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README.md removing special characters from project folder names Oct 9, 2018

README.md

Bioconda packaging of the Regulatory Sequence Analysis Tools (RSAT)

Representative: Jacques van Helden

Community


ELIXIR-FR / IFB-core

Leads


  • Jacques van Helden
  • Morgane THOMAS-CHOLLIER

Background information


The software suite Regulatory Sequence Analysis Tools (RSAT; http://rsat.eu/) aims at analysing cis-regulatory elements in genomes. This well-known, highly-cited and well-maintained ressource running without interruption since 1998, is available on 6 Web servers (including a teaching server) managed by an international team (France, Spain, Mexico). RSAT servers support 10,032 genomes from all taxa. In 2017, RSAT servers treated 117.487 Web queries, 96.219 SOAP/WSDL requests, and the stand-alone version was downloaded 234 times. The installation process is however heavy, due to the diversity of languages (Perl, C, C++, python, R) and numerous library dependencies. The goal of this BioHackathon application is to package RSAT with bioconda.

Expected outcomes


At the end of the BioHackathon the suite should become fully installable under BioConda, with a single command line: conda install -c bioconda rsat The bioconda packaging will provide an effort-less installation of the RSAT suite on Linux, macOS, and Windows operating systems (via a docker image). The installed package will enable to run the tools on the command line, and we will evaluate the possibility to optionally deploy a local Web server and Web services on the user machine.

Expected audience


RSAT team: knowledge of current installation of RSAT. Potential participants:

  1. Jacques van Helden (Aix-Marseille Université, Marseille, France),
  2. Morgane Thomas-Chollier (Ecole Normale Supérieure, Paris, France),
  3. Bruno Contreras (ARAID & Estación Experimental de Aula Dei-CSIC, Zaragoza, Spain).

Conda packaging: Unix environment, Docker images. Potential hackers (to be confirmed):

  1. Gildas Le Corguillé (Station Biologique de Roscoff, France),
  2. Anthony Bretaudeau (Université de Rennes, France)
  3. Other specialists might be sollicitated in ELIXIR bioconda task force.

Expected hacking days: 4 days, 3 days

Related works and references


GitHub or any other public repositories of your FOSS products (if any)


RSAT git repository is currently restricted to the development team, but the source code (under aGPLv3 licence) is freely available in the form of a tarball downloadable from http://rsat.eu/.

Hackers