GrEMBOSS Project

With the growth of genome databases and the implied complexity for processing such information within bioinformatics research, there is a need for computing power and massive storage facilities which can be provided by Grid infrastructures. EMBOSS is a free Open Source sequence analysis package specially developed for the needs of the bioinformatics and molecular biology user community. This work describes the deployment of EMBOSS over the EELA and EGEE Grids, both gLite middleware-based infrastructures. This work is focused on rewriting the I/O EMBOSS libraries (AJAX) to use the GFAL from the LCG/EGEE middleware. This library allows the use of files registered on the catalog service which are contained in the storage elements of a Grid. Submitting a job into a Grid is not an intuitive task. This work also describes an adhoc mechanism to allow bioinformaticians to concentrate on the EMBOSS command, instead of acquiring advanced knowledge about Grid usage. The results obtained so far demonstrate the functionality of GrEMBOSS, and represent an efficient and viable alternative for “gridifying” other bioinformatic applications.

Instructions

Option A. Download GrEMBOSS.

You can download the GrEMBOSS_X.X.X.tgz distribution file for compilation (below on the attachments section).
Uncompress on your server and make sure you configure it in this way:

% ./configure --prefix=/DESIRED/INSTALLATION/PATH/FOR/GREMBOSS --disable-shared --enable-static

Option B. Converting EMBOSS to GrEMBOSS.

To manually convert EMBOSS to GrEMBOSS (without taking care of the available EMBOSS version), you should download the EMBOSS_to_GrEMBOSS-README.txt file (on the attachments section), and follow the instructions.

Attachment	Size
EMBOSS_to_GrEMBOSS-README.txt	6.04 KB
GrEMBOSS_Catania-paper_V9.pdf	308.77 KB
EMBOSS_to_GrEMBOSS_5.0.0.tgz	2.58 KB
GrEMBOSS_5.0.0.tgz	19.9 MB
gremboss_ui.pl	5.85 KB
upload-SE.pl	16.85 KB