[BioRuby] rake

[MISHIMA, Hiroyuki]

Hi Yannick and all,

I will try to answer your questions....

Yannick Wurm wrote (2010/12/22 19:06):
> Hiro-san's comment about Pwrake for workflows convinced me to
> finally have a look at Rake.
>
> So I was trying to make a Rakefile that gives me a tree from the
> gblocks run on the cordon alignment from the backtranslated protein
> alignment from the protein sequence from nucleotide squences. But I
> think I quickly bumped into a killer limitation with rules: that
> they apparently only do one level of inference
>
> And I quote from
> http://onestepback.org/articles/buildingwithrake/rulelimitations.html
>
 >> rule ".c" =>  [".y"] do |t| yacc(t.source) end
>> rule ".o" =>  [".c"] do |t| compile_c(t.source) end
 >> If lex.y exists
>> … Rake will not Build lex.c from lex.y and lex.o from lex.c.
>

> Is this limitation still true? Or is something else wrong with my
> code? Do you have a workaround?

Rakefile:
rule ".c" => [".y"] do |t|
   puts "run yacc(#{t.source})"
   touch t.source.ext('c')
end

rule ".o" => [".c"] do |t|
   puts "run compile_c(#{t.source})"
   touch t.source.ext('o')
end

$ touch lex.y
$ rake lex.o
run yacc(lex.y)
touch lex.c
run compile_c(lex.c)
touch lex.o

Hmm.. it seems to work well.. Do I make misconception about the slide?

> And question two: lets say I want a generic rule that cleans up fasta
> sequences (so that if I require 'aasdflkjsalkfjasdlkj.fasta', the
> file aasdflkjsalkfjasdlkj should be run through Emboss' seqret. Is
> that possible? The following hasn't been working:
>> rule ".fasta" =>  "" do |task|
 >>   sh "seqret -sequence
>> #{task.prerequisites.join} -outseq #{task.name}"
 >> end

Try dynamic definition using the "file" method.

Rekefile (put all the files to be cleaned into the source directory):
SOURCES = FileList["source/*"]
SOURCES.each do |src|
   file "#{src}.fasta" => src do |t|
     sh ["segret",
         "-sequence #{t.prerequisites.join(" ")}",
         "-outseq #{t.name}",
        ].join(" ")
   end
end
task :default => SOURCES

Sometimes the "rule" methods can be complicated because it basically
assumes that all files have one extension (not ".tar.gz" but ".tgz").
Recently I prefer to use "file" instead of "rule". Because Rakefiles
are Ruby codes themselves, dynamic definition using the file methods are
more flexible. However, I think some hack introducing some new methods
(Rake DSL syntax) can make the description simpler...

Thanks,
Hiro
-- 
MISHIMA, Hiroyuki, DDS, Ph.D.
COE Research Fellow
Department of Human Genetics
Nagasaki University Graduate School of Biomedical Sciences