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Update install instructions
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flying-sheep committed Jan 18, 2021
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Expand Up @@ -35,9 +35,9 @@ To work with the latest version `on GitHub`_: clone the repository and `cd` into
its root directory. To install using symbolic links (stay up to date with your
cloned version after you update with `git pull`) call::

flit install -s # from an activated venv or conda env
flit install -s --deps=develop # from an activated venv or conda env
# or
flit install -s --python path/to/venv/bin/python
flit install -s --deps=develop --python path/to/venv/bin/python

If you intend to do development work, there are some extra dependencies you'll want.
These can be install with `scanpy` via::
Expand All @@ -52,21 +52,19 @@ If you want to let conda_ handle the installations of dependencies, do::
beni pyproject.toml > environment.yml
conda env create -f environment.yml
conda activate scanpy
flit install -s
flit install -s --deps=develop

On Windows, you might have to use `flit install --pth-file`
if you are not able to give yourself the `create symbolic links`_ privilege.
Be aware that a `conda bug`_ might prevent `conda list` from working then.

.. _create symbolic links: https://docs.microsoft.com/en-us/windows/security/threat-protection/security-policy-settings/create-symbolic-links
.. _conda bug: https://github.com/conda/conda/issues/9074

Docker
~~~~~~
If you're using Docker_, you can use the minimal `fastgenomics/scanpy`_ image from the Docker Hub.
If you're using Docker_, you can use e.g. the image `gcfntnu/scanpy`_ from Docker Hub.

.. _Docker: https://en.wikipedia.org/wiki/Docker_(software)
.. _fastgenomics/scanpy: https://hub.docker.com/r/fastgenomics/scanpy
.. _gcfntnu/scanpy: https://hub.docker.com/r/gcfntnu/scanpy
.. _bioconda: https://bioconda.github.io/

Troubleshooting
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