Fwd: GBrowse 2.0 HOWTO documentation & broken links

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Fwd: GBrowse 2.0 HOWTO documentation & broken links

girlwithglasses
See issue 1 in the forwarded message - does this need to be altered in
the GBrowse wiki documentation?


---------- Forwarded message ----------
From: Weeks, Nathan <[hidden email]>
Date: Fri, Aug 3, 2012 at 8:10 AM
Subject: GBrowse 2.0 HOWTO documentation & broken links
To: "[hidden email]" <[hidden email]>


Hello,

I have a couple of GBrowse wiki issues to report:

1. The GBrowse 2.0 HOWTO (http://gmod.org/wiki/GBrowse_2.0_HOWTO)
   describes the "fulltext" option as searching through "notes,
attributes and descriptions";
   however, from the Region.pm code, I've determined that
Bio::Graphics::Browser2::Region.pm
   searches only the "Note" attribute by default, unless a list of
attributes to be searched is
   specified in the "search attributes" option in the GENERAL section.
It would be nice
   to document this in the GBrowse 2.0 HOWTO.

2. The links to the GBrowse 2.0 "Usage" and "Configure" tutorials at
    http://gmod.org/wiki/GBrowse#On-line_documentation
   are broken.

Regards,

--
Nathan Weeks
IT Specialist
USDA-ARS Corn Insects and Crop Genetics Research Unit




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--
Amelia Ireland
GMOD Community Support Specialist || http://gmod.org

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Re: GBrowse 2.0 HOWTO documentation & broken links

Jim Hu
Not sure, but I think that sometimes the search behavior differs with the db adaptor being used...

Jim

On Aug 8, 2012, at 5:49 PM, Amelia Ireland wrote:

See issue 1 in the forwarded message - does this need to be altered in
the GBrowse wiki documentation?


---------- Forwarded message ----------
From: Weeks, Nathan <[hidden email]>
Date: Fri, Aug 3, 2012 at 8:10 AM
Subject: GBrowse 2.0 HOWTO documentation & broken links
To: "[hidden email]" <[hidden email]>


Hello,

I have a couple of GBrowse wiki issues to report:

1. The GBrowse 2.0 HOWTO (http://gmod.org/wiki/GBrowse_2.0_HOWTO)
  describes the "fulltext" option as searching through "notes,
attributes and descriptions";
  however, from the Region.pm code, I've determined that
Bio::Graphics::Browser2::Region.pm
  searches only the "Note" attribute by default, unless a list of
attributes to be searched is
  specified in the "search attributes" option in the GENERAL section.
It would be nice
  to document this in the GBrowse 2.0 HOWTO.

2. The links to the GBrowse 2.0 "Usage" and "Configure" tutorials at
   http://gmod.org/wiki/GBrowse#On-line_documentation
  are broken.

Regards,

--
Nathan Weeks
IT Specialist
USDA-ARS Corn Insects and Crop Genetics Research Unit




This electronic message contains information generated by the USDA
solely for the intended recipients. Any unauthorized interception of
this message or the use or disclosure of the information it contains
may violate the law and subject the violator to civil or criminal
penalties. If you believe you have received this message in error,
please notify the sender and delete the email immediately.



--
Amelia Ireland
GMOD Community Support Specialist || http://gmod.org

------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
Gmod-gbrowse mailing list
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=====================================
Jim Hu
Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054



------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
Gmod-gbrowse mailing list
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