Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Added 'Detailed installation guide for pygraphviz issue' section #48

Merged
merged 1 commit into from
Sep 11, 2023
Merged

Added 'Detailed installation guide for pygraphviz issue' section #48

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
17 changes: 15 additions & 2 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand All @@ -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`.
Expand Down Expand Up @@ -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