can Jbrowse have both blat and blast search tool on the same machine?

[Michael Thang]

Hi there,

I am wondering if the Jbrowse/Apollo allows to have both Blat and Blast as the search tool? can I do the following in the groovy.config file?

    sequence_search_tools {
        blast_nuc {
            search_exe = "/usr/local/bin/blastn"
            search_class = "org.bbop.apollo.sequence.search.blast.BlastCommandLine"
            name = "Blast nucleotide"
        }
        blast_prot {
            search_exe = "/usr/local/bin/tblastn"
            search_class = "org.bbop.apollo.sequence.search.blast.BlastCommandLine"
            name = "Blast protein to translated nucleotide"
        }

        blat_nuc {
            search_exe = "/usr/local/bin/blat"
            search_class = "org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide"
            name = "Blast nucleotide"
        }
        blat_prot {
            search_exe = "/usr/local/bin/blat"
            search_class = "org.bbop.apollo.sequence.search.blat.BlatCommandLineProteinToNucleotide"
            name = "Blast protein to translated nucleotide"
        }

    }

thanks,

[Nathan Dunn]

It should work. 

NAthan

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