~~NOTOC~~
===== Installation =====
==== SEQLinkage Docker Image ====
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 [[docker-guide|jump-start guide]] to it up on your system. Otherwise you can pull the docker image and run it:

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

<code bash>
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'
</code>\\
So next time you can simply run

<code bash>
seqlink -h
</code>\\
to evoke the program instead of having to type ''docker run'' command.

==== Supporting Data ====
Supporting data as well as older versions of the software can be downloaded [[http://bioinformatics.org/seqlink/download/|here]].

==== Install from Source ====
=== Latest source code download ===
[[http://bioinformatics.org/seqlink/ccount/click.php?id=3|{{icons:download.png?64}}]]

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 [[https://github.com/gaow/SEQLinkage/blob/master/Dockerfile|Dockerfile]] helpful.

=== Dependencies ===
To successfully compile the program from source you need to have on your OS ''gcc'' (version 4.9+) [[http://swig.org|''swig'']] and [[http://continuum.io/downloads|''anaconda'']] installed.

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

<code bash>
sudo apt-get install gcc g++ build-essential libbz2-dev swig
</code>\\
Then download and install [[http://continuum.io/downloads|Anaconda]] scientific Python distribution.

=== Compile from source ===
<code bash>
python setup.py install
</code>\\
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

<code bash>
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
</code>\\
==== Developmental Version ====
''SEQLinkage'' is [[https://github.com/gaow/SEQLinkage|on github]] since version 1.0.0. We welcome your contributions through github!