From ad4e05631ef662ca9143590dec538124e9968e1e Mon Sep 17 00:00:00 2001 From: bio-la Date: Wed, 6 Mar 2024 16:49:51 +0100 Subject: [PATCH] update to readme --- README.md | 21 +++++++++++++++++---- 1 file changed, 17 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 2cd8ad9d..b9744d72 100644 --- a/README.md +++ b/README.md @@ -27,13 +27,26 @@ Available workflows: See [installation instructions here](https://panpipes-pipelines.readthedocs.io/en/latest/install.html) +We recommend installing panpipes in a conda environment, we provide a minimal conda config file in `pipeline_env.yaml` + +``` +conda env create --file=pipeline_env.yml +``` + +In this environment, you can install nightly version of panpipes, i.e. cloning this repo and installing it from main. + +``` +git clone https://github.com/DendrouLab/panpipes.git +cd panpipes +pip install -e . +``` + + Oxford BMRC Rescomp users find additional advice in [docs/installation_rescomp](https://github.com/DendrouLab/panpipes/blob/main/docs/installation_rescomp.md) ## Releases -`panpipes v0.4.0` is out [now](./CHANGELOG.md)! - -The `ingest` workflow now expects different headers for the RNA and Protein modalities. +Since `panpipes v0.4.0` ,the `ingest` workflow expects different headers for the RNA and Protein modalities from the previous releases. Check the example [submission file](https://github.com/DendrouLab/panpipes/blob/main/docs/usage/sample_file_qc_mm.md) and the [documentation](https://panpipes-pipelines.readthedocs.io/en/latest/usage/setup_for_qc_mm.html) for more detailed instructions. ## Citation @@ -45,4 +58,4 @@ bioRxiv 2023.03.11.532085; doi: https://doi.org/10.1101/2023.03.11.532085](https ## Contributors Created and Maintained by Charlotte Rich-Griffin and Fabiola Curion. -Additional contributors: Sarah Ouologuem, Devika Agarwal, Lilly May, Kevin Rue-Albrecht, Lukas Heumos. +Additional contributors: Sarah Ouologuem, Devika Agarwal, Lilly May, Kevin Rue-Albrecht, Giulia Garcia, Lukas Heumos.