VariantProcessing

VariantProccessing

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.

Prerequisites

Bedtools:

For Fedroa 13, 14 and EPEL5/6 users, run the following command line command:

$ yum install BEDTools

For Debian/Ubuntu users:

$ apt-get install bedtools

For OSX users with Homebrew installed:

$ brew tap homebrew/science
$ brew install bedtools

Or alternatively wiht the MacPort system:

$ port install bedtools

BedOPS: (For troubleshooting tips, refer to BedOPS Linux systems: BedOPS required GCC 4.8.2 which allows support of C++11 features that is used by BedOPS You can check the version of your GCC with

$ gcc --version

If you have a compiler older than 4.8.2, use your preferred package manager to upgrade/install 4.8.2 ie. (Ubuntu)

$ sudo apt-get install gcc-4.8
$ sudo apt-get install g++-4.8
$ sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.8 50
$ sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 50

Some static libraries may also need to be installed: ie. (CentOS or RH-like environment)

$ sudo yum install libstdc++-static
$ sudo yum install glibc-static

or Ubuntu:

$ sudo apt-get install libc6-dev
$ sudo apt-get install build-essentials

Next, install a git client of your choice if you do not already have one installed

Then, clone the BedOPS Git repository:

$ git clone https://github.com/bedops/bedops.git

Then go into the top-level of the local copy of the repository and run the following:

$ cd bedops
$ make

Then once it has been build, install the compiled binaries and scripts to a local bin directory:

$ make install

Finally, copy the extracted binaries to a location of your choice:

Mac OSX:

Manual compilation: Check if you have Clang/LLVM 3.5 or grater installed:

$ clang -v

It is also recommended to install Apple Xcode and Command Line Tools (Preferences->Downloads options in Xcode)

Install a git client of your choice if you do not have one installed

Clone the git repository in an appropriate local direcctory:

$ git clone https://github.com/bedops/bedops.git

Run make in the loccal copy of the repository:

$ cd bedops
$ make

Next, run:

$ make install

Then copy the extracted binaries to a location of your choice:

$ cp bin/* /usr/local/bin

Bioconda:

Install the Miniconda package from Conda's website

Add the Conda channels for Bioconda if you have not already:

$ (conda config --add channels r)
$ conda config --add channels defaults
$ conda config --add channels conda-forge
$ conda config --add channels bioconda

Install the BedOPS package:

$ conda install bedops

Homebrew:

Ensure you have Clang/LLVM 3.5 or greater installed:

$ clang -v

Installing

A step by step series of examples that tell you how to get a development env running

Say what the step will be

Give the example

And repeat

until finished

End with an example of getting some data out of the system or using it for a little demo

Running the tests

Explain how to run the automated tests for this system

Break down into end to end tests

Explain what these tests test and why

Give an example

And coding style tests

Explain what these tests test and why

Give an example

Deployment

Add additional notes about how to deploy this on a live system

Built With

• RStudio- The IDE used

Contributing

Versioning

We use SemVer for versioning. For the versions available, see the tags on this repository.

Authors

• Billie Thompson - Initial work - PurpleBooth

See also the list of contributors who participated in this project.

License

This project is licensed under the MIT License - see the LICENSE.md file for details

Acknowledgments

• Dr Anindya Dutta for providing the opportunity to work in his laboratory
• Ajay Chatrath for his mentorship and providing all the data and any insight for this package