Starting from version 1.0.0, binary release for Linux and MacOS are no longer supported. Instead we release Docker image for SEQLinkage which can be executed on both Linux and MacOS. Although overall execution time of a command may increase by over 10%, we believe for at least new users the straightforward installation and guaranteed reproducibility are well worth the loss in performances.

In order to run the docker image we provide, you should have Docker installed on your machine. If you do not have Docker, please follow this jump-start guide to it up on your system. Otherwise you can pull the docker image and run it:

docker pull gaow/seqlink
alias seqlink='docker run --rm --security-opt label:disable -t '\
	'-P -h SEQLinkage -w $PWD -v /tmp:/tmp -v $PWD:$PWD '\
	'-u $UID:${GROUPS[0]} -e HOME=/seqlink -e USER=$USER gaow/seqlink seqlink'
seqlink -h

It is recommended that you add the alias to your shell configuration script (~/.bashrc on Linux and ~/.bash_profile on Mac)

alias seqlink='docker run --rm --security-opt label:disable -t '\
	'-P -h SEQLinkage -w $PWD -v /tmp:/tmp -v $PWD:$PWD '\
	'-u $UID:${GROUPS[0]} -e HOME=/seqlink -e USER=$USER gaow/seqlink seqlink'

So next time you can simply run

seqlink -h

to evoke the program instead of having to type docker run command.

Supporting data as well as older versions of the software can be downloaded here.

SEQLinkage was developed during 2013 - 2014 on Debian 8.0 with Python 2 and GCC 5.0. To set it up properly in nowadays computing environment (eg, using conda env) you might find this Dockerfile helpful.

To successfully compile the program from source you need to have on your OS gcc (version 4.9+) ''swig'' and ''anaconda'' installed.

Below are commands for installing dependency packages on Debian 8.0. It may also hold for Ubuntu based Linux.

sudo apt-get install gcc g++ build-essential libbz2-dev swig

Then download and install Anaconda scientific Python distribution.

python setup.py install

If the command above failed because it requires root privilege, you should instead run a local installation by

• Specifying lib and bin directories
• Modify the system environment variable to include these directores
  • you can write the export commands to your ~/.bashrc file to make it permanent

python setup.py install --install-platlib=/path/to/lib \
                        --install-scripts=/path/to/bin
export PATH=/path/to/bin:$PATH
export PYTHONPATH=/path/to/lib:$PYTHONPATH

SEQLinkage is on github since version 1.0.0. We welcome your contributions through github!