[maker-devel] Maker iPlant image

[Stein, Joshua]

Also please note that there is a tutorial available here, particularly important if you want to use in MPI mode.
https://pods.iplantcollaborative.org/wiki/display/sciplant/MAKER-P+Atmosphere+Tutorial

Josh

Joshua Stein, PhD
Manager, Sci. Informatics III
Cold Spring Harbor Laboratory
steinj at cshl.edu
http://ware.cshl.org/



On Mar 26, 2014, at 10:20 AM, "Childs, Kevin" <kchilds at plantbiology.msu.edu>
 wrote:

> Daniel,
> 
> There are a few small issues with the MAKER-P_2.28 image at iPlant.  I have been using the image successfully for more than a month.  I typically set several environmental variables immediately after starting an ssh session.
> 
> export PATH=$PATH:/opt/maker/bin:/opt/maker/exe/snap:/opt/maker/exe/augustus/bin:/opt/maker/exe/augustus/scripts/
> export ZOE=/opt/maker/exe/snap
> export AUGUSTUS_CONFIG_PATH=/opt/maker/exe/augustus/config
> export TMP=/tmp
> 
> The image will allow you to train SNAP, but training Augustus is not possible with the current image.  Augustus training requires blat which was not installed in this image.  There is also an issue where training Augustus requires that you write to the /opt/maker/exe/augustus/config/species/ directory which requires some inconvenient directory hacking.  I've worked this all out on a forked image (currently private), but I have not had the time to contact Joshua Stein to suggest some modifications to his public image.
> 
> Augustus should work with a stock hmm on this image.
> 
> I have not attempted to use GeneMark, and of course, fgenesh is a completely different story.
> 
> Kevin Childs
> 
> 
> ---
> Kevin Childs, PhD
> 
> Assistant Professor - Fixed Term
> Plant Biology Department
> Michigan State University
> 
> kchilds at plantbiology.msu.edu
> 517-775-2844 (m)
> 517-353-5969 (l)
> 
> On Mar 25, 2014, at 10:24 AM, Carson Holt wrote:
> 
>> --> /opt/maker/bin/maker
>> 
>> It looks like most preinstalled software is under /opt on the image.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> From: Daniel Standage <daniel.standage at gmail.com>
>> Date: Tuesday, March 25, 2014 at 7:24 AM
>> To: Maker Mailing List <maker-devel at yandell-lab.org>
>> Subject: [maker-devel] Maker iPlant image
>> 
>> Greetings,
>> 
>> I launched an instance from the Maker-P 2.28 image (c5104d19-b4a2-4304-beb2-4921ac61c1ca), but was unable to find the location of the installed software. All I could find was an example data set on the Desktop, but the "maker" program was not in the path and the contents of "/usr/local/src" are empty. Could you please advise on how to run Maker in iPlant Atmosphere? Thanks.
>> 
>> --
>> Daniel S. Standage
>> Ph.D. Candidate
>> Computational Genome Science Laboratory
>> Indiana University
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> 
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