Re: [galaxy-dev] Packaging pycurl on toolshed

So far I have been trying to avoid this, but I would like to see packaged pycurl on the toolshed now. This is where my package sits: https://testtoolshed.g2.bx.psu.edu/repository?repository_id=534efefdbab02103 and this is the error: Traceback (most recent call last): File "setup.py", line 563, i

Re: [galaxy-dev] setting SGE arguments in galaxy (cloudman)

The default args will apply to all the tools. Tool-specific args will apply only for the tool you specify and those overwrite the default (ie, arguments will not add up). On Thu, Aug 14, 2014 at 2:53 PM, Jim McCusker wrote: > Perfect, thanks! That's in addition to the default arguments? > > > >

Re: [galaxy-dev] setting SGE arguments in galaxy (cloudman)

Perfect, thanks! That's in addition to the default arguments? On Thu, Aug 14, 2014 at 2:52 PM, Enis Afgan wrote: > If I'm understanding your question correctly (ie, have the ability to > specify SGE requirements on a per-tool basis), then yes. You'd do something > like this in universe_wsgi.i

Re: [galaxy-dev] setting SGE arguments in galaxy (cloudman)

If I'm understanding your question correctly (ie, have the ability to specify SGE requirements on a per-tool basis), then yes. You'd do something like this in universe_wsgi.ini: [galaxy:tool_runners] bwa_wrapper = drmaa://-pe smp 2/ bowtie2 = drmaa://-pe smp 2/ On Thu, Aug 14, 2014 at 2:26 PM, Ji

[galaxy-dev] Is anyone using composite datatype uploads?

Hello everyone, We are considering to disable the deprecated upload tool form which is currently accessible through Tool panel > Get Data > Upload file. The new upload feature (icon at the top of the Tool panel) covers all of its functionality except uploading composite datatypes like e.g. Velvet.

Re: [galaxy-dev] setting SGE arguments in galaxy (cloudman)

thanks, I ended up doing subinvocations (submitting a job from within a job) because one tool in particular needs lots of memory. Is there a way to set these things on a per-tool basis (which would let me remove the subinvocation)? Jim On Thu, Aug 14, 2014 at 2:09 PM, Enis Afgan wrote: > Hi Ji

Re: [galaxy-dev] setting SGE arguments in galaxy (cloudman)

Hi Jim Try setting it like this: default_cluster_job_runner = drmaa://-w n -l mem_free=16G/ I've just tried it and worked fine. Sorry for a delay in getting back to you, Enis On Tue, Aug 5, 2014 at 6:44 PM, Jim McCusker wrote: > I have a galaxy/cloudman cluster where I would like to pass a "-

Re: [galaxy-dev] Upload file not working with new install

No sure if this will help but you may want to check this. We just fixed a problem from uploading small files via the ftp directory. Our nfs mount was set to cache file meta data about every 30 sec. This proved problematic when uploading a small fasta file that previously uploaded. Every time we

[galaxy-dev] Upload file not working with new install

Hi Team, I have installed a fresh version of Galaxy and am having an issue with the 'Upload File' tool. When I attempt to use it it just sits and spins. No data gets uploaded. I have looked through the universe.wsgi.ini file and cannot find anything there that stands out. Can you point me t

Re: [galaxy-dev] Question about composite blast datatypes

14.08.2014, 10:01, "Peter Cock" :On Wed, Aug 13, 2014 at 7:22 PM, Eric Rasche wrote: Hi Peter, I'm working on composite datatypes now (for PacBio SMRT cells). In the datatype I know I'll have files with variable names (e.g. .1, .2, .3) and after using the blast datattype as

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

I'm all in! :) 2014-08-14 17:11 GMT+02:00 Sebastian Schaaf : > 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 > > > 2014-08-14 15:

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

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 2014-08-14 15:21 GMT+02:00 graham etherington (TSL)

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

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: > > h

[galaxy-dev] Announcing the UK Galaxy Community

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: http://galaxy-community.org.uk/ The aims of Galaxy-UK are: * To bring the Galaxy community in the United Kingdom closer together * Identify and address

Re: [galaxy-dev] Workflow Loop

It's currently not possible to build loops into galaxy workflows. Major workflow engine enhancements are being worked on, but for an immediate solution you could drive something like this using the API if you wanted to. -Dannon On Thu, Aug 14, 2014 at 8:54 AM, Görkem Erdoğan wrote: > Hello Al

[galaxy-dev] Workflow Loop

Hello All, I have a little issue. I want create workflow with loop but workflow's nodes must use different settings in each loop steps.How can i do this? ___ Please keep all replies on the list by using "reply all" in your mail client. To m

Re: [galaxy-dev] Providing BLAST db in a data library

On Mon, Jul 28, 2014 at 9:43 AM, Peter Cock wrote: > On Mon, Jul 28, 2014 at 8:28 AM, Ulf Schaefer wrote: >> Dear Nate, dear Peter >> >> Sorry for the delay in replying. >> >> I can import both HTML and blastdb from a history to a data library. If >> I try to get the data out of the library into

Re: [galaxy-dev] Question about composite blast datatypes

On Wed, Aug 13, 2014 at 7:22 PM, Eric Rasche wrote: > Hi Peter, > > I'm working on composite datatypes now (for PacBio SMRT cells). In the > datatype I know I'll have files with variable names (e.g. .1, .2, .3) and > after using the blast datattype as reference material, I noticed that you > had c

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

Hi again, Has anyone had time to look into the traceback? Best, Martin From: martinchristianse...@hotmail.com To: jmchil...@gmail.com; n...@bx.psu.edu Date: Tue, 12 Aug 2014 15:59:53 +0200 CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] TypeError with 'dict' Hi guys, Thanks for t