From af574d1512f4c1538c085debfc88de8c1ef0d5a3 Mon Sep 17 00:00:00 2001 From: Ugur Bayindir Date: Mon, 11 Sep 2023 19:09:54 +0100 Subject: [PATCH] Added 'Detailed installation guide for pygraphviz issue' section --- README.md | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index dc5c333..c375095 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ STATUS: early Beta -A library for retreiving and leveraging the semantic context of ontogy annotation in [CxG standard](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/3.0.0/schema.md) [AnnData files](https://anndata.readthedocs.io/en/latest/). +A library for retrieving and leveraging the semantic context of ontology annotation in [CxG standard](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/3.0.0/schema.md) [AnnData files](https://anndata.readthedocs.io/en/latest/). Slide summarising intended functionality ![image](https://github.com/INCATools/pandasaurus_cxg/assets/112839/3082dcd2-dd2f-469d-9076-4eabcc83130d) @@ -13,6 +13,20 @@ Available on [PyPi](https://pypi.org/project/pandasaurus-cxg/0.1.1/) $ pip3 install pandasaurus_cxg +#### Detailed installation guide for pygraphviz issue + +During package installation, sometimes the pygraphviz package installation is failing on **macOS** due to Graphviz may be +installed in a location that is not on the default search path. In this case, it may be necessary to manually +specify the path to the graphviz include and/or library directories. To do that use following instructions and install +pygraphviz manually. + +``` +brew install graphviz +export CFLAGS="-I $(brew --prefix graphviz)/include" +export LDFLAGS="-L $(brew --prefix graphviz)/lib" +pip install pygraphviz +``` + ## Usage The `AnndataEnricher` and `AnndataAnalyzer` classes can be used both individually and in conjunction with the `AnndataEnrichmentAnalyzer` wrapper class. The `AnndataEnrichmentAnalyzer` class serves as a convenient way to leverage the functionalities of both `AnndataEnricher` and `AnndataAnalyzer`. @@ -60,4 +74,3 @@ https://github.com/INCATools/pandasaurus_cxg/blob/main/walkthrough.ipynb ## Roadmap https://github.com/INCATools/pandasaurus_cxg/blob/main/ROADMAP.md -