Installation

Dependencies

A working copy of Singularity is required. Singularity is best installed with sudo. While it is said to be possible to install as an unprivileged user with some features missing, MIPTools has yet to be tested on such an installation.

Singularity is available for most Linux systems, including high-performance clusters. It is also possible to install and use on Mac OS using virtual machines with a little bit of extra work.

Note that the snap package is a rapid way to install the go language required by Singularity (e.g., on Ubuntu/Debian: sudo snap install go --classic).

Quick Start

The MIPTools container, built and ready to use, can be downloaded here. You can download the development version or any previous release:

# Download the latest stable release
wget https://baileylab.brown.edu/MIPTools/download/miptools_v0.4.0.sif

# Download the development version
wget https://baileylab.brown.edu/MIPTools/download/miptools_dev.sif

Note

These prebuilt versions do not include the bcl2fastq software due to its license. You must build the container yourself if you plan to use MIPTools to demultiplex bcl files.

Install From Source

MIPTools can also be built from source using the definition file provided in the GitHub repository. You can install the most recent release using the following:

# Install stable version
git clone --branch v0.4.0 https://github.com/bailey-lab/MIPTools.git

You can alternatively install the development version:

# Install dev version
git clone https://github.com/bailey-lab/MIPTools.git

Next, build the container, and you should be all set to get started using MIPTools!

cd MIPTools
sudo singularity build miptools.sif MIPTools.def

miptools.sif is a single portable file which has all the programs needed for MIP design, data analysis, and a lot more.

Sudo Privileges

Warning

You must have sudo privileges to build the image. You do not need sudo to use the image.

If you want to run the container on an environment without sudo, either download a prebuilt image (see above) or build the container on your own machine where you do have sudo privileges and copy the image file to the computer without sudo. Note that the Singularity program itself must have been installed with sudo.

Demultiplexing

If you plan to use MIPTools to demultiplex bcl files, you must download bcl2fastq separately. Currently, you can download it from here. You must download the file: bcl2fastq2 Conversion Software v2.20 Installer (Linux rpm) and place it in the MIPTools/programs directory.

CPU Usage

The build process can take about 30-60 minutes to build, depending on the number of CPU cores available. By default, the build process will use 20 CPU cores. If the computer used for building the container has less then 20 CPU cores available, change the CPU_COUNT=20 value at the top of the MIPTools.def file to a suitable number before building the container. On the other hand, if the computer has additional CPU’s, by all means, use them by setting the same parameter to a higher value.