From f843d9d0dc08fd715ee64265ba4a1034439361a8 Mon Sep 17 00:00:00 2001 From: Sarah Bastkowski Date: Sun, 22 Oct 2023 19:09:46 +0100 Subject: [PATCH] Fixing README --- README.md | 29 +++-------------------------- 1 file changed, 3 insertions(+), 26 deletions(-) diff --git a/README.md b/README.md index b696a54..31a8178 100644 --- a/README.md +++ b/README.md @@ -134,7 +134,8 @@ sudo apt install r-base Before installing QuaTraDIS via conda, first [install conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html) and enable the bioconda channel as described [here](https://bioconda.github.io/). After which if you don't have mamba installed then we recommend you do this to make the installation process much faster. -We also recommend using a virtual environment with python pinned to 3.10. +We also recommend using a virtual environment with python pinned to 3.10. This should help to avoid version mixups. +[conda virtual environment](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html). Rough steps are described here (adapt as needed for your system): ```bash @@ -153,35 +154,11 @@ mamba install -c conda-forge -c bioconda quatradis ``` -Quatradis installs several conda dependencies, to avoid version mixups you might want to install QuaTraDIS in it's own - -[conda virtual environment](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html). -To do this instead of running the commands above which install QuaTraDIS to your base environment you can install into -an environment called 'quatradis_env' (can be renamed to whatever you like) like so: - -```bash -# Install mamba if you haven't already. Its necessary to install this in the base environment -conda install -c conda-forge mamba - -# Create the virtual environment -conda create --name quatradis_env - -# Activate the virtual environment -conda activate quatradis_env - -# Install quatradis -mamba install -c conda-forge -c bioconda quatradis - -# For now to workaround an issue with the bioconda recipe it may be required to install the latest pysam version as -# sometimes an old incompatible version gets installed -mamba install -c conda-forge -c bioconda pysam=0.19.1 -``` - Remember that if using virtual environments you will need to activate it everytime prior to using QuaTraDIS: ```bash # Activate the virtual environment called quatradis -conda activate quatradis_env +conda activate quatradis # Run your tradis command... tradis