From 077d73839f5e81673055fa89242709ec97e610f0 Mon Sep 17 00:00:00 2001 From: Kelly Sovacool Date: Mon, 18 Sep 2023 18:30:51 -0400 Subject: [PATCH] docs: move pip install instructions to contributing guide resolves #64 --- .github/CONTRIBUTING.md | 13 +++++++++++++ README.md | 12 +----------- 2 files changed, 14 insertions(+), 11 deletions(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 9ee47114..400b7ac5 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -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. diff --git a/README.md b/README.md index 401deac0..acf3c362 100644 --- a/README.md +++ b/README.md @@ -7,10 +7,6 @@ 🚧 **This project is under active development. It is not yet ready for production use.** 🚧 -## Getting started - -TODO - ## Usage ### champagne CLI @@ -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 @@ -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 ```