January 2013 - galaxy-dev - lists.galaxyproject.org

gatk lite
by mark.rose＠syngenta.com 04 Jan '13

04 Jan '13

Hello Is it possible to redirect the GATK tools in my local installation of Galaxy to use GATK Lite (which is free) rather than GATK. If so what files would need to be altered and how? I'm particularly interested in getting the "Depth of Coverage" tool to work. Thanks much Mark This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.

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issue with galaxy server running samtools merge
by chodon sass 03 Jan '13

03 Jan '13

hi, i am trying to merge several bam files with samtools merge on the galaxy server. i did this a few days ago with the same files successfully but when i tried to run this merge on the same files again, i have had some strange behavior from galaxy server. first, the commands didn't start to run for several hours. seconde, they are taking a very long time - this morning they are still running! there are only 3 bams in each merge command and on my home computer this take seconds to minutes. i don't think there is anything wrong with the file format, as the command ran successfully a few days ago on the same files. could there be something going on on the galaxy server side? thanks! chodon

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Galaxy cloud: Tool execution generated the following error message
by Alicia C 03 Jan '13

03 Jan '13

*Hi * *Happy New Year!* *I hope this is the correct email to contact re. Galaxy cloud. I tried to run Galaxy on the cloud, I could upload the file but could not go beyond simple function "operate on genomic intervals". Is this normal? This is my first time using the Galaxy on the cloud. Hope to hear from you soon. Thank you. * *Best wishes* *alicia* * * * * *Dataset 7: Join on data 1 and data 5* Tool execution generated the following error message: /mnt/galaxyTools/galaxy-central/lib/galaxy/__init__.py:79: UserWarning: Module markupsafe was already imported from /usr/local/lib/python2.6/dist-packages/MarkupSafe-0.11-py2.6-linux-x86_64.egg/markupsafe/__init__.pyc, but /mnt/galaxyTools/galaxy-central/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg is being added to sys.path self.check_version_conflict() Dataset generation errors *Dataset 8: Intersect on data 1 and data 5* Tool execution generated the following error message: /mnt/galaxyTools/galaxy-central/lib/galaxy/__init__.py:79: UserWarning: Module markupsafe was already imported from /usr/local/lib/python2.6/dist-packages/MarkupSafe-0.11-py2.6-linux-x86_64.egg/markupsafe/__init__.pyc, but /mnt/galaxyTools/galaxy-central/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg is being added to sys.path self.check_version_conflict()

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Re: [galaxy-dev] Where is the output of tools stored in Galaxy?
by Hans-Rudolf Hotz 03 Jan '13

03 Jan '13

Please keep all replies on the list by using "reply all"! You can write a wrapper around tophat2 and redirect the output to any directory you want - as long as galaxy has write access to the directory. However, the output will no longer be accessible as a history item. Regards, Hans On 12/27/2012 11:19 AM, Sachit Adhikari wrote: > Hi Hans, > > Oh yes it is stored in database/files. What I wanted to know was if I > can change the output path of one or two tools. Let's say if I want to > change the path of tophat2, what should I do? > > Thanks, > > Sachit > > On Thu, Dec 27, 2012 at 9:38 AM, Hans-Rudolf Hotz <hrh(a)fmi.ch > <mailto:hrh@fmi.ch>> wrote: > > Hi Sachit > > > They are stored in ~/database/files/ > > and you can change it by changing the value for "file_path" in the > 'universe_wsgi.ini' file. > > Regardd, Hans > > > > > On 12/26/2012 11:40 AM, Sachit Adhikari wrote: > > Hello Everyone, > > *Merry Christmas and Happy New Year* > * > > * > I was wondering where are the output of the tools stored in the > machine > where the galaxy is hosted? And, can I change the path of the > output of > the tools? > > Thanks, > > Sachit > > > > > _____________________________________________________________ > 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/ > >

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backtrace when attempting to view a shared workflow
by Langhorst, Brad 03 Jan '13

03 Jan '13

File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 202 in display_by_username_and_slug return self.display(trans, stored_workflow) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 218 in display self.get_stored_workflow_steps( trans, stored_workflow ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/base/controller.py', line 668 in get_stored_workflow_steps module = module_factory.from_workflow_step( trans, step ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py', line 402 in from_workflow_step return self.module_types[type].from_workflow_step( trans, step ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py', line 217 in from_workflow_step module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 2120 in params_from_strings return params_from_strings( self.inputs, params, app, ignore_errors ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/parameters/__init__.py', line 94 in params_from_strings value = params[key].value_from_basic( value, app, ignore_errors ) File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/parameters/grouping.py', line 444 in value_from_basic current_case = rval['__current_case__'] = value['__current_case__'] TypeError: 'NoneType' object is unsubscriptable -- Brad Langhorst langhorst(a)neb.com<mailto:langhorst@neb.com>

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Re: [galaxy-dev] Galaxy for SNP chip data
by Dave Clements 03 Jan '13

03 Jan '13

Arthur, On Mon, Dec 31, 2012 at 2:03 PM, Goldberg, Arthur P < arthur.p.goldberg(a)mssm.edu> wrote: > > We have SNP microarrays about hundreds of subjects. In particular, samples > were processed on the Illumina Infinium HumanExome BeadChip, with 951,117 > markers.. Our project is collaborative, so we've a couple of dozen users in > multiple countries. I'm happy to run my own Galaxy instance and create user > accounts. > > But I need to be able to upload tables (in tsv files) describing the > subjects, with attributes such as IDs, phenotype, gender, age, etc. And > then I want to associate data files (idat, GenomeStudio genotype, etc.) > with the subjects. Does Galaxy support this functionality, or can I add it > easily? > A default installation can do a lot with TSV files, so I think that part is easy. Can you provide more information on how you want to associate the files? What will that association look like? If you just want file names in additional columns, then I think that should be workable too. If you are looking for more sophisticated bundling, Galaxy does have support for complex data types where you can bundle together multiple files, but I haven't worked with it yet, and I suspect it is non-trivial. ( *Can someone on the list comment on that?*) > > Feel free to forward this email if you're not the right person to answer > it. > > I did! I have forwarded this to the Galaxy development list. Thanks, Dave C. BR > A > > --- > Arthur Goldberg > Associate Professor of Psychiatry > Seaver Autism Center - Mount Sinai School of Medicine > Seaver Center, Room ABE-33 > 212-241-4229 > Arthur.Goldberg(a)mssm.edu > > > > > -- <http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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Repository not found after pull
by Franco Caramia 03 Jan '13

03 Jan '13

Hi list, I installed the Homer tool from the main toolshed. Then I uninstalled it and made a pull for the new galaxy revision. When I tried to re-install Homer I got a HTTP:NOT FOUND error... My guess is that the url for the original Homer is stored in the DB (and it got changed on the new revision) and is trying to clone it and not finding it.. Any ideas on how to fix this? And If this is the case it should be added to the bug list.... Thanks, Franco This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.

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January 2013 Galaxy Update
by Dave Clements 02 Jan '13

02 Jan '13

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Frames Compatible Browser
by Duren, Ryan P 02 Jan '13

02 Jan '13

I am trying to view html results from the SeqPos Tool on Galaxy/Cistrome Main, but keep receiving "Please use a frames compatible browser when viewing this output" message. I have tried this in Google Chrome, IE9, and Firefox but receive the same message in all three browsers.

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MGTAXA taxonomic prediction does not work...
by Edlund, Anna 02 Jan '13

02 Jan '13

Hello. My name is Anna Edlund and I have loaded several files containing contigs of assembled metgenomic data to generate taxonomic predictions. However, no one of the jobs I submitted yesterday afternoon are finished. Do you know what the problem is? How can I make MGTAXA work faster? Any help with this is very appreciated. Thank you! Anna

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