[maker-devel] MAKER Install

[Carson Holt]

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
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