From f61b6b0ed5414ea45770ad7ab3b3ac851811ac67 Mon Sep 17 00:00:00 2001 From: Fabiola Curion Date: Tue, 30 Apr 2024 13:40:16 +0200 Subject: [PATCH] Update install.md --- docs/install.md | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/docs/install.md b/docs/install.md index cf4d0746..59a88786 100644 --- a/docs/install.md +++ b/docs/install.md @@ -53,6 +53,10 @@ pip install 'panpipes[spatial]' ``` The extra `[spatial]` includes the `squidpy`, `cell2location`, and `tangram-sc` packages. +The packages we support are in active development. We provide installation instructions to deal with the issues encountered, which we test in our [github actions](https://github.com/DendrouLab/panpipes) +- To install a version of panpipes that has a working MultiVI please install panpipes with `pip install 'panpipes[multivipatch]'` +- To install a version of panpipes to run old scvi-tools models in the refmap workflow, please install panpipes with `pip install 'panpipes[refmap_old]'` + ## Option 2: Install nightly panpipes version with preconfigured conda config file @@ -81,6 +85,11 @@ To install the spatial dependencies from the repo, use pip install .[spatial] ``` +The packages we support are in active development. We provide installation instructions to deal with the issues encountered, which we test in our [github actions](https://github.com/DendrouLab/panpipes) +- To install a version of panpipes that has a working MultiVI please install panpipes with `pip install '.[multivipatch]'` +- To install a version of panpipes to run old scvi-tools models in the refmap workflow, please install panpipes with `pip install '.[refmap_old]'` + + Panpipes requires the unix package `time`. You can check if it installed with `dpkg-query -W time`. If `time` is not already installed, you can install it using: