[apollo] Setting up blast on Apollo 2.0.5

[Nathan Dunn]

Tyler,

Sorry for the delay in response. I’m going to forward this to the list, as I think there are probably a few more solutions to this than I may have iterated.

I think you should be able to just configure the apollo-config.groovy to replace blat with blast.

apollo{
sequence_search_tools {
blat_nuc {
search_exe = "/usr/local/bin/blat"
search_class = "org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide"
name = "Blat nucleotide"
tmp_dir = "/opt/apollo/tmp"
}
blast_nuc {
search_exe = "/usr/local/bin/blastn"
search_class = "org.bbop.apollo.sequence.search.blast.BlastCommandLine"
name = "Blast nucleotide"
tmp_dir = "/opt/apollo/tmp"
}
}
}

For the organism in question you would have to set it as the blat directory in the organism panel (yes, this could be done better) or somehow pass it in as an option.

You should be able to monitor catalina.out log to see what is actually getting run.

Let us know if you run into trouble.

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory

Nathan,
I'm a postdoc at the Unversity of Oregon. I've configured a server to run Apollo and I really appreciate all over your work creating such an awesome plugin. The lab I'm in works with microRNA and we are trying to blast/blat small oligos to our nematode genomes. In the source code I noticed some java bits about blast and I'm wondering if (and how) it's possible to use the blast program for searching the genomes instead of blat.
Any help would be great.
Sincerely,
Tyler Hether
--
Tyler D Hether, PhD
Institute of Ecology and Evolution
335 Pacific Hall
5289 University of Oregon
Eugene, OR 97403-5289