[galaxy-dev] DRMAA broken following SGE update. How to fix?

Hi, Following a recent update to our SGE, DRMAA is failing to load in galaxy. The reason being that the path has changed. How do I change the path for galaxy to find the libdrmaa module? Cheers, Chris -- Dr Chris Cole Senior Research Associate (Bioinformatics) College of Life Sciences

Re: [galaxy-dev] Galaxy Cluster Configuration

Christoph Ruttkies wrote: Dear Galaxy-Dev Team, I have a problem concerning the integration of galaxy into a cluster environment. Galaxy is installed on a server that has access to the local cluster network and is configured as a submit host for the Sun Grid Engine running on the cluster

Re: [galaxy-dev] HOW TO RETRIEVE DATA FROM HISTORY??!!

Assaf Gordon wrote: Hi Colin, colin molter wrote, On 08/05/2011 01:54 PM: Is there a way to directly move/copy data from your galaxy history to a given location in the filesystem of the same galaxy server? Said differently, there is a nice way to import data from the server to

Re: [galaxy-dev] regarding updating data libraries

Sridhar A Malkaram wrote: Hi, I was wondering if there is a method of updating datasets in a data library, which was created using the option, Upload files from filesystem paths and selecting Link to files without copying into Galaxy. An update operation should reflect any changes that

Re: [galaxy-dev] Selective storage of galaxy files

Dave Walton wrote: Dear Galaxy developers, Our institution is trying solve our storage problem (we need lots, especially for NGS data, and someone needs to fund it). What we would like to be able to do, is based on some criteria control in what location a file gets written to disk. This

Re: [galaxy-dev] Adding Libraries

Tanguy LE CARROUR wrote: Dear Nate! On Wed, 2010-09-01 at 17:21 +0200, Tanguy Le Carrour wrote: On Wed, 2010-09-01 at 11:14 -0400, Nate Coraor wrote: This would be a great case for use of the (experimental) API. Set 'enable_api = True' in the config and then have a look at the

Re: [galaxy-dev] upload.py fails with files having commas in file name

Chorny, Ilya wrote: The ftp upload module fails when a file has a comma in the file name for example test.bam works but when copied to test,test.bam that file fails. Hi Ilya, Thanks for letting us know. This has been fixed in 5921:94688ff06248. --nate Cheers, Ilya Ilya Chorny

Re: [galaxy-dev] Selective storage of galaxy files

Ravi Madduri wrote: Nate I brought this issue up at the users conference and I wanted to bring it up again. How does somebody like us keep track of new development like this and how can we contribute? Hi Ravi, The best way is probably to ask on the dev list whether we are, or have

Re: [galaxy-dev] problem with build_chrom_db.py

Hi Curt, The development team has characterized the issue and a correction is pending. For now, the best work-around is to just ignore the error files. Thank you for reporting the problem! Best, Jen Galaxy team On 5/31/11 8:37 AM, Nate Coraor wrote: Curt Palm wrote: I've been

Re: [galaxy-dev] Tool Config Syntax Wiki page, actions tag

Hi Peter, Sorry for the delay in response. The outputs data actions tagset will allow you to set metadata, including e.g. column assignments (start,end,strand,etc) for tabular (interval) files. A somewhat complicated example of this is the cut tool (tools/filters/cutWrapper.xml), which sets

[galaxy-dev] BWA wrapper error

Hi all, I'm seeing the following error when I try to use the galaxy BWA wrapper for SOLID data : An error occurred running this job:Could not determine BWA version The alignment failed. Error aligning sequence. /bin/sh: bwa: not found Any suggestions in figuring out what this error has to

Re: [galaxy-dev] Boolean options in toolconfigs: yes/no vs. give/omit flag.

On Mon, Aug 22, 2011 at 5:29 PM, Samuel Lampa samuel.la...@scilifelab.uu.se wrote: Hi, I'm trying to parse the XML toolconfig format, for generating a lightweight command config wizard in an Eclipse based product. I wonder: Boolean parameters for some tools (such as the emboss/textsearch