galaxy-dev August 2014

galaxy-dev@lists.galaxyproject.org

65 participants
102 discussions

August 11, 2014 Galaxy Distribution
by Jennifer Jackson 15 Aug '14

15 Aug '14

August 11, 2014 Galaxy Distribution <http://wiki.galaxyproject.org/News/2014_08_11_Galaxy_Distribution> / <https://www.docker.com/>/ _Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2014_08_11>___ /Highlights:/// .Security alert <http://tinyurl.com/nhgmbc5>from July 31st, upgrade now .Citations <http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E…>: DOIs, bibtex, and much much more . Docker, docker,DOCKER <http://wiki.galaxyproject.org/Admin/Tools/Docker>. You voted, we've/got it/, with a little help from our friends (you!) . Significant Workflow, API, Job, Tool Shed, and Dataset management updates . Fixes, tunings, plus just a drop of ? Gossip *getgalaxy.org <http://wiki.galaxyproject.org/Admin/Get%20Galaxy>* *galaxy-dist.readthedocs.org <http://galaxy-dist.readthedocs.org/>* *bitbucket.org/galaxy/galaxy-dist <http://bitbucket.org/galaxy/galaxy-dist>* *new*: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable *upgrade*: $ hg pull $ hg update latest_2014.06.02 /Thanks for using Galaxy!/ The Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam>

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Re: [galaxy-dev] TypeError with 'dict'
by Björn Grüning 15 Aug '14

15 Aug '14

Hi Martin, please keep galaxy-dev in the CC list. Am 12.08.2014 um 08:51 schrieb Martin Christiansen: > Hi Björn, > > Most certainly. I have posted it below. > > <tool id="screen_reads" name="Screen Reads"> -> add here a version number version="0.1" > <description>against hg19</description> > > <command interpreter="bash">screen_reads.sh $Project.input $Project.samples $Project $Samples </command> > > <inputs> > <conditional name="Project"> > <param name="input" type="select" label="Select project"> > <option value="galaxy_test1">galaxy_test1</option> > <option value="Untitled Folder">Untitled Folder</option> -> is the white space really needed? If so $Project.input will be two words. Use "${Project.input}" to convert it to onw argument > </param> > <when value="galaxy_test1"> > <param name="samples" type="select" label="Select samples" display="checkboxes" multiple="True"> > <option value="147406386-700171390">147406386-700171390</option> > <option value="158256496-700097688">158256496-700097688</option> > <option value="158337416-700013715">158337416-700013715</option> > <option value="158337416-700097837">158337416-700097837</option> > <option value="158357646-700035237">158357646-700035237</option> > <option value="158458797-700014562">158458797-700014562</option> > <option value="158479027-700014724">158479027-700014724</option> > <option value="158479027-700097196">158479027-700097196</option> > <option value="158499257-700014837">158499257-700014837</option> > <option value="158499257-700098561">158499257-700098561</option> > <option value="158742018-700015181">158742018-700015181</option> > <option value="158802708-700015245">158802708-700015245</option> > <option value="158802708-700015250">158802708-700015250</option> > <option value="158802708-700099803">158802708-700099803</option> > <option value="158802708-700119165">158802708-700119165</option> > <option value="158822939-700014954">158822939-700014954</option> > <option value="158883629-700015113">158883629-700015113</option> > <option value="158883629-700100227">158883629-700100227</option> > <option value="158883629-700112812">158883629-700112812</option> > <option value="158924089-700099307">158924089-700099307</option> > </param> > </when> > <when value="Untitled Folder"> > <param name="samples" type="select" label="Select samples" display="checkboxes" multiple="True"> -> you don't have any <option> here. > </param> > </when> > </conditional> > </inputs> > > <outputs> > <data format="tabular" name="Project" label="Project" from_work_dir="/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.input"/> > <data format="tabular" name="Samples" label="Samples" from_work_dir="/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.samples"/> > </outputs> -> I'm not sure this will work. workdir is a special dir Galaxy creates for you. It will be the working directory where your program get's called. So assume your program creates foo.sam files. You can specify it like from_work_dir='foo.sam' The input handling looks also a little bit strange. You do not specify any input file in Galaxy. That is not really Galaxy like :) Cheers, Bjoern > <help> > Reads screened against hg19. > </help> > </tool> > > Best, > Martin > >

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Internal Server Error when trying to install a tool from the Tool shed
by audrey michel 15 Aug '14

15 Aug '14

Hi, We get the following error when we try to install any tool from the Tool shed when using the Admin panel: Internal Server ErrorGalaxy was unable to successfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. *The error has been logged to our team.* We would be grateful if you could advise on this issue. Kind Regards, Audrey Michel Baranov Lab School of Biochemistry & Cell Biology University College Cork Ireland

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Re: [galaxy-dev] unable to stob jobs
by John Chilton 15 Aug '14

15 Aug '14

Fantastic - thanks for the update! I hope it is okay - I am cc'ing the -dev list so if people search on this problem in the future and search the can see what the problem turned out to be and how to fix it. Enjoy your job killing. -John On Fri, Aug 15, 2014 at 12:47 PM, Michael Mason <MMason(a)benaroyaresearch.org> wrote: > Hi John, > > Just an update on the hypothesis. Our server guy figured out that the nfs > memory setting was such that Galaxy used all the memory. He believes this > resulted in no memory for jobs to be killed. He changed the setting so > that there is some leftover memory when I am using Galaxy at an all out > pace and I was able to kill jobs this morning. > Thanks again. > Mike > > On 8/15/14 9:32 AM, "John Chilton" <jmchilton(a)gmail.com> wrote: > >>Very interesting - whenever you get a chance I would try to kill >>simple jobs when Galaxy is not under load to verify the problem is >>related to Galaxy's job load. If you still have problems I would then >>try again to get that stack trace. >> >>Good luck, >> >>-John >> >>On Wed, Aug 13, 2014 at 6:46 PM, Michael Mason >><MMason(a)benaroyaresearch.org> wrote: >>> Hi John, >>> >>> We actually went ahead and recovered an archived instance from Friday. >>> This should should be the same build though. Because of the archived >>> instance I believe we lost the stack trace but I'll check with the IT >>> folks. >>> Thanks for your help. Below is the tip call. BTW we are using Galaxy >>>with >>> fastq's from a Fluidigm's C1 machine. This means we often run 100-200 >>> libraries on a single flow cell. The resulting 100-200 libraries tend to >>> tax Galaxy. But it tends to handle it though this may be the root cause >>>of >>> our difficulty killing jobs. >>> >>> tip >>> 13753:d3b1f484c4b6bbb3daa50fa167eef97a384890b3 >>> latest_2014.06.02 >>> 13742:8a863a311a6c9f14b302799bffcf94df9186fef7 >>> release_2014.06.02 >>> 13712:7e257c7b10badb65772b1528cb61d58175a42e47 >>> latest_2014.04.14 >>> 13085:68a8b0397947c732b28207d465d3f3c4e2a7a8a0 >>> release_2014.04.14 >>> 13064:9e53251b0b7e93b9563008a2b112f2e815a04bbc >>> release_2014.02.10 >>> 12440:5e605ed6069fe4c5ca9875e95e91b2713499e8ca >>> release_2013.11.04 >>> 11218:26f58e05aa1068761660681583821e21e6cbf7ab >>> release_2013.08.12 >>> 10392:1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 >>> release_2013.06.03 >>> 9943:524f246ca85395082719ae7a6ff72260d7ad5612 >>> security_2013.04.08 >>> 9292:2cc8d10988e03257dc7b97f8bb332c7df745d1dd >>> release_2013.04.01 >>> 9231:75f09617abaadbc8cc732bb8ee519decaeb56ea7 >>> release_2013.02.08 >>> 8794:1c717491139269651bb59687563da9410b84c65d >>> release_2013.01.13 >>> 8530:a4113cc1cb5eaa68091c9a73375f00555b66dd11 >>> >>> >>> >>> >>> On 8/13/14 1:39 PM, "John Chilton" <jmchilton(a)gmail.com> wrote: >>> >>>>When was the last time you updated Galaxy - we fixed a bug that would >>>>be causing this behavior several releases ago. >>>> >>>>Otherwise - additional information would help - like are you using the >>>>DRMAA job runner or the newer specialized Slurm job runner and are >>>>there any details in the Galaxy log that might be helpful? I would >>>>expect to see a stack trace of some kind if there are problems like >>>>this. If there are no stack traces and you have an update-to-date >>>>Galaxy - perhaps checking the SLURM logs for errors might also provide >>>>additional insight. >>>> >>>>-John >>>> >>>>On Tue, Aug 12, 2014 at 12:10 PM, Michael Mason >>>><MMason(a)benaroyaresearch.org> wrote: >>>>> Hello all, >>>>> >>>>> I am running a Galaxy instance on slurm. I am unable to stop jobs via >>>>>the >>>>> admin "Manage Jobs" window. Via postgres, there are no jobs in the job >>>>> table. Any thoughts? >>>>> I realize this may not be dev but I am at a loss of what to do. >>>>> Thanks >>>>> Mike >>>>> ________________________________ >>>>> --CONFIDENTIALITY NOTICE--: The information contained in this email is >>>>> intended for the exclusive use of the addressee and may contain >>>>>confidential >>>>> information. If you are not the intended recipient, you are hereby >>>>>notified >>>>> that any form of dissemination of this communication is strictly >>>>>prohibited. >>>>> www.benaroyaresearch.org >>>>> >>>>> ___________________________________________________________ >>>>> 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, please use the interface at: >>>>> http://lists.bx.psu.edu/ >>>>> >>>>> To search Galaxy mailing lists use the unified search at: >>>>> http://galaxyproject.org/search/mailinglists/ >>> >>> ________________________________ >>> --CONFIDENTIALITY NOTICE--: The information contained in this email is >>>intended for the exclusive use of the addressee and may contain >>>confidential information. If you are not the intended recipient, you are >>>hereby notified that any form of dissemination of this communication is >>>strictly prohibited. www.benaroyaresearch.org > > ________________________________ > --CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.org

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How set the working and temp directories in external drive
by Juan Vladimir de la Rosa Medina 15 Aug '14

15 Aug '14

Hi, now I am trying to set the working and temp directories of Galaxy enviroment in a external drive, but I do not know how to do this task. I know that universe_wgsi.ini file has a section called Files and directories, with diferent options like job_working_directory, collect_outputs_from, file_path and new_file_path. However, I do not know if these are the options to be set or if there are other options. I also do not know how to set these options. Can anybody help me or point me to a tutorial? Thanks

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Packaging pycurl on toolshed
by Saket Choudhary 15 Aug '14

15 Aug '14

My attempt to 'package' pycurl on testtoolshed fails with the following error: src/pycurl.c: In function ‘do_multi_info_read’: src/pycurl.c:3549:15: warning: call to ‘_curl_easy_getinfo_err_string’ declared with attribute warning: curl_easy_getinfo expects a pointer to char * for this info [enabled by default] src/pycurl.c: In function ‘do_curl_getinfo’: src/pycurl.c:2888:19: warning: call to ‘_curl_easy_getinfo_err_curl_slist’ declared with attribute warning: curl_easy_getinfo expects a pointer to struct curl_slist * for this info [enabled by default] error: could not create '/usr/local/share/doc': Permission denied A local install worked fine. Is this because of libcurl-devel missing on toolshed instance?

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setting SGE arguments in galaxy (cloudman)
by Jim McCusker 14 Aug '14

14 Aug '14

I have a galaxy/cloudman cluster where I would like to pass a "-l mem_free=16G" parameter when galaxy submits the job to SGE. I've tried adding it like this: default_cluster_job_runner = drmaa://-l mem_free=16G/ (it was: default_cluster_job_runner = drmaa:/// ) but now the jobs don't even submit. Am I wiping out other important parameters? How should I do this? Thanks, Jim

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Announcing the UK Galaxy Community
by graham etherington (TSL) 14 Aug '14

14 Aug '14

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 the needs of the community * Encourage interaction and collaboration. Galaxy-UK is also an information hub for events such as: * UK based Galaxy training courses * UK based talks involving Galaxy * Information on the location of UK Galaxy servers * Anything else that might be pertinent to bring the UK Galaxy users/admins together as a community We will be organising both online meetings and physical meetings, so keep an eye on the site for these events. Best wishes, The Galaxy-UK Team.

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Question about composite blast datatypes
by Eric Rasche 14 Aug '14

14 Aug '14

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Workflow Loop
by Görkem Erdoğan 14 Aug '14

14 Aug '14

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?

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galaxy-dev August 2014