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docs: move pip install instructions to contributing guide
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resolves #64
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kelly-sovacool committed Sep 18, 2023
1 parent f4d501b commit 077d738
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13 changes: 13 additions & 0 deletions .github/CONTRIBUTING.md
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Expand Up @@ -25,3 +25,16 @@ Keep the changelog up to date with all notable changes in `CHANGELOG.md`[^2].
## VS code extensions

If you use VS code, installing [nf-core extension pack](https://marketplace.visualstudio.com/items?itemName=nf-core.nf-core-extensionpack) is recommended.

## Installation

For testing and debugging, We recommend installing the dev version of champagne in editable mode to a user-specific location.

```
git clone https://github.com/CCBR/CHAMPAGNE
mkdir -p ~/bin/champagne
pip install -e CHAMPAGNE -t ~/bin/champagne
export PATH="$HOME/bin/champagne/bin:$PATH"
```

Then you can run your local version of champagne, make edits to the code as needed, and run your edited version again without reinstalling it.
12 changes: 1 addition & 11 deletions README.md
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Expand Up @@ -7,10 +7,6 @@

🚧 **This project is under active development. It is not yet ready for production use.** 🚧

## Getting started

TODO

## Usage

### champagne CLI
Expand All @@ -19,13 +15,6 @@ You can run champagne from the command line.
The CLI includes helper steps for execution on supported
high performance computing clusters including Biowulf and FRCE.

Install the champagne CLI:

```sh
cd CHAMPAGNE
pip3 install .
```

Run the test dataset using the test profile:

```sh
Expand All @@ -39,6 +28,7 @@ champagne run -profile singularity --outdir results/test --input assets/samplesh
```

Run preview to view that steps that will run without actually executing any code:

```sh
champagne run -profile ci_stub -preview
```
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