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Question: installation of perl modules from toolshed
1
gravatar for biomonika
4.2 years ago by
biomonika • 60
United States
biomonika • 60 wrote:

Hello,

I am writing custom tool for Galaxy that uses perl scripts. These perl scripts use specific perl modules and therefore I need to make sure that those perl modules are installed.

What is the recommended way to install perl modules from tool_dependencies.xml?

I have found following code that installs modules from test toolshed:

https://github.com/bgruening/galaxytools/blob/master/test_repositories/setup_perl_environment/tool_dependencies.xml

I haven't found equivalent for main toolshed so far. If I stick to test toolshed, is this the recommended way or is there any other way how to easily install perl modules for custom tools in toolshed?

Thank you.
perl toolshed modules • 1.3k views
ADD COMMENT • link •
modified 3.7 years ago by mateusbellomo • 10 • written 4.2 years ago by biomonika • 60
2
gravatar for Bjoern Gruening
4.2 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi Monika,

yes I would recommend this solution, but there are not so many users of this approach. But I will try to assist you to get it running. The main advantage with this approach is that you can depend on your own perl version. Independently of the system perl version. I will migrate the perl package and bioperl to the main toolshed today.

Ciao,

Bjoern
ADD COMMENT • link written 4.2 years ago by Bjoern Gruening ♦ 5.1k
0
gravatar for mateusbellomo
3.7 years ago by
mateusbellomo • 10
mateusbellomo • 10 wrote:

Hi Bjoern,

I'm trying to do the same. I've created a tool that needs 'LWP::UserAgent', 'XML::Twig' and 'FileHandle' perl modules. I've found your package on github and on tool_shed and I want to know how to use it so my tools works correctly.

 

Thanks

 

Mateus
ADD COMMENT • link written 3.7 years ago by mateusbellomo • 10

Hello Mateus please create a new question instead of using this one. That keeps it clean for the others to use.

ADD REPLY • link written 3.7 years ago by Martin Čech ♦♦ 4.9k

Sorry. I'm creating another question right now.

ADD REPLY • link written 3.7 years ago by mateusbellomo • 10
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