ${ENV_NAME} +source ${ENV_NAME}/bin/activate +pip install cellxgene +``` + + #### In my _prepare_ command I received the following error `Warning: louvain module is not installed, no clusters will be calculated. To fix this please install cellxgene with the optional feature louvain enabled` Louvain clustering requires additional dependencies, so we don't include them by default. For now, you need to specify that you want these packages by using diff --git a/docs/index.md b/docs/index.md index a2cc0790..58776714 100644 --- a/docs/index.md +++ b/docs/index.md @@ -10,7 +10,7 @@ _cellxgene_ is an interactive data explorer for single-cell transcriptomics data ## getting started -_cellxgene_ requires **Python 3.6** +_cellxgene_ **only** supports Python 3.6. We recommend [installing _cellxgene_ into a conda or virtual environment.](/faq.html#how-do-i-create-a-python-36-environment-for-cellxgene) Install the package. ``` bash