SPARQLing genomics
This project provides programs to extract RDF triplets from commonly used file formats in genomics.
It also provides a web-based environment to explore the RDF triplets once inserted in a triple store.
The complete documentation is available in the doc/ directory.
Dependencies
To build the programs in this repository, the following tools are required:
- GNU Autoconf, GNU Automake, pkg-config and GNU Make
- HTSlib
- Libgcrypt
- Raptor2
- GNU Guile
Installation and development environment with GNU Guix
The following command creates an environment wherein all required tools to construct the project's programs are available:
$ guix environment -l environment.scm
Do the usual autotools dance to build everything:
[env]$ autoreconf -vfi
[env]$ ./configure
[env]$ make
Or change the last step to build individual components, like vcf2rdf:
[env]$ make -C tools/vcf2rdf
Starting the web interface
To start the web interface, run:
[env]$ web/sg-web
Further reading
Please read the manual in the doc/ directory. A PDF can be built using:
$ guix environment -l environment.scm --ad-hoc texlive
[env]$ make doc
Alternatively, a is also available.