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docs: use snakemake
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visze authored Dec 15, 2023
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Expand Up @@ -38,15 +38,15 @@ Set up conda with snakemake environment

This pipeline uses python2.7 and python3.6 with additional R scripts in a Snakemake pipeline. The ``.yml`` files provided will create the appropriate environments and is completely handled by MPRAsnakeflow. The whole pipeline is set up to run on a Linux system.

Install the the conda environment. The general conda environment is called ``mprasnakeflow``.
Install the the conda environment. The general conda environment is called ``snakemake``.

.. code-block:: bash
cd MPRAsnakeflow
conda create -c bioconda -c conda-forge -n mprasnakeflow snakemake
mamba create -c conda-forge -c bioconda -n snakemake snakemake
# activate MPRAsnakeflow
conda activate mprasnakeflow
# activate snakemake
conda activate snakemake
To deactivate the environment, use:

Expand All @@ -61,6 +61,6 @@ Quick test

.. code-block:: bash
conda activate mprasnakeflow
conda activate snakemake
snakemake --help

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