Installation

Please follow the guide below to install MetaChat and its dependent software.

System requirements

MetaChat was developed and tested on Linux (U), macOS and Windows operating systems. Linux and macOS is recommended.

Python requirements

MetaChat was developed and tested using python 3.9. We recommend using mamba or conda to manage Python environments.

Installation using pip

We suggest setting up MetaChat in a separate mamba or conda environment to prevent conflicts with other software dependencies. Create a new Python environment specifically for MetaChat and install the required libraries within it.

mamba create -n metachat_env python=3.9 r-base=4.3.2
mamba activate metachat_env
pip install metachat

if you use conda, r-base=4.3.2 may not included in the channels. Instead, you can r-base=4.3.1 in conda.

Now you can check if metachat can sucessfully import in Python:

import metachat as mc

MetaChat requires two additional R packages in one downstream analysis: tradeseq and clusterexperiment. These can be easily installed through the mirror in Bioconda.

mamba install bioconda::bioconductor-tradeseq=1.16.0
mamba install bioconda::bioconductor-clusterexperiment=2.22.0

Make sure you add the Bioconda channel to your environment. if you haven’t already, add the Bioconda channel to your Conda configuration (https://bioconda.github.io/):

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

Since Bioconda is only supported on Linux (64-bit and AArch64) and macOS (x86_64), installation on other systems requires the use of the Bioconductor.

mamba install -c conda-forge r-biocmanager --no-update-deps

BiocManager::install("tradeSeq")

Hint: This way of installation may result in errors when installing some dependency packages. Our recommendation is to use conda or mamba for these dependencies and try BiocManager::install("tradeSeq") again.

Troubleshooting

Problem: Unable to install gseapy

If you get error: can't find Rust compiler during the installation of gseapy, please try installing the rust compiler via mamba install rust.

Problem: Unable to install pydpc

If you get error during the installation of pydpc, please try pip install --use-pep517 pydpc==0.1.3.

While installing in Windows system, you may get the error:

error: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": http://visualstudio.microsoft.com/visual-cpp-build-tools/

You can sovle this problem as following steps:

  1. Visit the Visual Studio website to download and install the latest version of Microsoft C++ Build Tools (https://visualstudio.microsoft.com/visual-cpp-build-tools/).

  2. Select installation options: During installation, you can choose to install all default options to ensure the C++ compiler and necessary build tools are included. If Visual Studio is already installed, you can select to install only the C++ tools.

  3. Set environment variables: After installation, you may need to manually set the environment variables so that the system can locate the correct build tools. Follow these steps to set the environment variables: (i) Open the Control Panel, navigate to “System and Security” -> “System” -> “Advanced system settings.”; (ii) In the “System Properties” window, click the “Environment Variables” button ; (iii) In the “System Variables” section, find and edit the variable named Path. (iv) Add the installation path of Microsoft C++ Build Tools to the Path variable. The typical path is similar to C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.xx.xx\bin\Hostx64\x64, but it may vary depending on your installation version and system configuration.

Continuous updating…

Feel free to contact us if you encounter any other problems with the installation.