gmod location on ubuntu filesystem

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gmod location on ubuntu filesystem

Volodymyr Zavidovych
Hello

I'm trying to install Chado on my desktop Ubuntu as described here:

I've installed all dependencies and perl modules. Now I'm stuck at this point: "Then, back in the gmod directory: <bunch of make commands>"

Where exactly is the gmod directory? It doesn't exist under /usr/local/gmod

I apologize if I'm missing something simple.

Thank you
Volodymyr



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Re: gmod location on ubuntu filesystem

Scott Cain
Hi Volodymyr,

There does seem to be a step missing there: down load gmod/chado from here:

  http://sourceforge.net/projects/gmod/files/gmod/chado-1.22/

and extract it with

  tar zxvf chado-1.22.tar.gz

and cd into the resulting chado directory (this how to was originally
written before I changed the name of the package from "gmod" to
"chado").

I've marked that page as "needs editing" so I don't forget to fix it
(hopefully sometime in the next few days).

Thanks,
Scott


On Thu, Sep 6, 2012 at 1:18 AM, Volodymyr Zavidovych
<[hidden email]> wrote:

> Hello
>
> I'm trying to install Chado on my desktop Ubuntu as described here:
> http://gmod.org/wiki/Installing_Chado_on_Ubuntu_HOWTO
>
> I've installed all dependencies and perl modules. Now I'm stuck at this
> point: "Then, back in the gmod directory: <bunch of make commands>"
>
> Where exactly is the gmod directory? It doesn't exist under /usr/local/gmod
>
> I apologize if I'm missing something simple.
>
> Thank you
> Volodymyr
>
>
>
> ------------------------------------------------------------------------------
> 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-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>



--
------------------------------------------------------------------------
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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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/
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Re: gmod location on ubuntu filesystem

Volodymyr Zavidovych
Thanks Scott!

I have another question. After running "make ontologies" I got the similar error for Gene Ontology, Chado Feature Properties, and Plant Ontology:

fetching files for Chado Feature Properties
  +load/etc/feature_property.obo
    loading...Cannot quote a reference at /home/zavidovych/perl5/lib/perl5/DBIx/DBStag.pm line 3736.
System call 'stag-storenode.pl -d 'dbi:Pg:dbname=chado;host=localhost;port=5432' --user zavidovych  --password 565$frWdi  tmp/load/etc/feature_property.oboxml' failed: 256
failed: 256 at lib/Bio/Chado/Builder.pm line 367, <STDIN> line 1.
make: *** [ontologies] Error 1

Apparently this is because DBStag installation didn't go smoothly:

Test Summary Report
-------------------
t/cvterm.t    (Wstat: 65280 Tests: 0 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 9 tests but ran 0.
Files=15, Tests=64, 47 wallclock secs ( 0.20 usr  0.03 sys +  5.10 cusr  0.76 csys =  6.09 CPU)
Result: FAIL
Failed 1/15 test programs. 0/64 subtests failed.
make: *** [test_dynamic] Error 255

Do you know what could be causing test failure for DBStag? I installed it manually as described

Thanks
Volodymyr

On Thu, Sep 6, 2012 at 10:17 AM, Scott Cain <[hidden email]> wrote:
Hi Volodymyr,

There does seem to be a step missing there: down load gmod/chado from here:

  http://sourceforge.net/projects/gmod/files/gmod/chado-1.22/

and extract it with

  tar zxvf chado-1.22.tar.gz

and cd into the resulting chado directory (this how to was originally
written before I changed the name of the package from "gmod" to
"chado").

I've marked that page as "needs editing" so I don't forget to fix it
(hopefully sometime in the next few days).

Thanks,
Scott


On Thu, Sep 6, 2012 at 1:18 AM, Volodymyr Zavidovych
<[hidden email]> wrote:
> Hello
>
> I'm trying to install Chado on my desktop Ubuntu as described here:
> http://gmod.org/wiki/Installing_Chado_on_Ubuntu_HOWTO
>
> I've installed all dependencies and perl modules. Now I'm stuck at this
> point: "Then, back in the gmod directory: <bunch of make commands>"
>
> Where exactly is the gmod directory? It doesn't exist under /usr/local/gmod
>
> I apologize if I'm missing something simple.
>
> Thank you
> Volodymyr
>
>
>
> ------------------------------------------------------------------------------
> 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-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
Ontario Institute for Cancer Research



--
Volodymyr Zavidovych
Pratt School of Engineering '14
Duke University
919-641-9169



------------------------------------------------------------------------------
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/
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