RNAplot

[David Hoover]

Hi all,

We have recently moved our mirror to a new host, and I noticed that the RNAplot executable we have is 32-bit, likely obtained from UCSC. I'd like to avoid requiring extra compatibility libraries. The default version of RNAplot (v2.1.9) won't work.

How does UCSC handle RNAplot these days? Are the postscript files pre-made ahead of time? Do you still hack the code?

Curious,
David Hoover
HPC @ NIH

[Maximilian Haeussler]

Hi David,

I'm not sure what exactly you mean with "do you still hack the code", but you can download an up-to-date RNAplot in various formats (e.g. binary) from http://www.tbi.univie.ac.at/RNA/ and replace the 32Bit version with it. GBIB for example is using a current version, as the 32Bit RNAPlot doesn't work in the virtual machine.

If you don't want to put your RNAplot binary into the cgi-bin directory, you can specify the full path with the hg.conf statement rnaPlotPath, this statement is also documented in src/product/ex.hg.conf.

cheers

Max

--

[David Hoover]

Hi Max,

Back in 2011 Hiram sent me a 32-bit "magic" version of RNAplot that Jim Kent had built years before. That version no longer works on our new server host without 32-bit compatibility libraries.

I now realize the current version of RNAplot from the ViennaRNA v2.1.9 package should work, but there were some other missing libraries on the server host. So, instead I compiled a static version and pushed it out to the server host. Everything's good now.

Thanks for being patient,

David