Manual installation

IgDiscover requires quite a few other software tools that are not included in most Linux distributions (or mac OS) 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 installed from requirements.txt in the last step with the pip install command. The instructions below are written for Linux and require modifications if you want to try this on OS X.

Note

We recommend the much simpler installation via Conda instead of using the instructions in this section.

Install non-Python dependencies

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

1. Install Python 3.6 or newer. It may already be installed on your system. On a sufficiently recent Debian or 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 PEAR:

   Install from https://www.h-its.org/downloads/pear-academic/.

5. Install IgBLAST:

   wget ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.17.1/ncbi-igblast-1.17.1-x64-linux.tar.gz
   tar xvf ncbi-igblast-1.17.1-x64-linux.tar.gz
   mv ncbi-igblast-1.17.1/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.

6. Install VSEARCH:

   wget https://github.com/torognes/vsearch/archive/v2.22.1.tar.gz tar xzf v2.22.1.tar.gz cd vsearch-2.22.1 ./autogen.sh ./configure CFLAGS=”-O3” CXXFLAGS=”-O3” make make install # as root or sudo make install

7. 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 install IgDiscover and its dependencies:

    git clone https://gitlab.com/gkhlab/igdiscover22.git
cd igdiscover22
pip install -r requirements.txt
pip install -e ./

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.