steremma / gridcg Goto Github PK

Measure the space used in the the grid storage systems, as well as the storage needed locally for retrieving the full programs output. Test with a big dataset (95 fasta files, all vs all)

Create a Java package to handle possible post-processing requests.
Examples are filtering of the phylogenetic profiles (etc filter profiles with less than x Aces) and
collapse of phylogenetic profiles in order to create organism profiling.

Edit the ExpandBBH package in order to handle resubmission and job monitoring.
Create a package ExpandPhylo and make sure it also works for plain Phylo profiles.
Test it with small - moderate - big datasets.

Run 1 BBH and 1 complete Phylo query, using the 95 Fasta files as input. Measure time for both queries in the following 3 manners:

1. Total time: The time between the 1st submit and the last job retrieval. Expected to be in the order of 1 week.
2. Job time: The time between a jobs submission and its output retrieval. This should be measured for each job. Take resubmissions into consideration here!
3. Running time: The time in which a job runs on the WN. Measure this for each job.