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Installation

SEQPower Docker Image

Starting from version 1.1.0, binary release for Linux and MacOS are no longer supported. Instead we release Docker image for SEQPower which can be executed on both Linux and MacOS. Although overall execution time of a command may increase by over 10%, we believe the straightforward installation and guaranteed reproducibility are well worth the loss in speed.

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


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

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


So next time you can simply run

spower -h


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 here.

Install from Source

Source code download

Dependencies

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

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


Then download and install Anaconda scientific Python distribution.

Compile from source

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


Developmental Version

SEQPower is on github since version 1.1.0. We welcome your contributions through github!