From 22f2e116c1c6d967814853e14ddf6b070c51289f Mon Sep 17 00:00:00 2001 From: Francisco Zorrilla Date: Sat, 27 Jul 2024 17:01:51 +0100 Subject: [PATCH] Update README.md --- config/README.md | 26 +++++++------------------- 1 file changed, 7 insertions(+), 19 deletions(-) diff --git a/config/README.md b/config/README.md index e681b95..8c98643 100644 --- a/config/README.md +++ b/config/README.md @@ -12,26 +12,14 @@ Make sure to inspect and set up the two config files in this folder. ## 🛢️ Environments -Set up three conda environments: -1. `mamba`: Used for installing mamba and setting up subsequent environments from recipe files -2. `metagem`: Contains most `metaGEM` core workflow tools, Python 3 & Snakemake>=5.10.0,<5.31.1 -3. `metawrap` Contains `metaWRAP` and its dependencies, Python 2 - -### 1. mamba - Conda can take *ages* to solve environment dependencies when installing many tools at once, we can use [mamba](https://github.com/mamba-org/mamba) instead for faster installation. -``` -conda create -n mamba mamba -``` +Set up two environments: +1. `metagem`: Contains most `metaGEM` core workflow tools, Python 3 & Snakemake>=5.10.0,<5.31.1 +2. `metawrap` Contains `metaWRAP` and its dependencies, Python 2 -Activate mamba environment to quickly set up subsequent environments. - -``` -source activate mamba -``` -### 2. metaGEM +### 1. metaGEM Clone metaGEM repo @@ -69,10 +57,10 @@ Alternative method: create metaGEM env using recipe .yml file mamba env create --prefix ./envs/metagem -f envs/metaGEM_env.yml ``` -Deactivate mamba env and activate metaGEM env +Deactivate activate metaGEM env ``` -source deactivate && source activate envs/metagem +source activate envs/metagem ``` Install pip tools @@ -81,7 +69,7 @@ Install pip tools pip install --user memote carveme smetana ``` -### 3. metaWRAP +### 2. metaWRAP It is best to set up `metaWRAP` in its own isolated environment to prevent version conflicts with `metaGEM`. Note that `metaWRAP v1.3.2` has not migrated from python 2 to python 3 yet.