Feature Request: Ability to specify a directory to read xml files for tool configuration
Right now for each tool I have, I have to list the xml file per tool in tool_conf.xml. I'd like to specify a directory that Galaxy will scan for a list of xml files and load all of them. So instead of: <section id="myTools" name="Custom Tools"> <tool file="mytools/tool1.xml" /> <tool file="mytools/tool2.xml" /> .... </section> I can do: <section id="myTools" name="Custom Tools"> <tool file="mytools/*.xml" /> </section> I'd add this to Trello but unfortunately my company blocks the site.
Hi Ryan, have you looked at this option? # Set to True to enable monitoring of tools and tool directories # listed in any tool config file specified in tool_config_file option. # If changes are found, tools are automatically reloaded. Watchdog ( # https://pypi.python.org/pypi/watchdog ) must be installed and # available to Galaxy to use this option. Other options include 'auto' # which will attempt to watch tools if the watchdog library is available # but won't fail to load Galaxy if it is not and 'polling' which will use # a less efficient monitoring scheme that may work in wider range of scenarios # than the watchdog default. #watch_tools = False Cheers, Bjoern Am 11.06.2015 um 18:09 schrieb Ryan G:
Right now for each tool I have, I have to list the xml file per tool in tool_conf.xml. I'd like to specify a directory that Galaxy will scan for a list of xml files and load all of them. So instead of:
<section id="myTools" name="Custom Tools"> <tool file="mytools/tool1.xml" /> <tool file="mytools/tool2.xml" /> .... </section>
I can do:
<section id="myTools" name="Custom Tools"> <tool file="mytools/*.xml" /> </section>
I'd add this to Trello but unfortunately my company blocks the site.
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Ryan, This is possible using the relatively new tool_dir tag. <tool_dir dir="path/to/tools" /> This still looks in the tool path like other the normal tool tag. -John On Thu, Jun 11, 2015 at 1:16 PM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Ryan,
have you looked at this option?
# Set to True to enable monitoring of tools and tool directories # listed in any tool config file specified in tool_config_file option. # If changes are found, tools are automatically reloaded. Watchdog ( # https://pypi.python.org/pypi/watchdog ) must be installed and # available to Galaxy to use this option. Other options include 'auto' # which will attempt to watch tools if the watchdog library is available # but won't fail to load Galaxy if it is not and 'polling' which will use # a less efficient monitoring scheme that may work in wider range of scenarios # than the watchdog default. #watch_tools = False
Cheers, Bjoern
Am 11.06.2015 um 18:09 schrieb Ryan G:
Right now for each tool I have, I have to list the xml file per tool in tool_conf.xml. I'd like to specify a directory that Galaxy will scan for a list of xml files and load all of them. So instead of:
<section id="myTools" name="Custom Tools"> <tool file="mytools/tool1.xml" /> <tool file="mytools/tool2.xml" /> .... </section>
I can do:
<section id="myTools" name="Custom Tools"> <tool file="mytools/*.xml" /> </section>
I'd add this to Trello but unfortunately my company blocks the site.
___________________________________________________________ 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/
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Thank you John and Bjoern. I will take a look at both. On Thu, Jun 11, 2015 at 1:35 PM, John Chilton <jmchilton@gmail.com> wrote:
Ryan,
This is possible using the relatively new tool_dir tag.
<tool_dir dir="path/to/tools" />
This still looks in the tool path like other the normal tool tag.
-John
On Thu, Jun 11, 2015 at 1:16 PM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Ryan,
have you looked at this option?
# Set to True to enable monitoring of tools and tool directories # listed in any tool config file specified in tool_config_file option. # If changes are found, tools are automatically reloaded. Watchdog ( # https://pypi.python.org/pypi/watchdog ) must be installed and # available to Galaxy to use this option. Other options include 'auto' # which will attempt to watch tools if the watchdog library is available # but won't fail to load Galaxy if it is not and 'polling' which will use # a less efficient monitoring scheme that may work in wider range of scenarios # than the watchdog default. #watch_tools = False
Cheers, Bjoern
Am 11.06.2015 um 18:09 schrieb Ryan G:
Right now for each tool I have, I have to list the xml file per tool in tool_conf.xml. I'd like to specify a directory that Galaxy will scan for a list of xml files and load all of them. So instead of:
<section id="myTools" name="Custom Tools"> <tool file="mytools/tool1.xml" /> <tool file="mytools/tool2.xml" /> .... </section>
I can do:
<section id="myTools" name="Custom Tools"> <tool file="mytools/*.xml" /> </section>
I'd add this to Trello but unfortunately my company blocks the site.
___________________________________________________________ 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/
participants (3)
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Björn Grüning -
John Chilton -
Ryan G