Just a "simple" question

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Just a "simple" question

filipegoncalo
Dear Sir/Madam

I am a Portuguese student,(Informatics and Health Care). I am working now on Bioinformatics as an internship in a specialized company! I have a question about Maker. I am working under a virtual machine running CentOS, and i already have installed all the Maker components, needed to run the program.
I was challenged to make an anotation. The first one I've ever made. Maybe that's why that i'm kind of lost :)
I have the genome in the .fasta format that i want to use to in the anotation. So, maker -CTL, then gedit the config files. On the  maker_opts.ctl, i wrote the name of the file (genome=sequence.fasta), and saved it. So far so good. But when i run maker, it outputs a fatal error, saying that the my genome does not exist!! So i suppose that i should have the genome, in a certain directory. Am i right?
Can you please give me a tip?

Best regards,
Filipe

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Re: Just a "simple" question

filipegoncalo
It's me again....i managed to figure it out somehow. just had to include the path on the config path. 
I've noticed that there's few information on maker, mainly for absolute beginners like me. I will have to write a long report in the end of my internship, describing step by step, from the installation of CentOS, going through  installing postgresql, chado, maker. It will be like a tutorial. I dont't know, maybe it could be helpfull for someone. I believe i could share it.



Anyway, thanks a lot.
Keep on the good work,
Filipe

2011/6/7 Filipe Bregieiro <[hidden email]>
Dear Sir/Madam

I am a Portuguese student,(Informatics and Health Care). I am working now on Bioinformatics as an internship in a specialized company! I have a question about Maker. I am working under a virtual machine running CentOS, and i already have installed all the Maker components, needed to run the program.
I was challenged to make an anotation. The first one I've ever made. Maybe that's why that i'm kind of lost :)
I have the genome in the .fasta format that i want to use to in the anotation. So, maker -CTL, then gedit the config files. On the  maker_opts.ctl, i wrote the name of the file (genome=sequence.fasta), and saved it. So far so good. But when i run maker, it outputs a fatal error, saying that the my genome does not exist!! So i suppose that i should have the genome, in a certain directory. Am i right?
Can you please give me a tip?

Best regards,
Filipe


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Re: Just a "simple" question

Carson Hinton Holt
Re: [maker-devel] Just a "simple" question I’m glad you were able to figure it out.  There is a MAKER tutorial at http://gmod.org/wiki/MAKER_Tutorial that might be useful.  It is from a class taught in 2010.  There is an update that reflects changes made for the same class taught in 2011, but the GMOD helpdesk operator position is being changed to another person.  So the update will have to wait for that to happen.

I would be very happy if you would share any documentation you produce.  It would be helpful in further updating the wiki, I am sure it would be useful for Chado as well.  Here is their tutorial http://gmod.org/wiki/Chado_Tutorial

Thanks,
Carson



On 6/7/11 7:54 AM, "Filipe Bregieiro" <filipegoncalo.duarte@...> wrote:

It's me again....i managed to figure it out somehow. just had to include the path on the config path. 
I've noticed that there's few information on maker, mainly for absolute beginners like me. I will have to write a long report in the end of my internship, describing step by step, from the installation of CentOS, going through  installing postgresql, chado, maker. It will be like a tutorial. I dont't know, maybe it could be helpfull for someone. I believe i could share it.



Anyway, thanks a lot.
Keep on the good work,
Filipe

2011/6/7 Filipe Bregieiro <filipegoncalo.duarte@...>
Dear Sir/Madam

I am a Portuguese student,(Informatics and Health Care). I am working now on Bioinformatics as an internship in a specialized company! I have a question about Maker. I am working under a virtual machine running CentOS, and i already have installed all the Maker components, needed to run the program.
I was challenged to make an anotation. The first one I've ever made. Maybe that's why that i'm kind of lost :)
I have the genome in the .fasta format that i want to use to in the anotation. So, maker -CTL, then gedit the config files. On the  maker_opts.ctl, i wrote the name of the file (genome=sequence.fasta), and saved it. So far so good. But when i run maker, it outputs a fatal error, saying that the my genome does not exist!! So i suppose that i should have the genome, in a certain directory. Am i right?
Can you please give me a tip?

Best regards,
Filipe



Carson Holt
Graduate Student
Yandell Lab
http:/www.yandell-lab.org/
Eccles Institute of Human Genetics
University of Utah

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Re: Just a "simple" question

Marvin B Moore
Filipe,

We enthusiastically welcome community developed MAKER documentation, and we will happily host or link to any contributions that you develop during your internship.

B

On Jun 7, 2011, at 11:16 AM, Carson Holt wrote:

I’m glad you were able to figure it out.  There is a MAKER tutorial at http://gmod.org/wiki/MAKER_Tutorial that might be useful.  It is from a class taught in 2010.  There is an update that reflects changes made for the same class taught in 2011, but the GMOD helpdesk operator position is being changed to another person.  So the update will have to wait for that to happen.

I would be very happy if you would share any documentation you produce.  It would be helpful in further updating the wiki, I am sure it would be useful for Chado as well.  Here is their tutorial http://gmod.org/wiki/Chado_Tutorial

Thanks,
Carson



On 6/7/11 7:54 AM, "Filipe Bregieiro" <<a href="x-msg://450/filipegoncalo.duarte@gmail.com">filipegoncalo.duarte@...> wrote:

It's me again....i managed to figure it out somehow. just had to include the path on the config path. 
I've noticed that there's few information on maker, mainly for absolute beginners like me. I will have to write a long report in the end of my internship, describing step by step, from the installation of CentOS, going through  installing postgresql, chado, maker. It will be like a tutorial. I dont't know, maybe it could be helpfull for someone. I believe i could share it.



Anyway, thanks a lot.
Keep on the good work,
Filipe

2011/6/7 Filipe Bregieiro <<a href="x-msg://450/filipegoncalo.duarte@gmail.com">filipegoncalo.duarte@...>
Dear Sir/Madam

I am a Portuguese student,(Informatics and Health Care). I am working now on Bioinformatics as an internship in a specialized company! I have a question about Maker. I am working under a virtual machine running CentOS, and i already have installed all the Maker components, needed to run the program.
I was challenged to make an anotation. The first one I've ever made. Maybe that's why that i'm kind of lost :)
I have the genome in the .fasta format that i want to use to in the anotation. So, maker -CTL, then gedit the config files. On the  maker_opts.ctl, i wrote the name of the file (genome=sequence.fasta), and saved it. So far so good. But when i run maker, it outputs a fatal error, saying that the my genome does not exist!! So i suppose that i should have the genome, in a certain directory. Am i right?
Can you please give me a tip?

Best regards,
Filipe



Carson Holt
Graduate Student
Yandell Lab
http:/www.yandell-lab.org/
Eccles Institute of Human Genetics
University of Utah
<ATT00001..txt>

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543





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