Installation
If you have a working copy of singularity and have demultiplexed data, you can use our sif file (recommended approach, below). Due to licensing issues, if you want to use miptools to demultiplex your data (we’re just wrapping up illumina’s bcl2fastq demultiplexing program) you’ll need to download bcl2fastq, put it in our ‘programs’ folder, and build your own sif file from source.
Dependencies
A working copy of Singularity is required. Our tools only work when singularity is installed with administrative privileges with sudo. Administrative privileges are not required to run singularity.
Singularity is available for most Linux systems and is usually already installed on academic high-performance clusters. It is also possible to install and use on Mac OS using virtual machines with a little bit of extra work.
Easy Installation
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
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, simply 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
privilege 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. By default, the
build process will use 20 CPU cores. You can change this by editing the
CPU_COUNT=20
value at the top of the
MIPTools.def
file to a suitable number before building the container.