Gotoh

Gotoh is a simple sequence aligner used in several of the BC-CfE's bioinformatics tools.

The functionality is launched as a Docker container, and provided via a FastAPI interface.

By building extension modules, Gotoh can also be called from Python directly.

For details on the alignment algorithm used, see the following:

Gotoh, Osamu. "An improved algorithm for matching biological sequences."
    Journal of Molecular Biology, Volume 162, Issue 3 (1982): 705-708.

Gotoh, Osamu. "Optimal alignment between groups of sequences and its application
     to multiple sequence alignment." Computer applications in the biosciences: 
     CABIOS 9.3 (1993): 361-370.

Launching the webserver Docker container

To build the Docker container, use the included Makefile in the root directory. This is currently tested with make build-base. This builds the Docker image. You can launch the Docker image with make run-base-local. (Root permissions are needed to run these commands.)

Once the Docker image is running, you can launch the FastAPI using

cd /webserver/
./runserver.sh

There are two API endpoints /align_it (nucleotide) and align_it_aa (amino acid). See the FastAPI docs <local-address>/docs for details.

Python Bindings

To build Gotoh's Python bindings, you'll need to have the following installed:

• A supported Python interpreter (e.g. Python 3.9)
• The Python header files (apt install python-dev or yum install platform-python-devel on Linux, usualy installed by default on Windows)
• A C++ compiler

With these installed, you should be able to build the extension module with

    python setupy.py build

Alternately, you may install the gotoh module using pip by adding this repo to your requirements.txt file or similar method.

    git+https://github.com/cfe-lab/[email protected]#egg=gotoh&subdirectory=alignment/gotoh

Ruby Bindings

The /ruby directory contains the directory structure required to build a gem containing Gotoh's Ruby bindings. This gem, named gotoh, contains a module called Gotoh that holds the align_it and align_it_aa functions.

To build Gotoh's Ruby bindings (which are called "alignment" instead of "gotoh" for arbitrary historical reasons), you'll need to have the following installed:

• Ruby
• The Ruby header files (installed by default with DevKit on Windows or RVM on Linux)
• A C++ compiler

The "canonical" environment for testing and building this package is the dev container defined in the .devcontainer directory. This system is based on the cfe_ubuntu Ruby image based on Ubuntu 20.04 (this old version is required to run Ruby 2.2.2), and stripped down to only the parts necessary for Ruby. This environment is also used by the CI/CD pipeline for testing and building.

In this environment (or another suitable environment), you should be able to build the extension module using the build_gem.bash script. By default this will make a gem with the version number 0.1.0.pre; set the environment variable CFE_GOTOH_VERSION before building to assign a proper version number.

Manually building the Ruby bindings

If you want to manually build the bindings, e.g. for testing/debugging/development, copy /ruby/ext/gotoh/extconf.rb to the /alignment/gotoh/ directory and change the create_makefile('gotoh/gotoh') line to create_makefile('gotoh'); then run

    ruby extconf.rb  # generates a Makefile and other supporting files
    make

which will build gotoh.so, which can be required from Ruby.