Bioinformatics

In running ALLPATHS-LG, a short read genome assembler, on a Dell PowerEdge R920 with four Xeon E7-4860v2 processors running at 2.60GHz, I did one run with hyperthreading on and one with hyperthreading off. This was mainly to see if the increased cache size on the physical CPU core with hyperthreading off had a positive effect on performance.

I'll take all the anticipation away: Nope. Hyperthreading wins.

I wanted to install rpy and rpy2 on Red Hat Enterprise Linux 6. Here's how I did it. There have been several fixes in the rpy SVN repository that have not shown up in the version downloadable from SourceForge. Hopefully that's been fixed by now, but here's how I installed it by retrieving rpy directly from the repository.

First I made sure that the python-devel package was installed to avoid the error src/RPy.h:63:20: error: Python.h: No such file or directory:

yum install python-devel

I had installed perl5.12 from MacPorts. sudo port installed listed

The following is a transcript of an installation of miRNAkey on Mac OS X 10.6. Actually it has more do with installation of the prerequisites. There is a handy script included with the miRNAkey distribution but I elected to do it by hand since some version numbers had changed and the Fastx-Toolkit binaries were for 10.5, not 10.6.

Step 1: Install bwa

The Burrows-Wheeler Aligner can be downloaded from Sourceforge.