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Installation
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This workflow is intended only for GNU/Linux systems. Some of the rules invoke the GNU versions of commands like
sed
,grep
, andsort
, which may cause issues if you are on BSD systems like OpenBSD or macOS. The rules were not tested on BSD systems, so it might not be an issue, but I cannot say for certain. If using BSD systems, you may need to install the GNU versions of those commands and augment the rules to reflect those GNU commands. LepMak3r will 100% not work on Windows (unless using it inside a WSL).
Because it's a Snakemake workflow, there is no "true" installation of LepMak3r, which can be be considered good or bad depending on one's preferences. To get LepMak3r, simply clone the git repository and begin using it as the working directory for your project. That's it!
git clone https://github.com/pdimens/LepMak3r.git
cd LepMak3r
Alternatively, you can manually download and unzip the release.
Then, you will need to create the pre-configured conda environment provided with the LepMak3r repository:
conda env create -f conda_LepMak3r.yml
The new environment will be called lepmak3r
and can be activated with
conda activate lepmak3r
LepMak3r comes with all the necessary scripts in the scripts
folder, along with all the Lep-Map3 modules in the LM3
folder, a Snakefile with the target rule all
, a rules
folder, and all of it is configured to work out of the box (rather, out of that folder)!