docs/INSTALLATION.md

In lehner-lab/DiMSum: A pipeline for processing deep mutational scanning data

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Installation Instructions

System requirements

DiMSum is expected to work on all Unix-like operating systems.

Installing DiMSum and its dependencies using Conda (recommended)

The easiest way to install DiMSum is by using the bioconda package.

Firstly, install the Conda package/environment management system (if you don't already have it).

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

IMPORTANT: If in doubt, respond with "yes" to the following question during installation: "Do you wish the installer to initialize Miniconda3 by running conda init?". In this case Conda will modify your shell scripts (~/.bashrc or ~/.bash_profile) to initialize Miniconda3 on startup. Ensure that any future modifications to your $PATH variable in your shell scripts occur before this code to initialize Miniconda3.

After installing Conda you will need to add the bioconda channel as well as the other channels bioconda depends on. Start a new console session (e.g. by closing the current window and opening a new one) and run the following:

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

Next, create a dedicated Conda environment to install the DiMSum bioconda package and it's dependencies:

conda create -n dimsum r-base=4.0 fastqc=0.11 r-dimsum
conda activate dimsum

TIP: See here for more information about managing conda environments.

To check that you have a working installation of DiMSum, run the Demo

NOTE: If you're having graphics issues, try installing R Cairo v1.5:

conda install -c conda-forge r-cairo=1.5

Installing DiMSum dependencies using Conda

Alternatively, once Conda is installed (or if you already have it) you can install DiMSum dependencies alone by creating a Conda environment from the dimsum.yaml file.

Firstly, clone the DiMSum repository:

git clone https://github.com/lehner-lab/DiMSum.git

Then use it to create the environment for DiMSum dependencies and activate it:

conda env create -f DiMSum/dimsum.yaml
conda activate dimsum

Once DiMSum dependencies have been installed successfully you can then install DiMSum from source (you can skip the first step to clone the DiMSum repository).

Installing DiMSum dependencies manually

Installing DiMSum dependencies manually is not recommended. The easiest way to install DiMSum (and its dependencies) is by using the DiMSum bioconda package. See Installing DiMSum using Conda.

REQUIRED: Before installing DiMSum from source, please ensure that the following required software is installed:

• R >=v3.6
• Pandoc >=v1.17.2

Pandoc comes bundled with RStudio and the pandoc binary can be found in the RStudio bin/pandoc directory.

OPTIONAL: Additionally, if raw FASTQ files will be processed (with DiMSum WRAP), the following software needs to be installed:

• FastQC v0.11
• Cutadapt v2.4
• VSEARCH >=v2.17
• Starcode v1.3

NOTE: Please ensure that the $PATH vairable is set so that these external binaries are available from the command-line prompt. You can add a directory (containing an external binary or symblic link) to your path by adding the following line at the bottom of your ~/.bashrc or ~/.bash_profile file:

export PATH=EXTERNAL_BINARY_DIRECTORY:$PATH

Installing DiMSum from source (GitHub)

Installing DiMSum from source is not recommended. The easiest way to install DiMSum (and its dependencies) is by using the DiMSum bioconda package. See Installing DiMSum using Conda.

Before installing DiMSum from source, please ensure that the required software dependencies are available.

Firstly, clone the DiMSum repository:

git clone https://github.com/lehner-lab/DiMSum.git

Then, from the same location run R and enter:

if(!require(devtools)) install.packages("devtools")
#devtools::install_deps('DiMSum') #Uncomment this line to install DiMSum dependencies
devtools::install('DiMSum')

Finally, add the cloned DiMSum repository base directory to your path. You can do this by adding the following line at the bottom of your ~/.bashrc or ~/.bash_profile file:

export PATH=CLONED_DIMSUM_REPOSITORY:$PATH

Demo DiMSum

In order to test that you have a working installation of the DiMSum pipeline and all necessary software dependencies, run the Demo.

lehner-lab/DiMSum documentation built on April 10, 2024, 4:15 a.m.