Error when running 'make ontologies'

[Nicolas Joannin]

Hello,

I am trying to install a Chado database on my local machine.

I've followed the instructions found in install.CHADO file. But when I reach the make ontologies part, I get the following error message:

Nicolas$ make ontologies

./Build ontologies

Available ontologies:

[1] Relationship Ontology

[2] Sequence Ontology

[3] Gene Ontology

[4] Chado Feature Properties

[5] Plant Ontology

Which ontologies would you like to load (Comma delimited)? [0]  1,2,3,4

fetching files for Relationship Ontology

  +http://www.obofoundry.org/ro/ro.obo

    updated

    loading...sh: go2fmt.pl: command not found

sh: go-apply-xslt: command not found

System call 'go2fmt.pl -p obo_text -w xml /Users/Nicolas/data/vardb_chado/tmp/obo/OBO_REL/ro.obo | go-apply-xslt oboxml_to_chadoxml - > /Users/Nicolas/data/vardb_chado/tmp/obo/OBO_REL/ro.oboxml' failed: 32512

failed: 32512 at lib/Bio/Chado/Builder.pm line 346, <STDIN> line 1.

make: *** [ontologies] Error 2

I have installed GO::Parser, as specified in the install file.

I cannot locate any go2fmt.pl file, though... 

Any idea where the problem comes from?

Best regards,

Nicolas

Nicolas Joannin, Ph.D.

Bioinformatics Center

Kyoto University, Uji campus, Japan

[Scott Cain]

Hi Nicolas,

Are you familiar with the locate command?  Try try "locate go2fmt" to see if that turns anything up. If you don't know if the locate database has been updated since you installed, try "sudo updatedb" first. 

Also, are you sure go-perl was installed successfully?

Scott

Sent from my iPhone

[Nicolas Joannin]

Hi Scott,

Thanks for the quick reply!

I didn't know about "locate", so thanks for pointing it out!

Here's the result:

Nicolas$ locate go2fmt

/usr/local/ActivePerl-5.14/site/bin/go2fmt.pl

/usr/local/ActivePerl-5.14/site/man/man1/go2fmt.pl.1

As for the installation of go-perl... I simply tried to install GO::Parser through cpan, which tells me that it is up-to-date. Also, running perldoc GO::Parser gives me its documentation.

Beyond that, is there a different way to check that it is installed?

Is /usr/local/ActivePerl-5.14/site/bin/ supposed to be in my Path? Because it currently isn't... Could that be the problem?

Best regards,

Nicolas 

Nicolas Joannin, Ph.D.

Bioinformatics Center

Kyoto University, Uji campus, Japan

[Scott Cain]

That is almost certainly the problem. 

Sent from my iPhone

[Nicolas Joannin]

Hi Scott,

Easy fix then... Sorry I disturbed you for something so tribial.

Have a good week end!

Cheers,

Nicolas

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