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Re: [GMOD-devel] Trouble with Chado installation

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Re: [GMOD-devel] Trouble with Chado installation

Scott Cain
Hi Haritha,

I'm cc'ing the schema mailing list, since that's where we discuss Chado issues.  I haven't installed DBIx::DBStag on the command line/via cpan in a really long time.  Since you're using Ubuntu, I'd suggest that you use apt-get:

  sudo apt-get install libdbix-dbstag-perl

Virtually all (or actually all, I don't remember) prerequisites can be installed with apt-get on Debian and Ubuntu systems.  There is also a Debian package for Chado, but as I recall, it's pretty flawed, so I'd suggest not using it.

Also, if you plan on using Tripal at all, I'd suggest installing Chado with Tripal anyway, as it's easier.

Scott


On Thu, Nov 12, 2015 at 11:46 AM, Haritha Veeraghanta <[hidden email]> wrote:

Hello,

 

I am working on a genome project for BTI. I am trying to install Chado on my Ubuntu machine on postgres. I followed all the steps of the GMOD installation verbatim. I got the GMOD bundle installed. I am running into trouble with the DBIs::DBStag (DBIx::DBSchema is installed). When I reach the step “make” after the makefile.pl, I get repeated error at the same line in the script at:

 

t/cvterm.t ...... Cannot quote a reference at /home/hv66/Downloads/DBIx-DBStag-0.10/blib/lib/DBIx/DBStag.pm line 3736.

t/cvterm.t ...... Dubious, test returned 255 (wstat 65280, 0xff00)

 

I am not sure what I am missing. When I checked for the bundle installs, all others are up to date.

 

The result is FAIL, but I am pretty sure d it yesterday night, it showed me a PASS. I might be severely mistaken.

 

Please help me out,

 

Thanks

Haritha

 

--

 

Haritha Veeraghanta

Data Architect

Genomics & Open-source Breeding Informatics Initiative (GOBII)

[hidden email]

<a href="tel:%28607%29%20254-2734" value="+16072542734" target="_blank">(607) 254-2734

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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

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