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[WIP] added python=3.6 to kofamscan and created new khmer env #80

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[WIP] added python=3.6 to kofamscan and created new khmer env #80

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10 changes: 8 additions & 2 deletions doc/06_quality_control.md
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Expand Up @@ -178,10 +178,16 @@ srun -p bmh -J khmer -t 20:00:00 --mem=21gb -c 1 --pty bash

Since we changed computers, our conda environment was automatically deactivated.

Activate your project environment again:
Create a new environment:

```
conda activate dib_rotation
conda create -n khmer
```

> This step (creating a new environment) was necessary because `khmer` requires a different python version than we have installed in our `dib_rotation` environment. You can compare the two environments with `conda list -n dib_rotation` and `conda list -n khmer`... after we finish setting up the `khmer` environment though!

```
mamba activate khmer
```

### Install khmer
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2 changes: 1 addition & 1 deletion doc/10_annotating_amino_acid_sequences.md
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Expand Up @@ -36,7 +36,7 @@ kofamscan is not available as a conda package, but being able to use the KEGG fr
We'll create a new environment for kofamscan, and use conda to install all of its dependencies.

```
mamba create -n kofamscan hmmer parallel ruby kofamscan
mamba create -n kofamscan hmmer parallel ruby kofamscan python=3.6
conda activate kofamscan
```

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