[maker-devel] MAKER Install

[Daniel Standage]

Barry's and Carson's suggestions were helpful, and SNAP is no longer having
any problems. However, solving the SNAP problem made some other problems
evident.  When I ran maker using the sample data, there were some errors
generated by RepeatMasker (see maker_errors.log).  So I tried running
RepeatMasker with some sample data and got similar errors (see
repeat_masker_*.log). I then looked into all of RepeatMasker's
prerequisites, and everything seems to be working fine except for
cross_match.  It ran for about 5 seconds generating the output in
cross_match_*.log, and then would have a seg fault. I'm not really sure what
the problem is or how to address it.  Any suggestions?

Thanks,

Daniel Standage
Plant Genetics Lab
Brigham Young University

On Tue, Sep 22, 2009 at 9:21 PM, Carson Holt
<carson.holt at genetics.utah.edu>wrote:

> Snap requires you to specify the location of the installation directory,
> and will not automatically locate the HMM directory by itself.  To do this
> you must set the environmental variable ZOE to be the path to the snap
> installation directory.
> i.e. in you .bash_profile add something like the following.
>
> export ZOE=/usr/local/snap
>
> Please note that this is the location of the snap base directory and not
> the Zoe or HMM directories under snap.
>
> You will then need to restart your terminal or type 'source
> ~/.bash_profile' to finish loading all changes to your .bash_profile.
>
> When ZOE is not set, you must supply the full path to the HMM rather than
> just the name, i.e. snaphmm:/usr/local/snap/HMM/fly
>
> Let me know if that fixes it for you.
>
> Thanks,
> Carson
>
> 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
> _______________________________________________
> maker-devel mailing list
> maker-devel at yandell-lab.org
> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>
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