[galaxy-dev] May 2015 Galactic News (and 2 GCC2015 deadlines today)
Hello all, The *May Galactic News https://wiki.galaxyproject.org/GalaxyUpdates/2015_05* brings lots of Galaxy related news including: - *GCC2015 News https://wiki.galaxyproject.org/GalaxyUpdates/2015_05#GCC2015:_4-8_July.2C_Norwich_UK* - *Early Registration is Open https://wiki.galaxyproject.org/GalaxyUpdates/2015_05#Early_Registration_is_Open.21!* (and it closes 22 May) - *Poster Abstract Deadline is Today https://wiki.galaxyproject.org/GalaxyUpdates/2015_05#Poster_Abstract_Deadline_is_TODAY!* - *Registration and Lodging Scholarships Applications are due Today https://wiki.galaxyproject.org/GalaxyUpdates/2015_05#Registration_and_Lodging_Scholarships:_Applications_due_TODAY!*(restrictions apply) - Oliver Stegle of EBI https://wiki.galaxyproject.org/GalaxyUpdates/2015_05#Keynote_Speaker:_Oliver_Stegle will give the opening keynote. - Extend your trip https://wiki.galaxyproject.org/GalaxyUpdates/2015_05#Other_Events_Near_GCC2015 at nearby events. - Sponsorships from GigaScience and ELIXIR https://wiki.galaxyproject.org/GalaxyUpdates/2015_05#GCC2015_Sponsorships - And, 20+ events over the next 3 months https://wiki.galaxyproject.org/GalaxyUpdates/2015_05#Other_Events - New releases (Pulsar, Planemo) https://wiki.galaxyproject.org/GalaxyUpdates/2015_05#Releases and Tool Shed contributions https://wiki.galaxyproject.org/GalaxyUpdates/2015_05#ToolShed_Contributions : - 66 new publications https://wiki.galaxyproject.org/GalaxyUpdates/2015_05#New_Papers - Who's Hiring https://wiki.galaxyproject.org/GalaxyUpdates/2015_05#Who.27s_Hiring - The ReproGenomics Viewer https://wiki.galaxyproject.org/GalaxyUpdates/2015_05#New_Public_Galaxy_Server:_The_ReproGenomics_Viewer - New Community Log Board and Training Resource entries https://wiki.galaxyproject.org/GalaxyUpdates/2015_05#Galaxy_Community_Hubs And, other news https://wiki.galaxyproject.org/GalaxyUpdates/2015_05#Other_News as well. Dave Clements https://wiki.galaxyproject.org/DaveClements and the Galaxy Team https://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ ___ 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/
Re: [galaxy-dev] Possible to pass hostName to a tool?
This is actually way trickier than one might assume at first glace.
Galaxy generally doesn't know how it is deployed (do workers need to
hit the proxy or talk to wsgi directly, etc...), if the URL users
access Galaxy via will work for worker nodes, even if worker nodes
have consistent access.
I would recommend using something like
$__app__.config.galaxy_infrastructure_url in your cheetah template and
then url join that with /api. This is what Pulsar and the IPython
plugin use for instance to figure out where to send and fetch files
to/from. If deployers don't set that parameter
galaxy_infrastructure_url - Galaxy will do some guessing based on
typical configurations.
See also:
https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.ini.sample#L474
To allow deployers to configure this on per job destination basis - I
would actually fallback to this with something like:
--galxay_host_url
\${GALAXY_HOST_URL:-$__app__.config.galaxy_infrastructure_url}
This allows deployers to define GALAXY_HOST_URL for a particular host
if they need to but will make some reasonable default guesses
otherwise (which they can do directly in job_conf.xml for instance).
-John
On Fri, May 1, 2015 at 2:54 PM, Ben Bimber bbim...@gmail.com wrote:
Hello,
I apologize for the second email as this is related to a question from two
days ago. I am writing a galaxy tool that runs code that will query the
galaxy server. Within the tool wrapper XML, is there a way to write the API
URL of the current server? I dont see anything along these lines
documented.
Thanks in advance for any help,
Ben
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[galaxy-dev] Possible to pass hostName to a tool?
Hello, I apologize for the second email as this is related to a question from two days ago. I am writing a galaxy tool that runs code that will query the galaxy server. Within the tool wrapper XML, is there a way to write the API URL of the current server? I dont see anything along these lines documented. Thanks in advance for any help, Ben ___ 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/
