Manual installation

IgDiscover requires quite a few other software tools that are not included in most Linux distributions (or OS X for that matter) and which are also not available from the Python packaging index (PyPI) because they are not Python tools. If you do not use the recommended simple installation instructions via Conda, you need to install those non-Python dependencies manually. Regular Python dependencies are automatically pulled in when IgDiscover itself is installed in the last step with the pip install command. The instructions below are written for Linux and require if you want to try this on OS X.

Install non-Python dependencies

The dependencies are: MUSCLE, FastQC, VSEARCH, IgBLAST, PEAR, and – optionally – flash.

  1. Install Python 3. It most likely is already installed on your system, but in Debian/Ubuntu, you can get it with

    sudo apt-get install python3
    
  2. Create the directory where binaries will be installed. We assume $HOME/.local/bin here, but this can be anywhere as long as they are in your $PATH.

    mkdir -p ~/.local/bin
    

    Add this line to the end of your ~/.bashrc file:

    export PATH=$HOME/.local/bin:$PATH
    

    Then either start a new shell or run source ~/.bashrc to get the changes.

  3. Install MUSCLE. This is available as a package in Ubuntu:

    sudo apt-get install muscle
    

    If your distribution does not have a ‘muscle’ package or if you are not allowed to run sudo:

    wget -O - http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gz | tar xz
    mv muscle3.8.31_i86linux64 ~/.local/bin/
    
  4. Install VSEARCH:

    wget -O ~/.local/bin/vsearch https://github.com/torognes/vsearch/releases/download/v1.1.0/vsearch-1.1.0-linux-x86_64
    chmod +x ~/.local/bin/vsearch
    
  5. Install PEAR:

    wget http://sco.h-its.org/exelixis/web/software/pear/files/pear-0.9.6-bin-64.tar.gz
    tar xvf pear-0.9.6-bin-64.tar.gz
    mv pear-0.9.6-bin-64/pear-0.9.6-bin-64 ~/.local/bin/pear
    
  6. Install IgBLAST:

    wget ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.4.0/ncbi-igblast-1.4.0-x64-linux.tar.gz
    tar xvf ncbi-igblast-1.4.0-x64-linux.tar.gz
    mv ncbi-igblast-1.4.0/bin/igblast? ~/.local/bin/
    

    IgBLAST requires some data files that must be downloaded separately. The following commands put the files into ~/.local/igdata:

    mkdir ~/.local/igdata
    cd ~/.local/igdata
    wget -r -nH --cut-dirs=4 ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data
    wget -r -nH --cut-dirs=4 ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/database/
    wget -r -nH --cut-dirs=4 ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/optional_file/
    

    Also, you must set the $IGDATA environment variable to point to the directory with data files. Add this line to your ~/.bashrc:

    export IGDATA=$HOME/.local/igdata
    

    Then run source ~/.bashrc to get the changes.

  7. Install FastQC. Under Debian/Ubuntu:

    sudo apt-get install fastqc
    

    If you install it by hand, make sure you end up with a fastqc binary in the $PATH.

  8. Optionally, install flash:

    wget -O FLASH-1.2.11.tar.gz http://sourceforge.net/projects/flashpage/files/FLASH-1.2.11.tar.gz/download
    tar xf FLASH-1.2.11.tar.gz
    cd FLASH-1.2.11
    make
    mv flash ~/.local/bin/
    

Install IgDiscover

Install IgDiscover with the Python package manager pip, which will download and install IgDiscover and its dependencies:

pip3 install --user igdiscover

Both commands also install all remaining dependencies. The --user option instructs both commands to install everything into $HOME/.local.

Finally, check the installation with

igdiscover --version

and you should see the version number of IgDiscover.

You should now run IgDiscover on the test data set.