Installation

All the programs of MIPTools are packaged into a single file known as a singularity image or sif file.

If you have a working copy of singularity, you can use our sif file without the need to install anything else.

Obtaining MIPTools

The MIPTools sif file, built and ready to use, can be downloaded from here: https://baileylab.brown.edu/MIPTools/download/. This is the recommended approach for obtaining MIPTools.

You can download the development version or any previous release:

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

# Download the latest stable release
wget https://baileylab.brown.edu/MIPTools/download/miptools_v0.5.0.sif

If your machine has singularity installed, you can ignore the rest of this guide.

Sudo Privileges

There are two scenarios in which you might need sudo privileges:

First, you will need sudo in order to install singularity if it’s not already on your system.
Second, you will need sudo in order to build a sif file if you don’t want to use our prebuilt sif files.

If you want to run the container on an environment where you don’t have sudo privileges, either download a prebuilt image (recommended approach, see above) or build the image on a machine where you do have sudo privileges and copy the image file to the computer where you don’t have sudo privileges.

Obtaining Singularity

Singularity is available for most Linux systems and is usually already installed on academic high-performance clusters. Remember that you will need sudo permissions in order to install singularity in a way that is compatible with our pipelines. It is also possible to install and use on Mac OS using virtual machines with a little bit of extra work. We have tested two flavors of singularity. One is called apptainer and the other is singularity community-edition (aka singularity-ce).

Apptainer

Singularity can be installed from Apptainer using instructions from here: https://apptainer.org/docs/admin/main/installation.html

Specifically, if you’re using this on Linux, we would recommend using pre-built packages, which are available here under “assets”: https://github.com/apptainer/apptainer/releases

singularity-ce

Singularity-ce can be installed from here: https://docs.sylabs.io/guides/4.2/admin-guide/installation.html

Specifically, if you’re using this on Linux, we would recommend using pre-built packages, which are available here under “assets”: https://github.com/sylabs/singularity/releases

Advanced: Building a sif file from source

The MIPTools sif file can also be built from source using the build.sh shell script provided in the build folder of the GitHub repository. This could be useful if, for example, you want to tweak the behavior of MIPTools by editing the source code. This relies on a working copy of singularity and a machine with sudo privileges. You can install the most recent release using the following:

Step 1, clone the repository (either a stable version or the dev version):

# Clone stable version
git clone --branch v0.5.0 https://github.com/bailey-lab/MIPTools.git

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

Step 2, make any changes to the source code.

Step 3, build the sif file:

cd MIPTools/build
bash build.sh miptools.sif

miptools.sif is a single portable file which has all the programs needed for MIP design, data analysis, and a lot more. Once the sif file is built, you can copy or move the sif file anywhere (even onto a different computer).

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.