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Groovy tool for galaxy

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Groovy tool for galaxy

Anshul Tak
Hi,
I have a question regarding galaxy. Can I execute groovy scipts using galaxy? I installed groovy in galaxy docker image and all the dependencies. However, when I try to execute a tool which require groovy engine it says "/export/galaxy-central/database/job_working_directory/000/2/tool_script.sh: line 9: groovy: command not found"


So I understood the error that galaxy is not able to find groovy but ideally it should take the groovy engine as it is installed.
Can you give me some pointers to solve this issue?
--
With Regards,

Anshul Tak

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Re: Groovy tool for galaxy

Keith Suderman
We use Groovy (actually our own Groovy DSL interpreter) extensively so it looks like Groovy is not on the PATH that Galaxy is using.  Can you log in to the Docker instance and run Groovy scripts?  What does Galaxy think its $PATH is?

Keith

On Dec 26, 2016, at 3:23 AM, Anshul Tak <[hidden email]> wrote:

Hi,
I have a question regarding galaxy. Can I execute groovy scipts using galaxy? I installed groovy in galaxy docker image and all the dependencies. However, when I try to execute a tool which require groovy engine it says "/export/galaxy-central/database/job_working_directory/000/2/tool_script.sh: line 9: groovy: command not found"


So I understood the error that galaxy is not able to find groovy but ideally it should take the groovy engine as it is installed.
Can you give me some pointers to solve this issue?
--
With Regards,

Anshul Tak
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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