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Hello all,
I'm a biologist trying to be a bioinformatician, and I'm doing a local installation of MAKER on my own, which requires a bunch of perl modules (no problem) and external programs including RepeatMasker, BLAST, etc. While I'm not having issues with getting perl modules/dependencies for any of these programs (although it seems like all I've done for a few days), I'm clueless as to how to make MAKER recognize that I've installed these programs on my computer (power mac with 32gb ram- sufficient for what I'm doing).
How do I get MAKER to "see" BLAST? Et cetera? I suspect this is a common-UNIX-knowledge thing that I don't know because I don't have formal training in the area. Is there a file in the maker directory where I specify the directory locations of the external programs? I haven't been able to find one.
Thanks very much for your help!
EDIT: I solved my problem by continuing with the installation, which I thought would make my situation worse based on my reading of the README. Fortunately this wasn't so. After I proceeded with Build.PL I was able to use the Build command to download the external programs, which didn't work before. Obvious now, but I didn't realize that I would have to run Build.PL to completion at least once to make the commands from that perl script usable. Eesh. In any case, I ended up downloading all of the materials again, which is just one of the many self-teaching moments of this afternoon for me.
I'm a biologist trying to be a bioinformatician, and I'm doing a local installation of MAKER on my own, which requires a bunch of perl modules (no problem) and external programs including RepeatMasker, BLAST, etc. While I'm not having issues with getting perl modules/dependencies for any of these programs (although it seems like all I've done for a few days), I'm clueless as to how to make MAKER recognize that I've installed these programs on my computer (power mac with 32gb ram- sufficient for what I'm doing).
How do I get MAKER to "see" BLAST? Et cetera? I suspect this is a common-UNIX-knowledge thing that I don't know because I don't have formal training in the area. Is there a file in the maker directory where I specify the directory locations of the external programs? I haven't been able to find one.
Thanks very much for your help!
EDIT: I solved my problem by continuing with the installation, which I thought would make my situation worse based on my reading of the README. Fortunately this wasn't so. After I proceeded with Build.PL I was able to use the Build command to download the external programs, which didn't work before. Obvious now, but I didn't realize that I would have to run Build.PL to completion at least once to make the commands from that perl script usable. Eesh. In any case, I ended up downloading all of the materials again, which is just one of the many self-teaching moments of this afternoon for me.