seeker

R package

1. Install BiocManager.

   if (!requireNamespace('BiocManager', quietly = TRUE))
     install.packages('BiocManager')

2. If you use RStudio, go to Tools → Global Options… → Packages → Add… (under Secondary repositories), then enter:

   • Name: hugheylab
   • Url: https://hugheylab.github.io/drat/

   You only have to do this once. Then you can install or update the package by entering:

   BiocManager::install('seeker')

   Alternatively, you can install or update the package by entering:

   BiocManager::install('seeker', site_repository = 'https://hugheylab.github.io/drat/')

System dependencies

These instructions are for Unix-based systems. If you’re using Windows, you’re doing it wrong.

1. Download and install Aspera Connect. On Linux, you will likely have to download a tar.gz file (using wget or curl), untar it (using tar -zxvf), then run the resulting shell script. On macOS, you may have to install a browser extension first, then install Connect from a dmg file.

2. Install Miniconda. On Linux:

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

   On macOS:

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

3. Set up conda channels, including bioconda.

   conda config --add channels defaults
   conda config --add channels bioconda
   conda config --add channels conda-forge

4. Install the mamba package manager.

   conda install mamba -c conda-forge

5. Install the other command-line tools. The code below will install the packages into the base conda environment; use -n to specify a different environment. When using seeker, you will need to ensure that R is running with the given conda environment.

   mamba install refgenie trim-galore fastqc fastq-screen salmon multiqc

6. Optionally, configure refgenie. For example:

   mkdir -p ${HOME}/genomes
   refgenie init -c ${HOME}/genomes/genome_config.yaml

   Then you can add the following line to ~/.bashrc, ~/.bash_profile, or ~/.zshrc, depending on your OS and shell.

   REFGENIE="${HOME}/genomes/genome_config.yaml"

   Then source the file and run refgenie init.

7. Optionally, use refgenie to fetch the salmon index files for the mouse and human transcriptomes.

   refgenie pull hg38/salmon_sa_index
   refgenie pull mm10/salmon_sa_index

8. Optionally, fetch the genomes for fastq-screen. This takes a long time, so don’t bother unless you actually plan to run fastq-screen.

   fastq_screen --get_genomes