Question: Error installing 'perl' dependency
3
gravatar for Inquirer
11 months ago by
Inquirer70
Inquirer70 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!

ADD COMMENTlink modified 4 months ago by jakeflood0 • written 11 months ago by Inquirer70
3
gravatar for david.a.morais
11 months ago by
Canada
david.a.morais110 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 COMMENTlink written 11 months ago by david.a.morais110

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 REPLYlink modified 11 months ago • written 11 months ago by Inquirer70

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 REPLYlink written 9 months ago by danielfortin86100
0
gravatar for jakeflood
4 months ago by
jakeflood0
jakeflood0 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 COMMENTlink written 4 months ago by jakeflood0

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 REPLYlink written 4 months ago by jakeflood0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 100 users visited in the last hour