Installation and Dependencies

Installation

To install RetroDetector, clone the GitHub repository:

git clone https://github.com/tbenavi1/RetroDetector.git

Dependencies

RetroDetector is built on the Snakemake workflow management system. For full details on how to install Snakemake, please visit here. To summarize, the first step is to install mambaforge. If you have an x86_64 Linux machine then you can run the following commands:

wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
bash Mambaforge-Linux-x86_64.sh

If you don’t have this setup, you can download and install the file that corresponds to your OS and architecture, according to the table here.

You will then need to close and restart your terminal. If you want to prevent Conda from activating the base environment by default, you can run the following:

conda config --set auto_activate_base false

Now, you can install Snakemake:

conda activate base
mamba create -c conda-forge -c bioconda -n snakemake snakemake

Now, you can activate the snakemake environment using:

conda activate snakemake

In terms of dependencies, RetroDetector requires Snakemake, BWA, minimap2, Samtools, and EMBOSS. To keep things simple, you can run RetroDetector with the “–use-conda” flag and Snakemake will automatically set up the Conda environments with these dependencies. The dependencies will be installed into the current working directory without requiring any administrative privileges.

If you are able to run RetroDetector with the “–use-conda” flag, then you may return to Quick Start to continue with setting up RetroDetector for your project.

Otherwise you will need to install the dependencies manually. First you will need to install BWA and minimap2 in order to align the sequencing reads to the reference files. Full instructions can be found in the corresponding GitHub pages. To summarize, run the following commands in the folder where you normally install software:

git clone https://github.com/lh3/bwa.git
cd bwa
make
cd ..
git clone https://github.com/lh3/minimap2
cd minimap2
make
cd ..

Then, make sure to add the paths to BWA and minimap2 to your $PATH environment variable. For example, if your software directory is /user/software, you could run:

export PATH=/user/software/minimap2:$PATH
export PATH=/user/software/bwa:$PATH

Next, you will need to install Samtools. RetroDetector requires the Samtools consensus command, which was Please follow the instructions here to download and install the latest version of SAMtools and HTSlib. HTSlib is required in order to use bgzip. For example, if your software directory is /user/software, you could run the following (for SAMtools 1.15.1):

wget https://github.com/samtools/samtools/releases/download/1.15.1/samtools-1.15.1.tar.bz2
tar -xf samtools-1.15.1.tar.bz2
cd samtools-1.15.1
./configure --prefix=/user/software/samtools-1.15.1
make
make install
cd ..
wget https://github.com/samtools/htslib/releases/download/1.15.1/htslib-1.15.1.tar.bz2
tar -xf htslib-1.15.1.tar.bz2
cd htslib-1.15.1
./configure --prefix=/user/software/htslib-1.15.1
make
make install
cd ..

Finally, make sure to add the paths to SAMtools and HTSlib to your $PATH environment variable. For example:

export PATH=/user/software/samtools-1.15.1/bin:$PATH
export PATH=/user/software/htslib-1.15.1/bin:$PATH

To continue with setting up RetroDetector for your project, return to Quick Start.