Published on
2009 December 9 in
Personal.
Effective next month, I’ll be taking down this site. Most of the content have been successfully moved to my wordpress press account. Reasons for the move include [1] saving on web maintenance costs, [2] wordpress.com now has the features I need like posting equations and code, [3] I’m too lazy to regularly the wordpress.org engine to the latest version.
Please update your bookmarks and feedreaders to http://amespinosa.wordpress.com
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I keep forgetting where my scripts were in my home directories. Below is my ruby script to split a large FASTA [1] sequence into N sequences per file:
#!/usr/bin/env ruby
#
# Script: dumpseq.rb
# Description: Parses the a BLAST Fasta file and dumps each sequence to a
# file.
# Usage: dumpseq.rb [fasta_file]
require 'fileutils'
fasta_db = File.new(ARGV[0])
sno = 0
d = 0
file = nil
while true
x = fasta_db.readline("n>").sub(/>$/, "")
x =~ />(.*)n/
if sno % N == 0 # N seqs per query
file.close if file != nil
dir = sprintf("D%04d000", d / 1000)
FileUtils.mkdir_p dir
# short filenames
fname = sprintf "SEQ%07d.fasta", d
d += 1
file = File.new("#{dir}/#{fname}","w")
end
file << x
sno += 1
fasta_db.ungetc ?>
end
Its pretty hackish-looking. But then I found out that BioRuby [2] wrappers for parsing FASTA files.
[1] http://en.wikipedia.org/wiki/Fasta
[2] http://www.bioruby.org
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Because installing grid computing middleware can get you to this:
7th PANDA Grid Workshop, Bohol, Philippines, May 4 - 8, 2009
organised by
Ateneo de Manila University
Sponsored also by EPSRC, IoP, PPARC and the Royal Society of Edinburgh |
| The aim of the workshop is to bring together grid administrators and software developers in an informal setting, involving open discussions. The focus will include grid maintenance and monitoring and data production with PandaRoot.
Organising committee:
Rafael P. Saldana (Ateneo)
Kilian Schwarz (GSI)
Dan Protopopescu (Glasgow)
|
Contact person:
Address:
Holy Name University,
Lesage and Gallares Streets,
6300 Tagbilaran City,
Bohol, Philippines
|
Let’s look at the itinerary:
Tagbilaran City (May 3, 4, 5)
Metro Centre Hotel and Convention Center
Pres. Carlos P. Garcia Avenue
Tagbilaran City, Bohol
Philippines, 6300
Website: www.metrocentrehotel.com
Panglao Island (May 6, 7, 8, 9, 10)
Bohol Beach Club
Bo. Bolod, Panglao Island, Bohol 6340
Website: www.boholbeachclub.com.ph
Shet, gusto kong umuwi!!!
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Having workstations where you don’t have root access either means contacting support for installation or building your own software from source to get the latest version.
I started using git for code produced in my work. The build was successful with a simple “./configure; make ; make install” series of steps except for supporting access to subversion repositories. It was looking for the perl module SVN::Core to be able to function successfully. Googling about it will land you to the Alien::SVN CPAN module page. Its dependencies can be installed with the standard “install Module::Name” invocation in the CPAN shell. But the main package does not properly install in this environment. It is probably because of the tarball not containing the standard Makefile.PL. It has Build.PL instead. This script generates the Build that compiles the subversion library and its bindings. Then it generates a Makefile from Makefile.PL in the src/subversion/subversion/bindings/swig/perl/native directory. Below is the output of the script:
[Alien-SVN-1.4.6.0]$ ./Build
Running make
Running make swig-pl-lib
make: Nothing to be done for `swig-pl-lib'.
Running /usr/bin/perl Makefile.PL INSTALLDIRS=site
Writing Makefile for SVN::_Core
Writing Makefile.client for SVN::_Client
Writing Makefile.delta for SVN::_Delta
Writing Makefile.fs for SVN::_Fs
Writing Makefile.ra for SVN::_Ra
Writing Makefile.repos for SVN::_Repos
Writing Makefile.wc for SVN::_Wc
Running make
gcc -c -I/home/aespinosa/local/include/apr-0
...
The command /usr/bin/perl Makefile.PL INSTALLDIRS=site generates a build environment to install in /usr. This is not favorable for installation in userspace since you do not have permission to write on that directory. So this command will be rerun /usr/bin/perl Makefile.PL PREFIX=$USERDIR, where $USERDIR is the destination directory you want to.
Now you can successfully clone subversion repositories!
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Grid computing infrastructures were made to support execution of science applications at larger scales. One challenge today in running your science in these behemoth systems the requirement of “griddification” or “supercomputerification”. You need to know how to make the best of your hardware or grid sites in order to orchestrate beautiful workflows and process your science. So a lot of research has been done to create languages such as Swift to make life easier for these domain scientists.
I was debugging a science application for the last several months to run on petascale (100×10^3++ processors) systems. The main goal of the domain scientist was to process hundres of thousands data sequences. I got too much carried away in the debugging to make the application work and have only looked at 3000 of the set In other words, not much *real* work has been done.
Now I should always remember when debugging, remember the scientists who took pain in measuring this data or who can’t get data. (Much like an analogy of “finish your food because there are millions of children hungry in developing countries”).
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