Groovy tool for galaxy
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
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 <anshul.tak@gmail.com> 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/
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I thought I had read that newer versions of Galaxy were able to watch the tools directory and update the tools menu when any tool wrappers were added, deleted, or modified; basically the "Admin -> Reload a tool's configuration" without the administrator actually having to do anything. However, my Google searches are not turning up anything? Am I over-remembering something I had read or are my Google skills failing me? This is for an upcoming course that will involve students developing tools and pipelines. We want the teaching assistants to be able to update their master Galaxy instance with new tools without a lot of button clicks or a server restart. Thanks, Keith ---------------------- Keith Suderman Research Associate Department of Computer Science Vassar College, Poughkeepsie NY suderman@cs.vassar.edu
Hi Keith, Galaxy has been able to load tools after installation for quite some time, however that did not work for production setups that are using multiple job handler threads. We did indeed refine the tool loading to work for production servers starting with release 16.10 (it's mentioned in the release notes https://docs.galaxyproject.org/en/master/releases/16.10_announce.html). Aspects of this have been refined up to release 17.05, which should be the most reliable concerning this feature. No special options need to be set to use this, it should hopefully just work. Technically we watch the various shed_tool_conf.xml / tool_conf.xml files as well as the individual tool wrappers for changes and trigger a reload, which we speed up by caching the tool definitions. One thing we can't do at the moment is detect if a macro file that is included in a tool has changes, so in this case you'd still need to restart the galaxy instance unfortunately. There is another option (watch_tools, see https://github.com/galaxyproject/galaxy/blob/release_17.05/config/galaxy.ini... ) in the galaxy.ini that allows you to watch a directory of tools (i.e no installation from the toolshed or modification of a tool_conf,xml file necessary) that you can activate. If you want to use this feature you need to indicate in your tool_conf.xml file which directory you would like to monitor. The syntax is like this: <tool_dir dir="<directory to monitor>" recursive="true"/> (The recursive="true" is not necessary if you want to monitor a flat directory). Best, Marius On 20 August 2017 at 04:13, Keith Suderman <suderman@cs.vassar.edu> wrote:
I thought I had read that newer versions of Galaxy were able to watch the tools directory and update the tools menu when any tool wrappers were added, deleted, or modified; basically the "Admin -> Reload a tool's configuration" without the administrator actually having to do anything. However, my Google searches are not turning up anything? Am I over-remembering something I had read or are my Google skills failing me?
This is for an upcoming course that will involve students developing tools and pipelines. We want the teaching assistants to be able to update their master Galaxy instance with new tools without a lot of button clicks or a server restart.
Thanks, Keith
---------------------- Keith Suderman Research Associate Department of Computer Science Vassar College, Poughkeepsie NY suderman@cs.vassar.edu
___________________________________________________________ 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/
Thanks Marius, it was the release notes I had seen and what I was thinking about. - Keith
On Aug 20, 2017, at 2:48 AM, Marius van den Beek <m.vandenbeek@gmail.com> wrote:
Hi Keith,
Galaxy has been able to load tools after installation for quite some time, however that did not work for production setups that are using multiple job handler threads.
We did indeed refine the tool loading to work for production servers starting with release 16.10 (it's mentioned in the release notes https://docs.galaxyproject.org/en/master/releases/16.10_announce.html <https://docs.galaxyproject.org/en/master/releases/16.10_announce.html>). Aspects of this have been refined up to release 17.05, which should be the most reliable concerning this feature.
No special options need to be set to use this, it should hopefully just work. Technically we watch the various shed_tool_conf.xml / tool_conf.xml files as well as the individual tool wrappers for changes and trigger a reload, which we speed up by caching the tool definitions. One thing we can't do at the moment is detect if a macro file that is included in a tool has changes, so in this case you'd still need to restart the galaxy instance unfortunately.
There is another option (watch_tools, see https://github.com/galaxyproject/galaxy/blob/release_17.05/config/galaxy.ini... <https://github.com/galaxyproject/galaxy/blob/release_17.05/config/galaxy.ini.sample#L257>) in the galaxy.ini that allows you to watch a directory of tools (i.e no installation from the toolshed or modification of a tool_conf,xml file necessary) that you can activate. If you want to use this feature you need to indicate in your tool_conf.xml file which directory you would like to monitor. The syntax is like this:
<tool_dir dir="<directory to monitor>" recursive="true"/>
(The recursive="true" is not necessary if you want to monitor a flat directory).
Best, Marius
On 20 August 2017 at 04:13, Keith Suderman <suderman@cs.vassar.edu <mailto:suderman@cs.vassar.edu>> wrote: I thought I had read that newer versions of Galaxy were able to watch the tools directory and update the tools menu when any tool wrappers were added, deleted, or modified; basically the "Admin -> Reload a tool's configuration" without the administrator actually having to do anything. However, my Google searches are not turning up anything? Am I over-remembering something I had read or are my Google skills failing me?
This is for an upcoming course that will involve students developing tools and pipelines. We want the teaching assistants to be able to update their master Galaxy instance with new tools without a lot of button clicks or a server restart.
Thanks, Keith
---------------------- Keith Suderman Research Associate Department of Computer Science Vassar College, Poughkeepsie NY suderman@cs.vassar.edu <mailto:suderman@cs.vassar.edu>
___________________________________________________________ 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/ <https://lists.galaxyproject.org/>
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ <http://galaxyproject.org/search/>
---------------------- Keith Suderman Research Associate Department of Computer Science Vassar College, Poughkeepsie NY suderman@cs.vassar.edu
participants (4)
-
Anshul Tak -
Keith Suderman -
Marius van den Beek -
Suderman Keith