Preparation

2100-01-01 Introduction PV:

The MaChIAto consists of python and R with various packages other developers established. So the installation process is complex. However, you can quickly install MaChIAto using the docker container.

Install MaChIAto using the docker (Strongly Recommended)

Download and install Docker Desktop: https://docs.docker.com/engine/install/#desktop
Enter Docker settings menu to adjust the memory allocation (~10G of memory is recommmended)

Type the following commands in the terminal.

# Download Docker image for MaChIAto Classifier
docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato:latest python ../MaChIAto.py -h;
# Download Docker image for MaChIAto Aligner
docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_aligner:latest Rscript ../MaChIAtoAligner.R
# Download Docker image for collect_MaChIAto_data.py
docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/collect_machiato_data:latest python ../collect_MaChIAto_data.py;
# Download Docker image for MaChIAto Analyzer
docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_analyzer:latest Rscript ../MaChIAtoAnalyzer.R;
# Download Docker image for MaChIAto Reviewer
docker run --rm -v `pwd`:/DATA -w /DATA -i kazukinakamae/machiato_reviewer:latest Rscript ../MaChIAtoReviewer.R;

Then, if you wish, you can follow the manual below.

Quick Start: https://machiatopage.github.io/2100/01/02/Quick-Start/
Usage of MaChIAto Classifier: https://machiatopage.github.io/2022/06/22/Usage-of-MaChIAto-Classifier/
Usage of MaChIAto Aligner: https://machiatopage.github.io/2022/06/22/Usage-of-MaChIAto-Aligner/
Usage of collect_MaChIAto_data.py: https://machiatopage.github.io/2022/07/27/Usage-of-collect-MaChIAto-data-py/
Usage of MaChIAto Analyzer: https://machiatopage.github.io/2022/06/22/Usage-of-MaChIAto-Analyzer/
Usage of MaChIAto Reviewer: https://machiatopage.github.io/2022/06/22/Usage-of-MaChIAto-Reviewer/

Install MaChIAto within the conda environment (Deprecated)

The installation procedure is deprecated. We are not supporting the procedure because the environment is not stable and is difficult to reproduce.

MacOSX

Click HERE to download MaChIAto.

Alternatively, enter the following command terminal.

1	git clone https://github.com/KazukiNakamae/MaChIAto.git;

Install miniconda3, R (>version R-4.0.1), Xcode, and XQuartz according to the following instructions.

Change default shell

1. Set bash as default shell

1	chsh -s /bin/bash;

Install software

1	sudo xcodebuild -license;

4. install XQuartz from the XQuartz project

(xquartz.macosforge.org)

Build the environment using conda

1. Environment for MaChIAto_(MaChIAto Classifier)

conda create --name MaChIAto_env;
source activate MaChIAto_env;
conda install -c anaconda python=3.8;
pip install --upgrade pip;
pip install regex tqdm argparse biopython numpy matplotlib GPy gpyopt datetime pandas;
conda deactivate;

2. Environment for MaChIAtoAligner

conda create --name MaChIAto_Aligner_env;
source activate MaChIAto_Aligner_env;
conda install -c bioconda python=3.8 bwa=0.7.17 samtools=1.9;
conda deactivate;

3. Environment for MaChIAtoAnalyzer

conda create --name MaChIAto_Analyzer_env;
source activate MaChIAto_Analyzer_env;
conda install -c anaconda python=3.8 wget;
conda install -c bioconda emboss;
conda install -c bioconda oligoarrayaux;
pip install --upgrade pip;
pip install numpy regex tqdm pandas;
conda deactivate;

4. Environment for MaChIAtoReviewer

1
2
3

conda create -n MaChIAto_Reviewer_env --clone MaChIAto_Aligner_env;
source activate MaChIAto_Reviewer_env;
conda deactivate;

Linux

Click HERE to download MaChIAto.