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Commit 9ce173f2 authored by larissasa's avatar larissasa
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Update README.md

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...@@ -69,7 +69,7 @@ This workflow is designed to work on Linux-based operating systems. HPC Cluster ...@@ -69,7 +69,7 @@ This workflow is designed to work on Linux-based operating systems. HPC Cluster
To clone the repository, use the following command: To clone the repository, use the following command:
``` ```
git clone https://git.imp.fu-berlin.de/begendiv/radseq-pre-processing-pipeline.git git clone https://git.imp.fu-berlin.de/begendiv/radseq-preprocessing-pipeline.git
``` ```
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...@@ -98,7 +98,7 @@ If `conda command not found` please close and re-open your terminal for conda i ...@@ -98,7 +98,7 @@ If `conda command not found` please close and re-open your terminal for conda i
--- ---
<div id="creating-our-snakemake-conda-environment"></div> <div id="creating-our-snakemake-conda-environment"></div>
## Creating our GEP (Snakemake) Conda environment ## Creating our RADseq preprocessing (Snakemake) Conda environment
The pipeline requires the following software to run: The pipeline requires the following software to run:
...@@ -108,11 +108,11 @@ The pipeline requires the following software to run: ...@@ -108,11 +108,11 @@ The pipeline requires the following software to run:
- mamba = `1.4.1` - mamba = `1.4.1`
- pandas = `1.4.2` - pandas = `1.4.2`
The easiest method to install this software stack is to create a GEP conda environment with the provided `snakemakeEnvironment.yaml` (see ***Note***) The easiest method to install this software stack is to create a RADseq preprocessing conda environment with the provided `snakemakeEnvironment.yaml` (see ***Note***)
``` ```
conda env create -f /<your_path_to>/radseq-pre-processing-pipeline/setup/snakemakeEnvironment.yaml conda env create -f /<your_path_to>/radseq-preprocessing-pipeline/setup/snakemakeEnvironment.yaml
conda activate radPreprocessing conda activate radPreprocessing
...@@ -150,7 +150,7 @@ These are: ...@@ -150,7 +150,7 @@ These are:
## Running the workflow ## Running the workflow
From within the main workflow directory (`radseq-pre-processing-pipeline`) where the `Snakefile` is located (make sure your snakemake environment is activated), run with: From within the main workflow directory (`radseq-preprocessing-pipeline`) where the `Snakefile` is located (make sure your snakemake environment is activated), run with:
``` ```
snakemake --cores # --use-conda snakemake --cores # --use-conda
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