[maker-devel] Problem with features going against wrong organism

[Shane Brubaker]

Thanks Scott!

I just wanted to let you know that I did this as you instructed, and it has fixed the problem now!

Thanks for your help.

-----Original Message-----
From: Scott Cain [mailto:scott at scottcain.net]
Sent: Friday, January 22, 2010 8:13 AM
To: Shane Brubaker
Cc: GMOD GBrowse List; maker-devel at yandell-lab.org; Wayne Lam
Subject: Re: [maker-devel] Problem with features going against wrong organism

Hi Shane,

See:

  http://gmod.org/wiki/SVN#SVN_Read-only_Access

where the project name is "schema".  Then change directories to chado.
 From there you can

  perl Makefile.PL
  make
  sudo make install

Which will install loading tools but won't change the database.  While
the schema has changed slightly from the 1.0 release, it is not enough
to affect the way the loader works, so you can leave it as is.

Scott


On Fri, Jan 22, 2010 at 11:06 AM, Shane Brubaker
<SBrubaker at aurorabiofuels.com> wrote:
> Thanks Scott!
>
> Can you tell me exactly how/what to do to get a fresh checkout of the schema repository?  Is it an update to the actual database or to just the loading script?
>
> Appreciate the help!
>
>
> -----Original Message-----
> From: Scott Cain [mailto:scott at scottcain.net]
> Sent: Thursday, January 21, 2010 4:02 PM
> To: Shane Brubaker
> Cc: GMOD GBrowse List; maker-devel at yandell-lab.org; Wayne Lam
> Subject: Re: [maker-devel] Problem with features going against wrong organism
>
> Hi Shane,
>
> I meant to write you about this last week, but I was traveling and it
> slipped my mind.  Anyway, I think you are being bitten by a bug in the
> chado bulk loader that I fixed a month or so ago.  Try getting a fresh
> checkout of the schema repository.
>
> FYI: the best place to write about this is on the schema mailing list
> (gmod-schema at lists.sourceforge.net).
>
> Scott
>
>
> On Thu, Jan 21, 2010 at 6:11 PM, Shane Brubaker
> <SBrubaker at aurorabiofuels.com> wrote:
>> Hi, I sent an email earlier about this but didn't really hear back.
>>
>>
>>
>> I dug into the problem more (basically my transcriptome and other tracks
>> were not showing up on my test organism).  After looking at the error_log
>> and doing some debugging, I confirmed that new tracks I load onto a test
>> organism have a srcfeature_id which points to the same scaffold, but on my
>> production organism.
>>
>>
>>
>> I am definitely typing in the name of the test organism when I do the load
>> (I am using chado, gmod_gff3_bulk_load).
>>
>>
>>
>> I confirmed that if I change the srcfeature_id in the database, I can now
>> see the track.
>>
>>
>>
>> So I am wondering if anyone has seen this before?   And what do you
>> recommend I do next?  I could:
>>
>>
>>
>> 1)      Rebuild my entire system
>>
>> 2)      Try to debug what is happening (maybe in the load script?)
>>
>> 3)      Just write a script that fixes the problem by updating the
>> src_featureids
>>
>>
>>
>> Thanks,
>>
>> Shane
>>
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>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
> 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.
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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.