Download MPAQT

Begin by downloading MPAQT from GitHub. Clone the repository and set the MPAQT_DIR environment variable to the directory where you cloned the package:

git clone <https://github.com/csglab/MPAQT.git>
cd MPAQT

export MPAQT_DIR=$PWD
export PATH=$MPAQT_DIR:$PATH

For convenient access to the MPAQT tool from any location on your system, automate the assignment and accessibility by adding the variable to your bashrc file and updating the PATH variable:

echo "export MPAQT_DIR=$MPAQT_DIR" >> ~/.bashrc
echo 'export PATH=$MPAQT_DIR:$PATH' >> ~/.bashrc

Install Dependencies

To install and run mpaqt and its dependencies, you can use conda environments or container images with docker or apptainer (formerly singularity).

These are the dependencies for mpaqt:

Tools:
  - R (v4.3.3)
  - kallisto (v0.50.1)
  - bustools (v0.43.2)

R Packages:
  - data.table (v1.15.4)
  - dplyr (v1.1.4)
  - tidyr (v1.3.1)
  - stringr (v1.5.1)
  - magrittr (v2.0.3)
  - matrix (v1.6_5)
  - optparse (v1.7.5)
  - rtracklayer (v1.62.0)
  - Biostrings (v2.70.1)
  - Rsubread (v2.16.1)

Conda Environment

To create a virtual environment for mpaqt, use the environment.yml file available in the repository:

conda env create -f environment.yml

This command will create an environment called mpaqt which can be activated using:

conda activate mpaqt

Now, you can run mpaqt and analyze your data. For example, you can index your reference transcriptome using the mpaqt index command. Refer to the Tutorial page for further steps.

Docker Container Image

You can pull the container image from DockerHub:

docker pull csglab/mpaqt:0.3.1

Next, attach your desired output directory to /csglab/mpaqt/projects using the -v (volume) option in Docker: