Agenda

• EOT/Phylogenetics workflow update

• Most required components implemented in staging DE. This includes Muscle, RAxML, WindJammer, Phyml, DNAML, trait evolution applications.
• Sheldon developed generalized wrapper for PHYLIP programs, will integrate PROML, PROPARS, DNAPARS, NEIGHBOR
• Tool Redundancy (more than one choice) at most steps in the workflow
• Naim has a tool that can subsample the data; we could you some guidance on which taxa should be retained to represent key lineages. Data set must be small enough for real time demo.

• RAxML/RAxML-Lite update (John Cazes)

Installing MAFFT, MUSCLE, phyutility, sqlite, and bpp as modules on lonestar.
– Completed modules for MUSCLE and sqlite

– Still working on MAFFT. There's a problem with a general install due to hard
coded links created in the build process. I'll have to rewrite the makefile to remove
the links or create them in a separate install process.

– There's a similar problem with phyutility and a hard coded path.

– PHLAWD uses a few older bpp libraries that are incompatible with the latest libraries.
So, I will custom build the older libraries just for PHLAWD and install the latest versions for developers

– I will install PHLAWD once I'm past these road blocks.

RAxML
Provided sample RAxML batch scripts to Rion Dooley to integrate into a web service.
– I'm iterating with Rion on RAxML. Once RAxML is working, we'll install RAxML-Light and the Parsimonator.

Running RAxML-Light on 75k and 100k test cases provided by Stephen Smith. Completed 2 with different seeds. The 75k run takes ~60 hours including the Parsimonator run. The 100k case takes ~72 hours. These runs were performed on Lonestar on 36 cores.

Received Fernando Izquierdo's code and will begin porting it to Lonestar once I've finished installing the modules to support PHLAWD and future data pipeline codes.

• tool integration workshop (Nicole Hopkins)

• Sheldon to go to Gainsville to meet with Gordon Burleigh about his unnamed intake pipeline and give a iPlant seminar.