[galaxy-dev] disk space does not add up...

My glaaxy user data area is using 40T But the repots server only show usage of about 16T… Im nearly out of space and I’m not sure how to resolve the disparity. I have run the clearnup_datasets.py and other I’m running mainenance scripts like this: #!/bin/sh echo 'running galaxy maintenace

[galaxy-dev] tool xml to fetch choices from a URL

Hi: I need users to specify a project when they run a tool… I would like this to be a select list whose set of options comes from a remote url. What’s the best way to achieve that UI? Should I try to add a from_url attribute to the options tag? Thanks, Brad -- Brad Langhorst, Ph.D.

Re: [galaxy-dev] simple way to refer to the repository install directory from a tool

a tool documentation has a section on writing wrapper scripts that demonstrates the use of the new $__tool_directory__ variable - http://planemo.readthedocs.org/en/latest/writing_standalone.html#wrapping-a-script. Hope this helps, -John On Thu, Mar 26, 2015 at 1:06 PM, Langhorst, Brad langho

[galaxy-dev] anybody seen this class of error before?

InvalidRequestError: One or more mappers failed to initialize - can't proceed with initialization of other mappers. Original exception was: Class 'kombu.transport.sqlalchemy.Message' is not mapped galaxy.jobs.handler ERROR 2015-04-19 14:46:00,794 Exception in monitor_step Traceback (most recent

Re: [galaxy-dev] Galaxy server build

We run the galaxy server as a vm… for 0-30 simultaneous users on a similar size cluster. 16 virtual cores and 8G RAM. I use 4 web handlers and 2 job handlers behind nginx. Brad On Jul 14, 2015, at 1:13 PM, Benjamin Datko bda...@carc.unm.edumailto:bda...@carc.unm.edu wrote: Hello All, We am

[galaxy-dev] unexpanded macros

Hi: I just installed hisat2 and the data manager from the toolshed …. Some macros seem not to be expanded when I load the tool in the UI (even across galaxy restarts) e.g. I see @FTYPE@ instead of fastqsanger the data manager produces this error: Fatal error: Exit code 1 () Traceback (most

[galaxy-dev] No handlers could be found for logger "galaxy.config"

Hi: When I run set_user_disk_usage.py I get that message … Has something changed about logging? I don’t see anything in the python script that looks like “galaxy.config” related to a logging setup. Brad — Brad Langhorst, Ph.D. Development Scientist New England Biolabs

[galaxy-dev] package dependencies

Hi: I just tried to install khmer from the toolshed. I don’t think it’s installing correctly - but I don’t know if it’s a tool problem or something with my setup. the tool-dep directory has khmer/2.0/crusoe/package_khmer_2_0/c7702a7d26e8/ but it’s empty. This tool has a package dependency

Re: [galaxy-dev] Sample tracking / external services - still supported?

Hi Matthias: I think it’s abandoned, I’ve tried to use it with no success. I think it should be brought up to date or be removed to save people from wasting time trying to get it working. Brad -- Brad Langhorst, Ph.D. Development Scientist New England Biolabs > On Jan 20, 2016, at 3:06 AM,

Re: [galaxy-dev] Kallisto tool wrapper?

comment out the condition if package_name.lower().startswith("package_" + name.lower()): From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org<mailto:galaxy-dev-boun...@lists.galaxyproject.org>] on behalf of Langhorst, Brad [langho...@neb.com<

Re: [galaxy-dev] Workflow Compatibility

Hi Katherine: I’d recommend not having users type in paths if at all possible (they will make frustrating mistakes). If there is a selection of these maybe consider turining them into dropdown lists. Either way, these would be no different than e.g. user specified downsampling amounts. or

Re: [galaxy-dev] Jobs don't run for one user

-11-30 05:49:35.363694 | new | handler0 | 537201 | 2016-11-30 05:40:08.343855 | new | handler0 | 537200 | 2016-11-30 05:39:20.394128 | new | handler1 | 537199 | 2016-11-30 05:38:03.913992 | new | handler0 | So hander0 and handler1 Brad On Wed, Nov 30, 2016 at 4:14 PM, Lan

Re: [galaxy-dev] extract extra info (logs) from history

Flagstat might be a good choice here… Brad > On May 2, 2018, at 1:48 AM, Jochen Bick wrote: > > Hi Devon, > > do you mean Alignment Summary? How can I access that information and use it > for an other tool. > > Cheers Jochen > > > On 26.04.2018 14:14, Devon Ryan

[galaxy-dev] one dataset won't import

Hi Galaxy folks: We have one data set in a shared library that will not import to a history. I am able to import it using the page for that dataset, but not from the list of all datasets in the folder. I’m not sure the source of the error - this particular row does not look odd to me.= Any

[galaxy-dev] Re: How to include a large datafile in a bioconda package?

Hi: I’d be concerned about that file changing or disappearing and causing irreproducibility. If the URL were to a permanent location (e.g. NCBI or zenodo) maybe it’s ok. Could it be re-computed locally if necessary (like a genome index)? Maybe others know of examples where this is done. Brad