Installation

Quickstart

Try these instructions first. If they don’t work, continue reading below.

Linux

On Linux, open a terminal window and run these commands. Copy and paste each line separately:

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

Close the terminal window and open a new one. Then run:

conda install -c bioconda igdiscover
igdiscover --version

If the last command outputs the current version of IgDiscover, it worked! Skip to the next section if you have problems.

OS X/macOS

On macOS, follow the miniconda installation instructions. Then open a terminal window and run:

conda install -c bioconda igdiscover
igdiscover --version

If the last command outputs the current version of IgDiscover, it worked! Keep reading if you have problems.

Conda

IgDiscover is written in Python 3 and runs on Linux and OS X. Be aware that running on OS X is not as well tested as on Linux, yet.

IgDiscover is easy to install because the program itself and its dependencies are available as Conda packages. Conda makes it possible to install IgDiscover with a single command, but Conda itself needs to be installed first. Since IgDiscover depends on many programs that are not available in most Linux distributions (or OS X for that matter), we recommend using Conda, but non-Conda installation instructions are also available.

First, download and install miniconda. That page has instructions for both Linux and OS X. If you are on Linux, either follow the instructions there or try these commands:

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

Accept the license, and when you get the question “Do you wish the installer to prepend the Miniconda3 install location to PATH in your /home/.../.bashrc”, answer yes. If you don’t, you need to note down the export PATH=... that the installer prints somewhere and type it in every time before using Conda or IgDiscover.

Note

If you use zsh instead of bash (applies to Bio-Linux, for example), then you need to manually add the export PATH=... line to the end of the file /home/your-user-name/.zshrc instead. The conda installer does not do this for you!

Alternatively, change your default shell to bash by running chsh -s /bin/bash.

Next, close the terminal window and open a new one. Make sure that Conda is installed by typing in conda list. If everything is working, you should see a list of some packages andd IgDiscover can now be installed.

Install IgDiscover from the bioconda channel with this command:

conda install -c bioconda igdiscover python=3.5

The python=3.5 is needed because Conda comes with a default of Python 3.6, but bioconda offers only packages for Python 3.5.

Then make sure that it works by running

igdiscover --version

and you should see the version number of IgDiscover.

You should now run IgDiscover on the test data set.

If you cannot or do not want to use Conda, you need to follow the manual installation instructions.

Troubleshooting on OS X

If you get the error

ValueError: unknown locale: UTF-8

Then follow these instructions.

Troubleshooting on Linux

If you use conda and see an error that includes something like this:

ImportError: .../.local/lib/python3.5/site-packages/sqt/_helpers.cpython-35m-x86_64-linux-gnu.so: undefined symbol: PyFPE_jbuf

Or you see any error that mentions a .local/ directory, then a previous installation of IgDiscover is interfering with the conda installation.

The easiest way to solve this problem is to delete the directory .local/ in your home directory, see also how to remove IgDiscover from a Linux system.

Development version

To install IgDiscover directly from the most recent source code, read the developer installation instructions.