GATC04

6-28-2011

Attendance: Josh, Matt V., Shiran

Agenda:

Josh: update on RNA assembly annotation by alignment to reference genome

• https://pods.iplantcollaborative.org/wiki/display/ipg2p/RNA+Assembly+Annotation

Matt: update on infrastructure/tool integration

1.  Working on the communications layer between the DE and the HPC APIs. I'm about 75% done, though the core functions of the are complete and functional. Now it's pretty much clean up, adding convenience functions, documentation, and some refactoring
2. Rebalancing the SU allocations on the TeraGrid allocation now that I am the PI on it
3. Working with Yoon Kah Leow at U of Arizona to get decGPU running and tested on the GPGPU cluster. He is moving some larger data into the cluster today for a real run.
4. Confirming that Abyss-PE runs on Ranger under the largemem queue and writing a deployment of it under the JOBS API (just starting the latter)
5. On the TACC side, we are still struggling with a pesky authentication issue keeping most jobs submitted from the API from entering the queue. This is due to friction at the boundary of Globus, LDAP, token authentication over HTTP, and OpenSSH. Rion and Dennis are burning some serious brain cells on this.

Timeline: What can we accomplish by ASPB?

Answer:

1. Abyss-PE
2. FASTQC
3. Blast database Green Plants
4. Blastx parsing and analysis scripts
5. R script plotting