Error installing 'perl' dependency

Question: Error installing 'perl' dependency

23 months ago by

Inquirer • 80 wrote:

Hello everyone. I encounter an error whenever I try to install any repositories that have the 'perl' dependency, such as 'package_bioperl_1_6' or 'package_perl_xml_parser_expat_2_41'. In all cases I get an error similar to this one:

Tool shed repository: package_perl_xml_parser_expat_2_41

Tool shed repository changeset revision: 5d17b1a12107

Tool dependency status: Error

Tool dependency installation error: Error installing tool dependency perl version 5.18.1: Unable to locate the repository directory for revision 35f117d7396b of installed repository package_perl_5_18 owned by iuc.

Tool dependency installation directory: ./database/dependencies/perl/5.18.1/iuc/package_perl_xml_parser_expat_2_41/5d17b1a12

The repository package_perl_5_18 (revision 35f117d7396b) is already installed, but these the dependency resolver seems unable to locate it. I have Googled and a similar error was reported by others (1 and 2) in March 2016, but apparently it was due to a bug that has already been fixed. Is there still a bug or is there something wrong with my Galaxy instance? It is updated to 16.07.

Thanks for your attention!

perl toolshed dependencies error • 777 views

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modified 16 months ago by jakeflood • 0 • written 23 months ago by Inquirer • 80

23 months ago by

david.a.morais • 110

Canada

david.a.morais • 110 wrote:

Hi I had the same problem recently and the fix is pretty simple. You must install expat-devel (using a package manager), prior to install the tool using the tool shed. yum install expat-devel (on a CentOS) apt-get install expat-devel (Ubuntu) (not sure if on ubuntu this is called expat-devel).

After that re-install or use the repair repository on your Galaxy, it should install without a problem.

Cheers

ADD COMMENT • link written 23 months ago by david.a.morais • 110

Thanks for the suggestion, but it does not seem to work. The Ubuntu package libexpat-dev was already installed on my machine and adding expat did not help either. Also, the error seems to affect other packages besides package_perl_xml_parser_expat_2_41, so I am not sure this is exactly the problem.

ADD REPLY • link modified 23 months ago • written 23 months ago by Inquirer • 80

I can also confirm that I have libexpat-dev and lib-expat installed and also get the same original error:

Error installing tool dependency perl version 5.18.1: Unable to locate the repository directory for revision 35f117d7396b of installed repository package_perl_5_18 owned by iuc.

ADD REPLY • link written 22 months ago by danielfortin86 • 110

16 months ago by

jakeflood • 0

jakeflood • 0 wrote:

Does anyone have an answer for this? As stated before, previous posts (links above) say that this exact issue should have been fixed in a patch, but I'm still seeing this error. I'm running OS X, and tried installing expat (ver 2.2.2), restarting, and reinstalling package_perl_5_18 without any success. I did this by running:

brew install expat

I wasn't able to find expat-devel with brew or with port. Thanks!!

ADD COMMENT • link written 16 months ago by jakeflood • 0

I was able to get this properly installed on my Ubuntu (14.04) machine. Still having problems with my Mac (10.11.6), but I'll use Ubuntu here on out.

ADD REPLY • link written 16 months ago by jakeflood • 0

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