[galaxy-dev] Output file permissions different pbs:/// VS local:/// job runners

Hi all. When I run the FastQC tool using the default local job runner, it produces a folder of files with permission 664: -rw-rw-r-- 1 galaxy galaxy 17K Jul 5 17:29 duplication_levels.png -rw-rw-r-- 1 galaxy galaxy 1.6K Jul 5 17:29 error.png -rw-rw-r-- 1 galaxy galaxy 7.5K Jul 5 17:29 fastqc_

[galaxy-dev] Galaxy cleaning up after it self after jobs fail

I am running galaxy on a system that normally runs all jobs on the cluster, but some jobs need to be run locally...But when I restart galaxy when these jobs are running, those jobs fail (and I am fine with that)...But then when I check the logs, I see a lot of this kind of errors and the word CRITI

Re: [galaxy-dev] History items get REMOVED when using the API to run workflows

OK...I tried this and it no longer removes the entries from the history...Thanks!I do see that each of the new histories I create still have a reference to some of the other files I pick up from the library (such as dbSNP) but those entries in the history have the number "None" in stead of the usua

[galaxy-dev] Has anyone implemented PINDEL as a tool in their GALAXY

Hi,I am about to embark of embedding PINDEL into GALAXY since it is not available in the TOOLSHED.Before I do, I thought I check if someone has already done this and could send me their XML so I don't have to start from scratch...Thanks!Thon _

Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?

For anyone :) Please join us on Monday - Thanks, Ann On 7/5/2012 4:15 PM, Thon Deboer wrote: Is this conference open for anyone or just (self appointed?) Czars? :) Regards, Thon de Boer, Ph.D. Bioinformatics Guru +1-650-799-6839 thondeb...@me.com LinkedIn Profile

Re: [galaxy-dev] History items get REMOVED when using the API to run workflows

On Jul 5, 2012, at 5:40 PM, Anthonius deBoer wrote: > WOW...I guess I know how you guys that designed the API think :) > > Small other question...Is it possible (yet) to pass a parameter to the API > yet, that is NOT an input step? > Things that get defined in the workflow step such as {Analysis_

Re: [galaxy-dev] History items get REMOVED when using the API to run workflows

WOW...I guess I know how you guys that designed the API think :)Small other question...Is it possible (yet) to pass a parameter to the API yet, that is NOT an input step?Things that get defined in the workflow step such as {Analysis_Run} that get filled in at runtime?Now it reverts to "X__oc__Analy

Re: [galaxy-dev] History items get REMOVED when using the API to run workflows

On Jul 5, 2012, at 5:33 PM, Thon Deboer wrote: > data['no_add_to_history']="True" ? Should do it. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists,

Re: [galaxy-dev] History items get REMOVED when using the API to run workflows

Thanks for the fast reply... How do I add this to the "payload"? Is it part of ds_map or something else? data['workflow_id'] = data['history'] = data['ds_map'] = {} data['no_add_to_history']="True" ? or is it part of the actual definition of the input step? Thanks T

Re: [galaxy-dev] History items get REMOVED when using the API to run workflows

I see the bug you're running into. As a temporary solution, executing workflows via the API with 'no_add_to_history' in the payload should work as expected. I'll have a permanent fix out shortly. -Dannon On Jul 5, 2012, at 5:12 PM, Thon Deboer wrote: > Hi, > > I am continueing to struggle w

Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?

Is this conference open for anyone or just (self appointed?) Czars? :) Regards, Thon de Boer, Ph.D. Bioinformatics Guru +1-650-799-6839 thondeb...@me.com LinkedIn Profile On Jun 28, 2012, at 2:14 AM, Sebastian Schaaf wrote: > Also hello to everyone, > > As I browsed through those tabs which

[galaxy-dev] History items get REMOVED when using the API to run workflows

Hi, I am continueing to struggle with the API I have created a workflow execution engine that submits a workflow using the examples in the API (scripts/api). When I run the WF on data in the LIBRARIES everything works fine. But when I choose a HISTORY as my source of data, the WF executes f

Re: [galaxy-dev] Looking for recommendations: How to run galaxy workflows in batch

But this only works if you have a single dataset (such as a BAM file) for each workflow to run on. If you have pairs of files (such as paired end FASTQ files, not an uncommon workflow nowadays :) ) you need to resort to using the API, since there is no support for paired end sequencing in GALAXY

Re: [galaxy-dev] Liftover tool installation woes

Great news, very glad this worked. I'll add liftOver to our wiki with more specific instructions and add in the bit about explicit paths to the .loc file section as well. Should help others going forward. Thanks for taking the time to report back the solution to the list! Jen Galaxy team On 7

[galaxy-dev] Display with IGV local

HI Galaxy-team ! I 'am trying to display BAM files whith the * local* IGV. However D*isplay with IGV "local*" use the already running copy of IGV on the server machine. So I need evry time to run manually igv by the command above: java -Xmx750m -jar igv.jar Is there any way to do this automatic

[galaxy-dev] Job output not returned from Cluster

Hi all,   I have exactly the same problem as described here: http://gmod.827538.n3.nabble.com/Job-output-not-returned-from-cluster-td879580.html   All the SGE stuff is administrated in our company and unfortunately they know nothing about Galaxy and so it?s my task to get it running. Everyth

[galaxy-dev] Adding the tag in tool xml file

Hi, is it possible to add the tag in tool_xml_file ? how can i add new tag in tool_xml_file ? if anyone is working on this , guide me Regards shashi --- This e-mail

Re: [galaxy-dev] Liftover tool installation woes

Hi Jen! Definitely didn't forget to reset the server everytime I tried. The problem was solved when I fixed the relative path to the full path.. can't believe I was stuck forever because of such a small miss. Fixed! and everything working so far =) Thank you so much, SJ On Thu, Jul 5, 2012 at 4

Re: [galaxy-dev] Liftover tool installation woes

Hello Kwon, There are no known issues with the liftOver wrapper (tools / extract / liftOver_wrapper.py and liftOver_wrapper.xml). Three more troubleshooting ideas: 1 - This may sound simple, but have you restarted the database since you updated the .loc files? http://wiki.g2.bx.psu.ed