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Update README.md #166

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Jul 27, 2024
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Update README.md #166

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26 changes: 7 additions & 19 deletions config/README.md
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Expand Up @@ -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

Expand Down Expand Up @@ -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
Expand All @@ -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.

Expand Down