This repository implements converters and tools for working with NGS data in HPC or Hadoop cluster
You can find HPG BigData documentation and tutorials at: https://github.com/opencb/hpg-bigdata/wiki.
You can report bugs or request new features at GitHub issue tracking.
Releases notes are available at GitHub releases.
Roadmap is available at GitHub milestones. You can report bugs or request new features at GitHub issue tracking.
HPG BigData is versioned following the rules from Semantic versioning.
We recommend to contact HPG BigData developers by writing to OpenCB mailing list opencb@googlegroups.com. The main maintainers and developers are:
- Ignacio Medina (im411@cam.ac.uk) (Founder and Project Leader)
- Joaquín Tárraga (jtarraga@cipf.es)
- Jacobo Coll (jacobo.coll-moragon@genomicsengland.co.uk)
- Matthias Haimel (mh719@cam.ac.uk)
- Jose M. Mut (jmmut@ebi.ac.uk)
HPG BigData is an open-source and collaborative project. We appreciate any help and feeback from users, you can contribute in many different ways such as simple bug reporting and feature request. Dependending on your skills you are more than welcome to develop client tools, new features or even fixing bugs.
HPG BigData is mainly developed in Java and it uses Apache Maven as building tool. HPG BigData requires Java 8 and others OpenCB Java dependencies that can be found in Maven Central Repository.
Stable releases are merged and tagged at master branch, you are encourage to use latest stable release for production. Current active development is carried out at develop branch, only compilation is guaranteed and bugs are expected, use this branch for development or for testing new functionalities. Only dependencies of master branch are ensured to be deployed at Maven Central Repository, develop branch may require users to download and install other active OpenCB repositories:
- GA4GH: https://github.com/opencb/ga4gh (branch 'master')
- java-common-libs: https://github.com/opencb/java-common-libs (branch 'develop')
- biodata: https://github.com/opencb/biodata (branch 'develop')
To build the application, run ./build.sh on the main folder. It will create a new folder build. Find the launch scripts on build/bin, and some examples on build/examples.
These are other requirements:
- Java 1.8
- cmake, g++
- Libraries: libz, libsnappy, liblzma, libncurses
HPG BigData is an open-source and free project, you can download develop branch by executing:
imedina@ivory:~$ git clone https://github.com/opencb/hpg-bigdata.git
Cloning into 'hpg-bigdata'...
remote: Counting objects: 3206, done.
remote: Compressing objects: 100% (118/118), done.
remote: Total 3206 (delta 47), reused 0 (delta 0), pack-reused 3039
Receiving objects: 100% (3206/3206), 11.54 MiB | 1.35 MiB/s, done.
Resolving deltas: 100% (913/913), done.
Checking connectivity... done.
For command line options invoke:
imedina@ivory:~$ cd build/bin
imedina@ivory:~$ ./hpg-bigdata.sh
imedina@ivory:~$ ./hpg-bigdata-local.sh
As you can see there are three commands implemnted, each of them with different subcommands.
- sequence : to process FastQ sequence files
- alignment: to process BAM alignment files
- variant : to process VCF variant files
You can find more detailed documentation and tutorials at: https://github.com/opencb/hpg-bigdata/wiki.
JetBrains is supporting this open source project with:
