[InterMine Dev] Error downloading data via perl script

Lewis, Brian Andrew brilewis at iupui.edu
Thu Sep 8 15:42:56 BST 2011

Julie -

Well, I was able to get farther this time after creating the nntcmine.yml file in the config directory.  When I run the command: perl bin/download_data -e nntc_data InterPro I get the following error:

Cannot use setting from bin/../config/nntc_data.yml as it does not exist.

Usage: download_data -e flymine Uniprot

at bin/download_data line 88

        main::read_config('bin/../config/nntc_data.yml') called at bin/download_data line 59

So are there two files that need to exist?  Just to see what would happen I copied the nntcmine.yml file to nntc_data.yml and I got a different error when executing the download_data script:

Died at /usr/local/share/perl5/YAML/Loader.pm line 676, <$IN> line 1.

~ Brian

Date: Thu, 08 Sep 2011 09:21:22 +0100

From: Julie Sullivan <julie at flymine.org<mailto:julie at flymine.org>>

To: dev at intermine.org<mailto:dev at intermine.org>

Subject: Re: [InterMine Dev] Error downloading data via perl script

Message-ID: <4E687B02.6000405 at flymine.org<mailto:4E687B02.6000405 at flymine.org>>

Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Brian

Yes, sorry, we're in the middle of migrating to the new system although I thought the old scripts still worked.

Unfortunately the new system isn't documented yet but will be shortly.  In the meantime, here are the modules you need to install:


Then you add a configuration file to set the destination directories for the logs and data files.  Here's flymine's:


So create and update of the copy of that file:


Then you run the scripts like so:

bio/scripts/DataDownloader$ perl bin/download_data -e nntcmine

Or to run a single source, do this:

bio/scripts/DataDownloader$ perl bin/download_data -e nntcmine IntactVocabulary


                perl bin/download_data -h

list of available sources:

                perl bin/download_data -s

The perl modules are here, so you can see where the files are coming from:


Let me know if that works for you.



On 07/09/11 22:19, Lewis, Brian Andrew wrote:

> I recently discovered that there were shell scripts in bio/scripts that automatically download data from public database to a server directory.  When I tried running one of the scripts (get_psi_ontology), I got the following error:


> Can't locate DataDownloader.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 . /../../intermine/perl/lib/) at get_psi_ontology line 15.

> BEGIN failed--compilation aborted at get_psi_ontology line 15.


> Pretty easy fix - just install the perl module.  After that I tried running the script again and got almost the same error:


> Use of uninitialized value in concatenation (.) or string at get_psi_ontology line 13.

> Can't locate InterMine/DataDownloader.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 . /../../intermine/perl/lib/) at get_psi_ontology line 15.

> BEGIN failed--compilation aborted at get_psi_ontology line 15.


> I've tried adding a statement similar to the following below the push(@INC... statement but I keep getting the "Can't locate..." error.


> use '/usr/local/intermine_0_97/bio/scripts/DataDownloader/lib';


> Any suggestions?


> Thanks,

> Brian





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