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Alokito
2019-09-04 15:45:56 -04:00
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Readme.md
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@@ -10,24 +10,24 @@ Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zu
1. Set up a venv with 1. Set up a venv with
``` ```
python -m venv .cellxgene-gateway python -m venv .cellxgene-gateway
source .cellxgene-gateway/bin/activate source .cellxgene-gateway/bin/activate
``` ```
2. Install requirements with 2. Install requirements with
``` ```
pip install -r requirements.txt pip install -r requirements.txt
``` ```
3. Prepare a folder with .h5ad files, for example 3. Prepare a folder with .h5ad files, for example
``` ```
mkdir cellxgene_data mkdir cellxgene_data
wget https://github.com/chanzuckerberg/cellxgene/raw/master/example-dataset/pbmc3k.h5ad -O ../cellxgene_data/pbmc3k.h5ad wget https://github.com/chanzuckerberg/cellxgene/raw/master/example-dataset/pbmc3k.h5ad -O ../cellxgene_data/pbmc3k.h5ad
``` ```
4. Copy run.sh.example to run.sh: 4. Copy run.sh.example to run.sh:
``` ```
cp run.sh.example run.sh cp run.sh.example run.sh
``` ```
`run.sh` defines various environment variables: `run.sh` defines various environment variables: