[maker-devel] MAKER Install

[Daniel Standage]

Barry,

Thanks for the tip.  I had set the ZOE variable to the snap/Zoe directory
(that's what I understood from the snap README...the tests worked correctly
because I gave the explicit location of the files it needed).  When I
changed the ZOE variable to the snap root directory, things looked a lot
better.  It looks like I have another problem with my RepeatMasker
installation, but I need some time to look into this issue deeper.

Thanks!

Daniel Standage
Plant Genetics Lab
Brigham Young University

On Tue, Sep 22, 2009 at 7:55 PM, Barry Moore
<barry.moore at genetics.utah.edu>wrote:

> Daniel,
> Did you remember to set the ZOE environment variable for snap?  Something
> like this:
>
> export ZOE=where_snap_is_installed # for bash
>
> or this:
>
> setenv ZOE where_snap_is_installed # for tcsh
>
>
> On Sep 22, 2009, at 5:21 PM, Daniel Standage wrote:
>
> Hi all,
>
> I am trying to get Maker working on our system.  I finally have all of the
> prerequisites installed, and they all appear to be working fine.  I'm now
> using the example data to test maker and it is not working.  I created a
> directory for the test, copied over the test data, generated the control
> files, and made the following changes to the control files.
>
>    - In maker_bopts.ctl
>       - blast_type:ncbi
>    - In maker_opts.ctl
>       - genome:dpp_contig.fasta
>       - est:dpp_transcripts.fasta
>       - protein:dpp_proteins.fasta
>       - snaphmm:fly
>       - predictor:snap
>
> Then when I run maker (using the command maker maker_exe.ctl
> maker_opts.ctl maker_bopts.ctl), it gives the following error message.
>
> #----------------------
> FATAL: failed!!
> #----------------------
> ERROR: The snaphmm specified for Snap/Fathom in maker_opts.ctl does not
> exist.
>
> I verified that there is a "fly" file in SNAP's HMM directory, so I don't
> know what could be causing this.  Does anyone have any insight?
>
> Thanks,
>
> Daniel Standage
> Plant Genetics Lab
> Brigham Young University
> <ATT00001.txt>
>
>
>
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