Re: [galaxy-dev] Announcing the UK Galaxy Community

2014-08-14 Thread bjoern.gruen...@googlemail.com
Amazing! All the best from Germany! Bjoern 2014-08-14 15:21 GMT+02:00 graham etherington (TSL) graham.ethering...@sainsbury-laboratory.ac.uk: Dear UK Galaxy-devs, We're delighted to announce the launch of the UK Galaxy Community. Please visit the site and have a look around:

Re: [galaxy-dev] Announcing the UK Galaxy Community

2014-08-14 Thread bjoern.gruen...@googlemail.com
I'm all in! :) 2014-08-14 17:11 GMT+02:00 Sebastian Schaaf sch...@ibe.med.uni-muenchen.de : Not to say 'exemplary' - really great :). @Björn: phone call within the next days? Cheers, Sebastian bjoern.gruen...@googlemail.com schrieb: Amazing! All the best from Germany! Bjoern

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

2014-08-12 Thread bjoern.gruen...@googlemail.com
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] Issues with dependencies for toolshed packages

2014-08-06 Thread bjoern.gruen...@googlemail.com
Iry, are you seeing the same error with: https://toolshed.g2.bx.psu.edu/view/iuc/snpeff Cheers, Bjoern 2014-08-06 19:12 GMT+02:00 Iry Witham iry.wit...@jax.org: Hi Greg, That resolved the internal server error issue. Now I need to figure out the issue with the dependencies. I was

Re: [galaxy-dev] TestToolShed failure, Exception: History in error state.

2014-07-31 Thread bjoern.gruen...@googlemail.com
Hi Peter, 2014-07-31 10:57 GMT+02:00 Peter Cock p.j.a.c...@googlemail.com: Hi Dave, You are right that on closer inspection I've mixed tool_dependencies.xml and repository_dependencies.xml *again*. Evidentially my mental model does not match Greg's here: (*) I need to define a tool

Re: [galaxy-dev] Object-Store, setting filetypes crashes Galaxy

2014-06-13 Thread bjoern.gruen...@googlemail.com
Hi Nate, we encountered an addition bug related to the object-store: Traceback (most recent call last): File /usr/local/galaxy/galaxy- dist/lib/galaxy/jobs/runners/__init__.py, line 153, in prepare_job job_wrapper.prepare() File /usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py,

[galaxy-dev] Object-Store, setting filetypes crashes Galaxy

2014-06-12 Thread bjoern.gruen...@googlemail.com
Hi, I have configured to use the hierarchical object store but as soon as I try to reset the filetpye of a dataset Galaxy is crashing with: galaxy.objectstore DEBUG 2014-06-12 14:39:21,180 Using preferred backend 'files3' for creation of MetadataFile 5963 132.230.153.57 - - [12/Jun/2014:14:39:20

[galaxy-dev] Galaxy reports crashing with the latest stable release

2014-06-04 Thread bjoern.gruen...@googlemail.com
Hi, I encountered the following bug during my testing of the latest stable release: Error - type 'exceptions.AttributeError': 'SpecifiedDateListGrid' object has no attribute 'info_text' URL: http://galaxy.uni-freiburg.de:9001/jobs/specified_date_handler?specified_date=2014-06-04 File

Re: [galaxy-dev] IGV display_application configuration failed with require_login=TRUE

2014-02-04 Thread bjoern.gruen...@googlemail.com
Hi Vincent, I think there was an error that was fixed recently. If you can, please try yo upgrade or wait a few more days until the new galaxy-dist version is released. Bjoern 2014-02-04 navratil navra...@prabi.fr: Dear galaxy-dev team, We have configured a galaxy-dist server (stable

Re: [galaxy-dev] Cheetah code issue

2014-02-04 Thread bjoern.gruen...@googlemail.com
Hi, to access variables in a conditional you need to write something like that: $rangeorlist.rngstart $rangeorlist.rend $rangeorlist.stepsize Cheers, Bjoern 2014-02-04 Ketan Maheshwari ketancmaheshw...@gmail.com: Hi, While developing a tool, I am facing Cheetah code issue. I looked up the

Re: [galaxy-dev] filter tag in output, multiple criteria

2014-01-31 Thread bjoern.gruen...@googlemail.com
Hi, something like that is also possible: (( params['settingsType'] == custom and params['unmapped_read_file'] is True )) So I assume: outtype == 0 or outtype == 2 will also work. Cheers, Bjoern 2014-01-31 Geert Vandeweyer

Re: [galaxy-dev] bowtie2 toolshed installation

2014-01-31 Thread bjoern.gruen...@googlemail.com
Hi Alex, there is a difference in http://toolshed.g2.bx.psu.edu/view/devteam/package_bowtie2_2_1_0 and http://toolshed.g2.bx.psu.edu/view/devteam/bowtie_wrappers The package_* is installing the binary for you and can be used by other programs as well. bowtie_wrappers contains the actual wrappers

Re: [galaxy-dev] GATK2

2014-01-30 Thread bjoern.gruen...@googlemail.com
I have no clue what is happening. Attached is my working *.loc flile. See select-box is also filtered by the db-key of your dataset, but I think you habe hg19 as dbkey, otherwise you would not see the hg19 in the select box. There must be something wrong in you *.log file. 2014-01-30 Briand,