Re: [galaxy-dev] history box odd behaviour

Ok. Just filed a bug report. Alex -Oorspronkelijk bericht- Van: Langhorst, Brad [mailto:langho...@neb.com] Verzonden: maandag 13 februari 2012 17:38 Aan: Bossers, Alex CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] history box odd behaviour On Feb 13, 2012, at 11:22 AM, Bo

[galaxy-dev] Running workflows on mulitple paired-end data sets

Hi,Is there an intelligent way to run a workflow that starts with more than one pair of paired-end data sets in a workflow?I can run multiple workflows when there is a SINGLE input file, but in the case of many paired end workflows, you need to provide two paired samples and just adding another inp

Re: [galaxy-dev] Batch limit on Wokflows

OK, I've tried the latest revision og 'Galaxy-Central' and am still running into the same issue, when I try to run a work flow when there are 20+ datasets in my history. I might try setting it up on another machine to see if I run into the same issue. Thanks, Robert __

[galaxy-dev] 2012 Galaxy Community Conference (GCC2012): Now Accepting Abstracts

Hello all, Abstracts are now being accepted for oral presentations at the 2012 Galaxy Community Conference (GCC2012) . Submissions on any topics of interest to the Galaxy community are encouraged. Areas

Re: [galaxy-dev] Status on importing BAM file into Library does not update

On Feb 13, 2012, at 11:52 AM, Fields, Christopher J wrote: > On Feb 13, 2012, at 9:45 AM, Nate Coraor wrote: > >> On Feb 8, 2012, at 9:32 PM, Fields, Christopher J wrote: >> >>> 'samtools sort' seems to be running on our server end as well (not on the >>> cluster). I may look into it a bit mo

Re: [galaxy-dev] cufflinks could not move file as directed by from_work_dir

On Feb 13, 2012, at 11:07 AM, p.baska...@leeds.ac.uk wrote: > Hi Nate, > > I got the following error in the log file after running cufflinks on the > local instance of galaxy: > Hi Praveen, Please use the galaxy-dev mailing list (CC'd) for these types of questions so that you can receive a

Re: [galaxy-dev] LDAP authentification

On Feb 13, 2012, at 7:38 AM, Sarah Maman wrote: > Hello, > > I managed to connect to Galaxy to LDAP ;-) > Three points were blocking for me: > * Being root of my virtual machine can carry out tests > * I confused login / password of two LDAP, so I thought that my > authentication method was not

Re: [galaxy-dev] Galaxy server configuration question

On Feb 13, 2012, at 3:08 AM, Huayan Gao wrote: > Hi Nate. > > I am ok now. > > The code I copied from wiki was using galaxy_dist, while my folder name is > galaxy-dist. > After I changed the path in the code, the problem solved. Hi Huayan, I've updated the wiki to refer to galaxy-dist rat

Re: [galaxy-dev] Problem with self.object_store.exists in set_dataset_sizes.py

On Feb 10, 2012, at 7:06 AM, Peter Cock wrote: > Hi all, > > I've just updated our Galaxy to the current release 26920e20157f which > now includes quota support. This means I need to run > set_dataset_sizes.py in order to record the current usage, as > explained here: > http://wiki.g2.bx.psu.edu/

Re: [galaxy-dev] Error executing tool: 'hg19'

This bug has been fixed in galaxy-central but, as per one of the threads you found, has not made it to galaxy-dist yet. Try this: 1. assuming you haven't made any changes to datatypes_conf.xml, copy datatypes_conf.xml.sample to datatypes_conf.xml 2. visit the custom builds page (User tab --> Cus

Re: [galaxy-dev] Stalled upload jobs under "Admin", "Manage jobs"

On Feb 10, 2012, at 6:47 AM, Peter Cock wrote: > Hello all, > > I've noticed we have about a dozen stalled upload jobs on our server > from several users. e.g. > > Job IDUserLast Update ToolState Command LineJob > Runner PID/Cluster ID > 2352 21 hours ago

Re: [galaxy-dev] Uploading large file in browser

On Feb 9, 2012, at 7:05 PM, Nic Barker wrote: > Hi All, > Apologies for resurrecting an old thread, but an HTML5 chunk uploader as > Hyunsoo previously suggested would actually be very useful for my > organisation, in terms of streamlining our workflow for less technically able > users. I was w

Re: [galaxy-dev] Status on importing BAM file into Library does not update

On Feb 13, 2012, at 9:45 AM, Nate Coraor wrote: > On Feb 8, 2012, at 9:32 PM, Fields, Christopher J wrote: > >> 'samtools sort' seems to be running on our server end as well (not on the >> cluster). I may look into it a bit more myself. Snapshot of top off our >> server (you can see our local

Re: [galaxy-dev] history box odd behaviour

On Feb 13, 2012, at 11:22 AM, Bossers, Alex wrote: > > When I press the eye icon on the running blast history box it drops an error > in the mid panel that the xml is not there yet (XML-parse error). But than > the box changes to green while the blast is still running in the background > (che

[galaxy-dev] history box odd behaviour

Hi All, Since some of the last updates (I guess, since I didn't notice it before) I notice some odd behaviour of the history box when for instance doing BLAST searches on our local galaxy_central (latest version). When I run blastx as output xml it starts running fine (yellow box). I can start n

Re: [galaxy-dev] Status on importing BAM file into Library does not update

On Feb 8, 2012, at 11:58 AM, Ryan Golhar wrote: > Hi Nate - I finally got a chance to look at this briefly, but I must admit, > my Python skills are lacking. In the Bam class in binary.py, all I see are > calls to > > proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=open

Re: [galaxy-dev] Batch limit on Wokflows

Sorry for the delay, but I am using a galaxy-dist clone, and have updated to revision 26920e20157f+ tip. I'm still receiving the same issue with the revision. Maybe I should try out galaxy-central? Thanks, Robert From: Dannon Baker [dannonba...@me.com]

Re: [galaxy-dev] generate dynamic select list based on other input dataset

Hi Jeremy, I understood the tags help if you want to filter input data based on options in a .loc file, right? My aim is to extract the column names of an input dataset, present them in a selection box or dropdown list, let the user choose one, and process the input set (with two inputs, the inpu

Re: [galaxy-dev] Status on importing BAM file into Library does not update

On Feb 8, 2012, at 9:32 PM, Fields, Christopher J wrote: > 'samtools sort' seems to be running on our server end as well (not on the > cluster). I may look into it a bit more myself. Snapshot of top off our > server (you can see our local runner as well): > > PID USER PR NI VIRT RES

Re: [galaxy-dev] Error executing tool: 'hg19'

For completeness: this is a local galaxy instance running for few months now, updated recently (27 Jan 'release'). Hello Joachim, After a quick try with visualising track in Trackster (importing one chromosome of hg19 - which did not succeed BTW), none of

Re: [galaxy-dev] Error executing tool: 'hg19'

Hello Joachim, > > After a quick try with visualising track in Trackster (importing one > chromosome of hg19 - which did not succeed BTW), none of the tools in my > local galaxy appear to work. What are the steps you're taking to produce this issue? > They all send this error message: > > Er

Re: [galaxy-dev] generate dynamic select list based on other input dataset

Holger, Have you looked at how dynamic options work and whether they would be sufficient for your use? See the tag syntax for details: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cfilter.3E_tag_set To specifically address your problem: can you determine the particular place

Re: [galaxy-dev] Galaxy server configuration question

Hi Nate. I am ok now. The code I copied from wiki was using galaxy_dist, while my folder name is galaxy-dist. After I changed the path in the code, the problem solved. Best, Huayan On 13 Feb, 2012, at 11:40 AM, Huayan Gao wrote: > Hi Nate, > > I removed the proxy section in httpd fi

Re: [galaxy-dev] LDAP authentification

Hello, I managed to connect to Galaxy to LDAP ;-) Three points were blocking for me: * Being root of my virtual machine can carry out tests * I confused login / password of two LDAP, so I thought that my authentication method was not good while I was using the wrong password ... * It is better

[galaxy-dev] Error executing tool: 'hg19'

Hi, After a quick try with visualising track in Trackster (importing one chromosome of hg19 - which did not succeed BTW), none of the tools in my local galaxy appear to work. They all send this error message: Error executing tool: 'hg19' This bug has been reported before, but I was wondering