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3_Installation.md

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How to install MSIsensor-pro?

Directly using binary version

  wget https://github.com/xjtu-omics/msisensor-pro/raw/master/binary/msisensor-pro[v1.x.x]
  chmod +x msisensor-pro[v1.x.x]
  export PATH=`pwd`:$PATH

If some dynamic libraries are missing, you need to install them and add their paths to the LD_LIBRARY_PATH variable.

Install Using Docker

   docker pull pengjia1110/msisensor-pro   
   docker run pengjia1110/msisensor-pro msisensor-pro

When running msisensor-pro with Docker, please note that you need to map the local path to the internal Docker path using the -v option.

Install Using Bioconda

  conda install msisensor-pro=v1.2.0 # install v1.2.0 version of msisensor-pro with bioconda 
  conda install msisensor-pro # install latest version of msisensor-pro with bioconda

Install from source code

( Recommended For Developers )

Install the dependencies

Dependent packages including zlib, ncurses and nurses-dev are required for MSIsensor-pro. You may already have these prerequisite packages. If not, you need to run the following code to obtain dependent packages.

  • For Debian or Ubuntu:

    sudo apt-get install libbz2-dev zlib1g-dev libcurl4-openssl-dev libncurses5-dev libncursesw5-dev

  • For Fedora, CentOS or RHEL

    sudo yum install bzip2-devel xz-devel zlib-devel ncurses-devel ncurses

Build MSIsensor-pro from source code

  • clone the repository from our github

    git clone https://github.com/xjtu-omics/msisensor-pro

  • make

    cd msisensor-pro/
./INSTALL

  • install

    sudo mv binary/msisensor-pro /usr/local/bin/

    You can also choose to add the path of msisensor-pro to the PATH variable or run it directly using the absolute path.