Installation steps

This only needs to be done once. To run GenEditID, first download and install these dependencies using bioconda. Here are some platform specific instructions for MacOS and for Windows 10.

Install miniconda3

on MacOS run

  curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
  sh Miniconda3-latest-MacOSX-x86_64.sh

on Linux, run:

  curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
  sh Miniconda3-latest-Linux-x86_64.sh

For changes to take effect, close and re-open your current shell.

Set up the channels, it is important to add them in this order, so that the priority is set correctly (that is, conda-forge is highest priority).
```
  conda config --add channels defaults
  conda config --add channels bioconda
  conda config --add channels conda-forge
```
Install our dependencies: pear, seqkit and Git LFS into a specific conda environment called geneditid.
```
  conda create -n geneditid python=3.8 pear seqkit git-lfs
```
To activate this environment, use conda activate geneditid. To deactivate an active environment, use conda deactivate. To see a list of all of your environments, run conda env list. To remove this environment, run conda remove -n geneditid --all
Setup Git LFS for supporting the usage of large files, clone the GitHub repo GenEditID, setup GenEditID
```
  cd ~
  conda activate geneditid
  git lfs install
  git clone https://github.com/GenEditID/GenEditID.git
  cd GenEditID/
  ./scripts/setup_geneditid.sh
```
Due to large reference genomes files within the repository, the cloning step takes can take a while. Please wait till it completes before moving forward, thanks for your patience.

The active environment you are currently using is shown in parentheses () or brackets [] at the beginning of your command prompt.

(geneditid) $

if not, activate it using conda activate geneditid before running the next steps.

Back to the main manual

GenEditID Manual: detailed steps