Ryan Thomas | 20 Nov 16:36 2014
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Quick question regarding the content on fungalgenomes.org

Hey,

I hope you don't mind me contacting you today but I just have a few quick questions,

Would you be interested in sparking up a mutually beneficial relationship with me over some content submissions for your site?

We are basically looking to place a short and sweet 500 word article on your website with a link pointing to a page on my clients website with payment for your effort.

Let me know if it's of interest and we can get it moving.

Thanks!

Ryan Thomas - DMA
slap up media
ryan-nvjVByHBJPzd97z9P8fs216hYfS7NtTn@public.gmane.org

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Asma Riyaz | 24 Nov 20:36 2014
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gff3 file loading

Hi,

I am trying to load a gff3 file into chado, but it fails with the error below:

Sorting the contents of /etc/BioDIG/biodig/web/static/genomicFiles/new/Tribolium_casteneum/ChLG10_official_gene.gff3 ...

DBD::Pg::st execute failed: ERROR:  null value in column "parent" violates not-null constraint

DETAIL:  Failing row contains (ChLG10, TCOGS2:TC004355, null, ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Na..., null). at /usr/local/share/perl/5.18.2/Bio/GMOD/DB/Adapter.pm line 4722, <IN> line 3.

Inserting into the sort table failed:,

Probably due to this line: ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Name=TC004355;Alias=GLEAN_04355

I have checked to see if there are extra tab spaces but I couldn't find any.

How do I re-format these gff3 files so as to overcome this?

Thanks,

Asma




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Asma Riyaz | 24 Nov 18:48 2014
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Re-load gene ontologies into Chado

Hi,

I need to re-load the ontologies into Chado as I don't think the 1st installed all of it. According https://github.com/scottcain/chado_test/blob/master/chado/INSTALL.Chado, I will need to delete the temporary files but I don't know where to locate these. Could someone point me in the right direction for this?

Thank you 
Asma
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Samy Jeevan Karloss Antony | 18 Nov 09:09 2014
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Displaying Duplicated Regions

Hello,

Is there a “”built-in” way to display Duplicated regions within a genome as track in GBrowse? 

E.g. Parts of Chromosome 2 is a duplicated copy of Chromosome 1.  When some one looks at Chromosome 1 in
Gbrowse, I want to show the genes in the duplicated (Chromosome 2) region (and vice-versa) as a separate track.

Thanks,
Jeevan  
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Scott Cain | 13 Nov 20:38 2014
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LAST CALL! Re: GMOD user talks at PAG

Hi All,

Last call: does anybody else want to give a GMOD-related talk at PAG this January?  We already have some good talk proposals, but we could use a few more.

Scott


On Mon, Nov 10, 2014 at 3:04 PM, Scott Cain <scott <at> scottcain.net> wrote:
Hello,

I'm looking for some people to give talks about how you've used GMOD tools at your site at the Plant and Animal Genomes meeting in San Diego this January.  If you're already going to PAG, or are looking for an excuse to go to San Diego in January, I encourage you to send me a brief note with a title for your talk.  If you haven't registered for PAG but will give a talk, you can register at early bird pricing (a savings of $100 dollars I think).

Unfortunately, I'm running a little late with this announcement, so if you'd like to give a talk, please get back to me by November 13 (Thursday).

Thanks and I hope to see you in San Diego in a few months,
Scott


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



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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Scott Cain | 11 Nov 21:10 2014
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Re: Problem with installing GBrowse

Hi Hufeng,

Please keep this on the GBrowse mailing list (reply-all).

I don't understand why you haven't tried to update the version of Bio::Graphics first, since the GBrowse installer asked you to install it.

Can you point me to the documentation for ChiA-PET, because I have heard of people using ChiA-PET data with GBrowse2.

Scott


On Tue, Nov 11, 2014 at 2:44 PM, Hufeng Zhou <williamzhoubwh-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Dear Scott:

Thanks very much for your reply.

It is like this, I need to use a package called the ChiA-PET tool that
need to only use GBrowse version 1 (they mentioned on their manual,
version 2 won't work)

So I am trying to install the GBrowse version 1....

If I try to install Version 1.7

I will have following error

Installed Bio::Graphics version 1.654 is less than desired version 1.7.
You probably need to update your BioPerl to version 1.6 or better and
install Bio::Graphics separately from CPAN.

Died at Makefile.PL line 272, <DATA> line 192.


That is why I tried version. 1.66 it is the only package I can
install, but after I install it, I find version 1.66 can not even run
the example data.
An example in-memory database from yeast chromosome 1 has been
installed for you. Try it at this URL:
http://localhost/cgi-bin/gbrowse/yeast_chr1 (which can't be accessed).

I really need your help on this.


Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  +1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/


On Thu, Nov 6, 2014 at 8:43 AM, Scott Cain <scott-XkniDE3L5z0cWVvVuXF20w@public.gmane.org> wrote:
> Hi Hufeng,
>
> Sorry it took so long to get to this message; it was caught in the spam trap
> that doesn't allow non-members to post to the list.
>
> Is there a reason you aren't trying to install GBrowse2?  GBrowse 1.66 is
> extremely old.  What were the problems you had?
>
> If you really want to continue with 1.66, please look in the apache access
> log to see where apache is looking for the gbrowse cgi script, and then try
> to find where it did get installed.  Since distros are different with regard
> to where they put various files, it can be difficult for me to guess where
> they are.  One possible suggestion that sometimes trips up new users is
> this: if you tried to install GBrowse before you installed apache, the
> GBrowse installer may have created a /usr/local/apache directory for you.
> If it did, I suggest you remove that directory and reinstall GBrowse.
>
> Scott
>
>
> On Tue, Oct 28, 2014 at 12:56 PM, Hufeng Zhou <williamzhoubwh-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org>
> wrote:
>>
>> Hello:
>> I have some problem with GBrowse, during the installation it has some
>> errors so higher versions won't be able to install, I was only able to
>> install GBrowse-1.66.
>>
>> I can access http://localhost/gbrowse/ without any problems, and all the
>> html pages can be viewed, the problem is in the welcome page, it suggest me
>> to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the example data.
>> But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can not be
>> accessed, which shows not found error.
>>
>> I am wondering if it is GBrowse is not running? If there is any way to
>> resolve this issue? Thanks very much.
>>
>> After installation,
>> Best Regards,
>> Hufeng Zhou, Ph. D
>> Research Fellow at Brigham and Women's Hospital
>> Postdoc Research Fellow at Harvard Medical School
>> Phone:  +1-(617)-903-8599
>> Website: kiefflab.hms.harvard.edu/zhouhufeng/
>>
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse <at> lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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Alejandro Sepúlveda | 10 Nov 22:00 2014
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install_driver error

Hi to all:

I have a persistent error with gbrowse, with the next message:

install_driver(mysql) failed: Attempt to reload DBD/mysql.pm aborted. Compilation failed in require. at /usr/local/lib/perl5/site_perl/5.20.0/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 217.

I have reinstalled both DBB/mysql and DBI packages, without errors.

I’d really appreciate your help.

Cheers,

Alejandro
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Scott Cain | 10 Nov 21:04 2014
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GMOD user talks at PAG

Hello,

I'm looking for some people to give talks about how you've used GMOD tools at your site at the Plant and Animal Genomes meeting in San Diego this January.  If you're already going to PAG, or are looking for an excuse to go to San Diego in January, I encourage you to send me a brief note with a title for your talk.  If you haven't registered for PAG but will give a talk, you can register at early bird pricing (a savings of $100 dollars I think).

Unfortunately, I'm running a little late with this announcement, so if you'd like to give a talk, please get back to me by November 13 (Thursday).

Thanks and I hope to see you in San Diego in a few months,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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Scott Cain | 6 Nov 14:44 2014
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Re: Problem with installing GBrowse

I forgot to cc the GBrowse mailing list; Hufeng, please reply to this email so it stays on list.

Scott


On Thu, Nov 6, 2014 at 8:43 AM, Scott Cain <scott-XkniDE3L5z0cWVvVuXF20w@public.gmane.org> wrote:
Hi Hufeng,

Sorry it took so long to get to this message; it was caught in the spam trap that doesn't allow non-members to post to the list.

Is there a reason you aren't trying to install GBrowse2?  GBrowse 1.66 is extremely old.  What were the problems you had?

If you really want to continue with 1.66, please look in the apache access log to see where apache is looking for the gbrowse cgi script, and then try to find where it did get installed.  Since distros are different with regard to where they put various files, it can be difficult for me to guess where they are.  One possible suggestion that sometimes trips up new users is this: if you tried to install GBrowse before you installed apache, the GBrowse installer may have created a /usr/local/apache directory for you.  If it did, I suggest you remove that directory and reinstall GBrowse.

Scott


On Tue, Oct 28, 2014 at 12:56 PM, Hufeng Zhou <williamzhoubwh-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Hello:
I have some problem with GBrowse, during the installation it has some errors so higher versions won't be able to install, I was only able to install GBrowse-1.66.

I can access http://localhost/gbrowse/ without any problems, and all the html pages can be viewed, the problem is in the welcome page, it suggest me to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the example data. But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can not be accessed, which shows not found error.

I am wondering if it is GBrowse is not running? If there is any way to resolve this issue? Thanks very much.

After installation,
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  +1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/

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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



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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Hufeng Zhou | 28 Oct 17:56 2014
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Problem with installing GBrowse

Hello:
I have some problem with GBrowse, during the installation it has some errors so higher versions won't be able to install, I was only able to install GBrowse-1.66.

I can access http://localhost/gbrowse/ without any problems, and all the html pages can be viewed, the problem is in the welcome page, it suggest me to visit http://localhost/cgi-bin/gbrowse/yeast_chr1 for the example data. But this link http://localhost/cgi-bin/gbrowse/yeast_chr1 can not be accessed, which shows not found error.

I am wondering if it is GBrowse is not running? If there is any way to resolve this issue? Thanks very much.

After installation,
Best Regards,
Hufeng Zhou, Ph. D
Research Fellow at Brigham and Women's Hospital
Postdoc Research Fellow at Harvard Medical School
Phone:  +1-(617)-903-8599
Website: kiefflab.hms.harvard.edu/zhouhufeng/
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weidmao | 23 Oct 02:04 2014

Need help on Installation of GBrowse

I goe the following message when I was running the Build.PL script, is it
normal? Bcause I failed the test after this. ANy comments? Thanks.

Checking prerequisites...
  recommends:
    *  Bio::DB::BigFile is not installed
    *  Bio::DB::Sam is not installed
    *  Bio::Das is not installed
  * Do not worry if some "recommended" prerequisites are missing. You can
install *
  * them later if you need the features they provide. Do not proceed with
the     *
  * install if any of "REQUIRED" prerequisites are missing.                      
*
  *                                                                              
*
  * The optional Safe::World module does not currently run on Perl 5.10 or       
*
  * higher, and so cannot be installed.                                          
*

ERRORS/WARNINGS FOUND IN PREREQUISITES.  You may wish to install the
versions
of the modules indicated above before proceeding with this installation

Run 'Build installdeps' to install missing prerequisites.

**** WARNING
*****************************************************************************************
If you are upgrading from an earlier version of GBrowse and wish to use
named user accounts, please 
set "user_accounts" to 1 in /etc/gbrowse2/GBrowse.conf and run
bin/gbrowse_metadb_config.pl to 
create/update your user account database.

See /etc/gbrowse2/GBrowse.conf.new for suggested settings.
******************************************************************************************************
**** WARNING *********************************************************
You appear to have SELinux installed on this computer. This can
interfere with GBrowse operation. Please read the file
README.fedora_and_selinux in order to perform additional configuration
operations that may be necessary to run on this computer.
**********************************************************************
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'GBrowse' version '2.55'
Now run:
  ./Build test
  ./Build demo          (optional)
  ./Build install       (as superuser/administrator)
        -or-
  ./Build install_slave (optional, for slave installations)

Other useful targets:
  ./Build register      (to register your copy of GBrowse)
  ./Build reconfig      (to reconfigure install locations)
  ./Build demostop      (to stop the demo)

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