[galaxy-dev] Internal Server Error when trying to install a tool from the Tool shed

Hi, We get the following error when we try to install any tool from the Tool shed when using the Admin panel: Internal Server ErrorGalaxy was unable to successfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading

[galaxy-dev] August 11, 2014 Galaxy Distribution

August 11, 2014 Galaxy Distribution / / _Complete News Brief ___ /Highlights:/// .Security alert from July 31st, u

[galaxy-dev] FW: FW: Problems uploading files to a data library

Thanks guys, with your help I have fixed the problem. The upload tool was missing, because I put the same path for both tool_dependency_dir and tool_path in the universe_wsgi.ini file, they were pointing to the shed_tools directory, outside the Galaxy dir. I resolved the problem leaving tool_p

Re: [galaxy-dev] Galaxy server broken with install of latest changes

Hey Tony, Thanks for the error report. I'll look into this, but you can try two things really quickly to see if you can get galaxy started: 1) python scripts/fetch_eggs.py may fix up your egg situation 2) just delete the eggs folder of your galaxy distribution (/eggs) and start galaxy again. It

[galaxy-dev] Galaxy server broken with install of latest changes

Hi, I installed the latest set of changes to Galaxy, and now the Galaxy server will not start up. I am hoping someone can point me to the source of the problem and/or a fix. This morning my Galaxy server was running just fine. I did a hg incoming and was told that a fair number of changes w

Re: [galaxy-dev] Installed tool invisible in Galaxy

Aha, that's true! With the XML fixed, the installation dialogue changes, and displays the "Add new tool panel section" and subsequent parts of the page. This would *appear* to come from the check for includes_tools_for_display_in_tool_panel on line 1620 of lib/galaxy/webapps/galaxy/controllers/ad

Re: [galaxy-dev] Installed tool invisible in Galaxy

I think your tool has an XML error in it (the in_graph_filename param is not being closed) - I imagine this would prevent Galaxy from displaying the tool - cannot say if it is the only error though: -John On Tue, Aug 12, 2014 at 2:00 PM, Peter van Heusden wrote: > 1. Yes, its definite

Re: [galaxy-dev] Installed tool invisible in Galaxy

1. Yes, its definitely a delete (checked the box). 2. The tool, once added, creates: a. the correct directory structure in shed_tools/ b. an entry in the tool_shed_repository table that *appears* to be correct c. an entry in shed_tool_conf.xml with the annotation of the Graph section (where it wa

Re: [galaxy-dev] FW: Problems uploading files to a data library

You don't need a tool to upload - you need 'upload1' (i.e. tools/data_source/upload.xml) and it cannot come from the tool shed - this will make its id something other than upload1. You can make some modifications to it, relocate it, etc... but that needs to be there in some form. In universe_wsgi.

[galaxy-dev] FW: Problems uploading files to a data library

Thanks Nate, I must say that I did not have the upload tool in the tool_conf.xml because I am using the shed_tool_conf.xml to have a customized tools panel, and this xml file is empty by default. I've installed the upload tool throught the Galaxy main tool shed, I rebooted the system, and checke

Re: [galaxy-dev] Determining datatype inheritance in tool XML Cheetah

On Tue, Aug 12, 2014 at 5:31 PM, John Chilton wrote: > Fun question! I have opened a pull request with my answer - > https://bitbucket.org/galaxy/galaxy-central/pull-request/457/allow-cheetah-tool-templates-to-reason/diff. > > There are three different hacks you can use right now... here is a > di

Re: [galaxy-dev] Determining datatype inheritance in tool XML Cheetah

Fun question! I have opened a pull request with my answer - https://bitbucket.org/galaxy/galaxy-central/pull-request/457/allow-cheetah-tool-templates-to-reason/diff. There are three different hacks you can use right now... here is a diff against tools/filters/catWrapper.xml I was using the to test

[galaxy-dev] unable to stob jobs

Hello all, I am running a Galaxy instance on slurm. I am unable to stop jobs via the admin "Manage Jobs" window. Via postgres, there are no jobs in the job table. Any thoughts? I realize this may not be dev but I am at a loss of what to do. Thanks Mike --CONFIDEN

[galaxy-dev] Determining datatype inheritance in tool XML Cheetah

Hi all, I've just uploaded a simple sequence composition tool to the Test Tool Shed: https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_composition https://github.com/peterjc/pico_galaxy/commit/45669446f5a14fd90a8a0d9d7430499de2fb3493 This accepts multiple input in FASTA, FASTQ, or SFF format -

Re: [galaxy-dev] Installed tool invisible in Galaxy

Hey Peter, When you are deleting and reinstalling the tool - can you confirm for me that you are definitely deleting the tool and not just deactivating it? I don't know where to hack around from there - I think repositories are tracked in the database (tool_shed_repository) table, in shed_tool_co

Re: [galaxy-dev] bug?

Hey Brad, Pretty sure John is right here; I didn't realize we even had any of those unencoded id checks still around. John, I agree they should go away at this point. -Dannon On Sun, Aug 10, 2014 at 5:13 AM, John Chilton wrote: > Doubt this is job metrics related - fairly certain the problem

Re: [galaxy-dev] can't install numpy from toolshed

On Aug 12, 2014, at 10:15 AM, Sajdak, Doris wrote: > Hi Nate, > > Thanks for the fast response. You were right, python2-6-dev wasn’t > installed. I’m all for using 2.7 and that’s what’s installed on the system > but I don’t know how to do that in the virtual environment. Can you tell me >

Re: [galaxy-dev] can't install numpy from toolshed

Hi Nate, Thanks for the fast response. You were right, python2-6-dev wasn't installed. I'm all for using 2.7 and that's what's installed on the system but I don't know how to do that in the virtual environment. Can you tell me how to switch that? Sorry if that's a ridiculously basic questio

[galaxy-dev] Installed tool invisible in Galaxy

Hi there I updated a tool of mine recently, committed to the local toolshed, did the update from within the Admin panel and then got this error: Error - : 'Tool' object has no attribute 'citations' A restart of Galaxy seemed to fix the problem, but since then the tool could not be found - it is

Re: [galaxy-dev] can't install numpy from toolshed

On Aug 12, 2014, at 9:59 AM, Sajdak, Doris wrote: > I’m running Galaxy in a virtual environment as described here (OS is Debian > 3.2.54-2): > https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Use_a_clean_environment > > When I go to install package_numpy_1_7 from the to

Re: [galaxy-dev] TypeError with 'dict'

Hi guys, Thanks for the response. I have been able to work around the from_work_dir option. And here are the full traceback: galaxy.tools ERROR 2014-08-12 15:55:35,298 Exception caught while attempting tool execution: Traceback (most recent call last): File "/home/pcm692/galaxy-dist/lib/gala

[galaxy-dev] can't install numpy from toolshed

I'm running Galaxy in a virtual environment as described here (OS is Debian 3.2.54-2): https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Use_a_clean_environment When I go to install package_numpy_1_7 from the tool shed, I get the following errors: Running from numpy sourc

Re: [galaxy-dev] Problems uploading files to a data library

On Tue, Aug 12, 2014 at 3:03 AM, Juan Vladimir de la Rosa Medina < jvdelar...@hotmail.com> wrote: > Hi everyone, > > I recently have installed a local instance of galaxy in my computer, > everything worked fine until I changed the path for *library_import_dir* in > the *universe_wsgi.ini* file, to

Re: [galaxy-dev] Galaxy error

Hi Emily, We might be able to track this down on our side if you provide the URL and HTTP method that caused this error and the time it occurred at. Thanks, --nate On Aug 11, 2014, at 9:20 AM, John Chilton wrote: > Hello, > > Sorry for the delay - please keep all correspondences on galaxy

Re: [galaxy-dev] TypeError with 'dict'

Nate is right - full traceback would help. I am not sure it is the only problem - but these outputs do not look right: Galaxy isn't going to expand variables ($Project.input / $Project.samples) in the from_work_dir attribute so those are going to be taken as literal strings. That dire

Re: [galaxy-dev] TypeError with 'dict'

Hi Martin, If there's a full traceback instead of just this fragment, that'd certainly help with determining exactly where the problem is coming from. --nate On Aug 12, 2014, at 4:17 AM, bjoern.gruen...@googlemail.com wrote: > Hi, > > Galaxy stores all information about a tool and it's para

Re: [galaxy-dev] Bug report: within

I have applied your patch here (https://bitbucket.org/galaxy/galaxy-central/commits/19309418c86450b7f39691460eb430e100883cb4) and one correction to James' previous comment - multi-page tools actually do work through the API - this was required for multi-page tool testing via the API. -John On Tue

Re: [galaxy-dev] Bug report: within

Hey James thanks for the feedback! But on the other hand I know of no alternative to creating an input form with several steps/pages/subforms, or is there? Our group really wants something like this to enhance the user friendliness for some tools with rather complicated input stages... actually

Re: [galaxy-dev] Bug report: within

Philipp, Pages are seriously deprecated -- do not use them. Many things will not work, they are not supported in workflows, the API, et cetera. They only still exist for backward compatibility with ANCIENT tools. Thanks, James -- jt On Tue, Aug 12, 2014 at 4:59 AM, Hans-Philipp Brachvogel wr

[galaxy-dev] Bug report: within

Hello, I found that it is possible for tool-xmls defined with tags to also have multipage helps, but this feature is not really documented and also does not work because of a tiny bug. You can have multipage helps by writing something like this (if your tool has two s): Helpt

Re: [galaxy-dev] TypeError with 'dict'

Hi, Galaxy stores all information about a tool and it's parameters in a database. I suppose if something is wrong with your tool, under some circumstances, it can't be stored in the database. Cheers, Bjoern 2014-08-12 9:23 GMT+02:00 Martin Christiansen < martinchristianse...@hotmail.com>: > Hi

Re: [galaxy-dev] TypeError with 'dict'

Hi Björn, I'm using galaxy as a front-end to run a larger pipeline in the background. Originally I implemented the pipeline which had the same wrapper and was running fine. I have now begun to break it down into steps where this is the first step. The only thing I've changed is the output. How

Re: [galaxy-dev] TypeError with 'dict'

Hi Björn, It looks like this. against hg19 screen_reads.sh $Project.input $Project.samples $Project $Samples galaxy_test1 Untitled Folder 147406386-700171390 158256496-700097688

Re: [galaxy-dev] TypeError with 'dict'

Hi Martin, please keep galaxy-dev in the CC list. Am 12.08.2014 um 08:51 schrieb Martin Christiansen: Hi Björn, Most certainly. I have posted it below. -> add here a version number version="0.1" against hg19 screen_reads.sh $Project.input $Project.samples $Project $Samples

[galaxy-dev] Problems uploading files to a data library

Hi everyone,I recently have installed a local instance of galaxy in my computer, everything worked fine until I changed the path for library_import_dir in the universe_wsgi.ini file, to upload files to data libraries.I followed the Galaxy documentation to setup this feature:This is the path in