Maker 2 Installation Questions

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Maker 2 Installation Questions

Shane Brubaker
Hi, we just got Maker 2 and are very excited about it but have a few questions.

1. If we already have Maker 1, how would you recommend upgrading to Maker 2?  Can it just be installed on the same machine? It appears that maybe it could be installed right alongside Maker 1.  Do we need to remove Maker 1?

2.  Now that AB-BLAST is out, does Maker 2 support AB-Blast in place of WU-Blast?  (And for that matter, does RepeatMasker?).

3.  Are the gene predictors listed the only ones currently supported?  Is there any way to wrap in a new gene predictor, or does that need to be done completely separately?

4.  Is there any documentation available besides the README and INSTALL files?  I saw some information on the new release in the mailing list, but I was wondering if there was any more detailed documentation out there.


Thanks for your help!

- Shane Brubaker


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Re: Maker 2 Installation Questions

Carson Hinton Holt
Re: [maker-devel] Maker 2 Installation Questions
1. If we already have Maker 1, how would you recommend upgrading to Maker 2?  Can it just be installed on the same machine? It appears that maybe it could be installed right alongside Maker 1.  Do we need to remove Maker 1?

You can install it on the same machine as in another directory, or you can install over the top of MAKER 1.  All of MAKER’s libraries are internal, so it shouldn’t link back to any old libraries.  Just make sure that MAKER 2 is first in your path if you install both, so typing maker on the command line will bring up the correct version.

2.  Now that AB-BLAST is out, does Maker 2 support AB-Blast in place of WU-Blast?  (And for that matter, does RepeatMasker?).

I haven’t tested with AB-Blast yet, so I can’t say.  I need to convince Mark to buy me a license, right now AB-Blast has no free academic license which is a major departure from WU-Blast.  I’m using the BioPerl module Bio::SearchIO::blast to parse the BLAST reports.  It does fine on most flavors of BLAST, but I’m not sure how much AB-Blast output differs from WU-Blast, and there is no mention of updating BioPerl to support AB-Blast.  There may also be some command line differences.  RepeatMasker has confirmed that AB-Blast works just fine for them though.

3.  Are the gene predictors listed the only ones currently supported?  Is there any way to wrap in a new gene predictor, or does that need to be done completely separately?

Current supported predictors are SNAP, GeneMark, Augustus, and FGENESH.  Also you can pass predictions from any source into MAKER by putting the predictions into GFF3 format and setting the location of the file in the pred_gff option.  If you have any specific predictor in mind, you can also request it and I can add native support to MAKER, so you won’t have to go through the GFF3 step.

4.  Is there any documentation available besides the README and INSTALL files?  I saw some information on the new release in the mailing list, but I was wondering if there was any more detailed documentation out there.

I have prepared a tutorials for GMOD at http://gmod.org/wiki/MAKER_Tutorial .  It is from the GMOD summer school of the Americas in 2009.  The 2010 update should be available soon.  GMOD already has it on a separate non-public wiki.  It just needs to be moved into the public wiki, and I understand they will be doing that shortly.

I hope that helps.  Just let me know if there is anything else you need.

Thanks,
Carson


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Re: Maker 2 Installation Questions

Shane Brubaker
Re: [maker-devel] Maker 2 Installation Questions

Thanks very much Carson.

 

We actually have AB-BLAST now so we will try hooking it up and let you know how it works.

 

 

From: Carson Holt [mailto:[hidden email]]
Sent: Thursday, June 03, 2010 1:13 PM
To: Shane Brubaker; [hidden email]
Subject: Re: [maker-devel] Maker 2 Installation Questions

 

1. If we already have Maker 1, how would you recommend upgrading to Maker 2?  Can it just be installed on the same machine? It appears that maybe it could be installed right alongside Maker 1.  Do we need to remove Maker 1?

You can install it on the same machine as in another directory, or you can install over the top of MAKER 1.  All of MAKER’s libraries are internal, so it shouldn’t link back to any old libraries.  Just make sure that MAKER 2 is first in your path if you install both, so typing maker on the command line will bring up the correct version.


2.  Now that AB-BLAST is out, does Maker 2 support AB-Blast in place of WU-Blast?  (And for that matter, does RepeatMasker?).

I haven’t tested with AB-Blast yet, so I can’t say.  I need to convince Mark to buy me a license, right now AB-Blast has no free academic license which is a major departure from WU-Blast.  I’m using the BioPerl module Bio::SearchIO::blast to parse the BLAST reports.  It does fine on most flavors of BLAST, but I’m not sure how much AB-Blast output differs from WU-Blast, and there is no mention of updating BioPerl to support AB-Blast.  There may also be some command line differences.  RepeatMasker has confirmed that AB-Blast works just fine for them though.


3.  Are the gene predictors listed the only ones currently supported?  Is there any way to wrap in a new gene predictor, or does that need to be done completely separately?

Current supported predictors are SNAP, GeneMark, Augustus, and FGENESH.  Also you can pass predictions from any source into MAKER by putting the predictions into GFF3 format and setting the location of the file in the pred_gff option.  If you have any specific predictor in mind, you can also request it and I can add native support to MAKER, so you won’t have to go through the GFF3 step.


4.  Is there any documentation available besides the README and INSTALL files?  I saw some information on the new release in the mailing list, but I was wondering if there was any more detailed documentation out there.

I have prepared a tutorials for GMOD at http://gmod.org/wiki/MAKER_Tutorial .  It is from the GMOD summer school of the Americas in 2009.  The 2010 update should be available soon.  GMOD already has it on a separate non-public wiki.  It just needs to be moved into the public wiki, and I understand they will be doing that shortly.

I hope that helps.  Just let me know if there is anything else you need.

Thanks,
Carson



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Re: Maker 2 Installation Questions

Carson Hinton Holt
Re: [maker-devel] Maker 2 Installation Questions If it doesn’t work, let me know.  I can probably get Mark to buy a copy of AB-Blast so I can add support if necessary.

Thanks,
Carson


On 6/3/10 3:05 PM, "Shane Brubaker" <SBrubaker@...> wrote:

Thanks very much Carson.
 
We actually have AB-BLAST now so we will try hooking it up and let you know how it works.
 
 

From: Carson Holt [[hidden email]]
Sent: Thursday, June 03, 2010 1:13 PM
To: Shane Brubaker; maker-devel@...
Subject: Re: [maker-devel] Maker 2 Installation Questions

1. If we already have Maker 1, how would you recommend upgrading to Maker 2?  Can it just be installed on the same machine? It appears that maybe it could be installed right alongside Maker 1.  Do we need to remove Maker 1?
You can install it on the same machine as in another directory, or you can install over the top of MAKER 1.  All of MAKER’s libraries are internal, so it shouldn’t link back to any old libraries.  Just make sure that MAKER 2 is first in your path if you install both, so typing maker on the command line will bring up the correct version.

2.  Now that AB-BLAST is out, does Maker 2 support AB-Blast in place of WU-Blast?  (And for that matter, does RepeatMasker?).
I haven’t tested with AB-Blast yet, so I can’t say.  I need to convince Mark to buy me a license, right now AB-Blast has no free academic license which is a major departure from WU-Blast.  I’m using the BioPerl module Bio::SearchIO::blast to parse the BLAST reports.  It does fine on most flavors of BLAST, but I’m not sure how much AB-Blast output differs from WU-Blast, and there is no mention of updating BioPerl to support AB-Blast.  There may also be some command line differences.  RepeatMasker has confirmed that AB-Blast works just fine for them though.

3.  Are the gene predictors listed the only ones currently supported?  Is there any way to wrap in a new gene predictor, or does that need to be done completely separately?
Current supported predictors are SNAP, GeneMark, Augustus, and FGENESH.  Also you can pass predictions from any source into MAKER by putting the predictions into GFF3 format and setting the location of the file in the pred_gff option.  If you have any specific predictor in mind, you can also request it and I can add native support to MAKER, so you won’t have to go through the GFF3 step.

4.  Is there any documentation available besides the README and INSTALL files?  I saw some information on the new release in the mailing list, but I was wondering if there was any more detailed documentation out there.
I have prepared a tutorials for GMOD at http://gmod.org/wiki/MAKER_Tutorial .  It is from the GMOD summer school of the Americas in 2009.  The 2010 update should be available soon.  GMOD already has it on a separate non-public wiki.  It just needs to be moved into the public wiki, and I understand they will be doing that shortly.

I hope that helps.  Just let me know if there is anything else you need.

Thanks,
Carson


This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient.  Any review, copying, or distribution of this email (or any attachments thereto) by others is strictly prohibited.  If you are not the intended recipient, please contact the sender immediately and permanently delete the original and any copies of this email and any attachments thereto.

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