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[Merge on next release] Document how to install cellxgene prepare (#889)

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* Document how to install cellxgene prepare

after pr #887 merged

* formatting

* remove reference to cellxgene[louvain]
This commit is contained in:
Charlotte Weaver
2019-09-13 18:15:06 -07:00
committed by Bruce Martin
parent 84c815cc04
commit 0f520f2fd4
3 changed files with 26 additions and 23 deletions
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docs/getting-started.md
+12 -11
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@@ -56,6 +56,18 @@ The `launch` command assumes that the data is stored in the `.h5ad` format from
The `prepare` command is included to help you format your data. It uses `scanpy` under the hood. This is especially useful if you are starting with raw unanalyzed data and are unfamiliar with `scanpy`.
To install `cellxgene prepare` alongside `cellxgene launch`
```
pip install cellxgene[prepare]
```
If the aforementioned optional package installation fails, you can also install these packages directly:
```
pip install scanpy>=1.3.7 python-igraph louvain>=0.6
```
To prepare from an existing `.h5ad` file use
```
@@ -76,17 +88,6 @@ To see all options call
cellxgene prepare --help
```
**Note**: `cellxgene prepare` will only perform `louvain` clustering if you have the `python-igraph` and `louvain` packages installed. To make sure they are installed alongside `cellxgene` use
```
pip install cellxgene[louvain]
```
If the aforementioned optional package installation fails, you can also install these packages directly:
```
pip install python-igraph louvain>=0.6
```
## conda and virtual environments