NBIC & VIB Bioinformatics RPM Repository
NBIC and BITS (Bioinformatics facility of the VIB, http://www.bits.vib.be) are maintaining both Galaxy servers focusing on NGS data analysis. To ease administration on their servers, they will establish a Bioinformatics RPM Repository on bioinformatics tools, the primary focus being NGS tools. The purpose is to come to a stable repository of easily installable packages for the common bioinformatics tools that can be used in (for example) Galaxy.
Be welcome to join our effort, which is just starting. Interested, please email hailiang dot mei at nbic dot nl or bits at vib.be.
- Joachim Jacob
- Luc Ducazu
- David van Enckevort (User:David.van.enckevort)
- Adam Huffman
Wanting to get involved? Please contact hailiang dot mei at nbic dot nl or BITS for more information.
We will use a trac repository to host our spec files. The spec files will be stored in trunk with the basename of the application. Each released version of the spec file will be tagged with the basename + version of the program.
Based on the spec files we will create two repositories. One repository that has the latest version of the tools and adheres to the LSB file hierarchy. (i.e. will use the directories /usr/bin /usr/lib etc.) The second repository will have versioned RPMs for the different packages that can be installed in the directory structure proposed by the Galaxy Team: $GALAXY_APP/basename/version.
The packages will be signed by NBIC. We will publish the public key for the packages in the repository.
To build the RPM packages in a controlled manner we will use Mock. The build environment will be a CentOS 5 virtual machine.
Some more information on building RPMs:
- RPM Writing lab - For newbies such as Joachim
- RPM Guide
- Fedora Packaging Guidelines
- GuruLabs RPM Guide (PDF download)
- CheckInstall - to automate creation of packages for sources to compile
Orange color highlighted tools are the ones that we are working on.