Ruby Speed - install from apt-get or compile yourself?

sequenceserver
#1

I’ve mentioned before that Ruby itself appears to be the slowest component of my SequenceServer setup - NCBI Blast executes on all cores, often times completing in less time than the subsequent post-processing done by SequenceServer (which uses just one core). And I got to thinking - is this an optimization issue? Would I see better results if I downloaded the source for Ruby (2.0 at this point) and compiled it on my system rather than use the apt-get Ruby 1.9 that’s in the repositories?

Anyone have any thoughts/opinions?

#2

It's difficult to say if the performance gain would be noticeable b/w
compiled Ruby and the one from apt-get. Why don't you use
https://github.com/postmodern/ruby-install and try SS on Ruby
2.0? I use Ruby 2.0 on antgenomes.org.

install ruby-install: https://github.com/postmodern/ruby-install#install

then,

$ sudo ruby-install ruby
$ gem install sequenceserver

Yo
-- Priyam

#3

Hit send by mistake. I was saying,

You might need to say 'sudo gem install sequenceserver' instead. I
never use sudo with RubyGems, but I am not sure if that's because I
also use chruby (https://github.com/postmodern/chruby).

-- Priyam