December 2012 - galaxy-dev - lists.galaxyproject.org

Custom Builds Server eroor
by Shaun Webb 14 Dec '12

14 Dec '12

Hello I added a custom build to Galaxy, then deleted it and added a new build with the same name. Now whenever I try to acces my custom builds I am getting a server error. Can you point me towards any faults? Do I need to manually remove the custom builds from the database and if so where can I find them? Thanks Shaun Webb Error - <type 'exceptions.KeyError'>: u'ensembl_Current' URL: http://bifx-core.bio.ed.ac.uk:8080/galaxy/display_application/4100358d24a8f… File '/storage/home/galaxy/production/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/storage/home/galaxy/production/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/storage/home/galaxy/production/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/storage/home/galaxy/production/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/storage/home/galaxy/production/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/dataset.py', line 740 in display_application display_link = display_app.get_link( link_name, data, dataset_hash, user_hash, trans ) File '/storage/home/galaxy/production/galaxy-dist/lib/galaxy/datatypes/display_applications/application.py', line 189 in get_link return PopulatedDisplayApplicationLink( self.links[ link_name ], data, dataset_hash, user_hash, trans ) File '/storage/home/galaxy/galaxy_env/lib/python2.6/UserDict.py', line 22 in __getitem__ raise KeyError(key) KeyError: u'ensembl_Current' -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Fw: Questions about Install GATK on local instance
by ygong＠cpdr.org 14 Dec '12

14 Dec '12

Hi, Could anyone give me some suggestions about that? Thanks very much. Anthonel ----- Forwarded by Yixiao Gong/cpdr/hjf on 12/13/2012 10:50 AM ----- From: Yixiao Gong/cpdr/hjf To: galaxy-dev(a)lists.bx.psu.edu Date: 12/12/2012 02:52 PM Subject: Questions about Install GATK on local instance Hi, all, I'm installing GATK on galaxy local instance now and I have some questions may need your help. I downloaded the GATK2 from GATK website htt http://www.broadinstitute.org/gatk/download . the link is http://www.broadinstitute.org/gatk/auth?package=GATK I knew that on galaxy tool dependencies page http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies they gave the link for GATK 1.4 version but I can't figure out how to download and install it, and I noticed that GATK2 have all 1.x version features, so I installed GATK2. In the GATK 1.4 link (https://github.com/broadgsa/gatk ) that shown on http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies, there are multiple folders and files and I got really confused what I need to download. Even I choose "ZIP" to download a zip file, I counld not figure out whether it is the program package and don't know how to install it. Maybe this is the problem. But based on my understanding, GATK is just a set of java package, and all we need to do is put it into /tool-data/shared/jars folder, right? That is how I did it for GATK2. The GATK2 package include a folder called "resources" and a file called "GenomeAnalysisTK.jar" . I put them into /tool-data/shared/jars/gatk folder. I tested the installation following the instruction : http://gatkforums.broadinstitute.org/discussion/1200/how-to-test-your-gatk-… And I request a key from broadinstitute and followed the instruction on http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and… But the galaxy still gave me the error message as followed： ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A USER ERROR has occurred (version 2.2-16-g9f648cb): ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed ##### ERROR Please do not post this error to the GATK forum ##### ERROR ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. ##### ERROR Visit our website and forum for extensive documentation and answers to ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk ##### ERROR ##### ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option requires a GATK Key file. Please see http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and… for more information and instructions on how to obtain a key. ##### ERROR ------------------------------------------------------------------------------------------ I guess I may made mistakes in some point: 1. I should not install GATK2 but only GATK 1.4 so that Galaxy can use it. But I really don't know how to download and install it. I can't find the correct file. 2. GATK2 works on Galaxy but I did something wrong on installing it. Could anyone help me about this? It will be greatly appreciated. Thanks. Anthonel

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tools imported from toolshed stay in "waiting to run status"
by Philipe Moncuquet 13 Dec '12

13 Dec '12

Hi dev, We are running a local instance of Galaxy, last update was the November release (7148:17d57db9a7c0 I think). We are facing problem when trying to run tools that were imported via the toolshed. The never start and the status stays on "waiting to run". Other tools work fine, and this generic to all tools from toolshed. Any suggestions on where should I look to fix this ? Philippe

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Tophat for Illumina Error: Could not find Bowtie 2 index files
by greg 13 Dec '12

13 Dec '12

I'm seeing the error below when I try to run Tophat for Illumina. Has anyone seen this before? Could I have installed bowtie incorrectly or am I simply running with the wrong data/parameters? Thanks, Greg (I'm also really confused why the error is mentioned /tmp/* paths. I never assigned anything to /tmp in the universe_wsgi.ini. Where is it getting that from?) Error in tophat: [2012-12-13 13:55:01] Beginning TopHat run (v2.0.6) ----------------------------------------------- [2012-12-13 13:55:01] Checking for Bowtie Bowtie version: 2.0.2.0 [2012-12-13 13:55:01] Checking for Samtools Samtools version: 0.1.18.0 [2012-12-13 13:55:01] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (/tmp/4036894.1.f04.q/tmp4TrEQQ/dataset_75.*.bt2)

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Re: [galaxy-dev] Impersonate a User
by Edward Hills 13 Dec '12

13 Dec '12

Hi Greg, Try clicking the logout button. That should logout of the user you are impersonating and back into you. Although, this does have a few quirks also and may log you right out. Don't forget that when you are impersonating someone the history may not be automatically loaded and you will have to do that manually. Cheers, Ed

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Local galaxy
by Jennifer Jackson 13 Dec '12

13 Dec '12

Repost to mailing list ___________________________________________________________ For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev Hi I am doing NGS analysis in our local galaxy, I would like to access the output files for further analysis. I do have an account on the server where galaxy is installed, so I would like to access the output files without actually downloading them( aince they are huge). Can you please tell me where I can find my (local galaxy) output files on the server ? Is it stored under databases ? Thanks. Selvi Ramalingam Sent from my iPhone -- Jennifer Jackson http://galaxyproject.org

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Server Error / Edit attribut of a dataset generated by a tool
by Sarah Maman 13 Dec '12

13 Dec '12

Hello, One of my users gets the following message when he wishes to edit the attribute of a dataset which is generated by using a tool (same problem as it is a tool provided by Galaxy or a tool coded by us). Do you have any idea? Thanks in advance, Sarah Maman URL: http://sigenae-workbench.toulouse.inra.fr/galaxy/datasets/b9580783e2098a2b/… File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 111 in __call__ return self.app( environ, start_response ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/controllers/dataset.py', line 600 in edit refresh_frames=refresh_frames ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 722 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 733 in fill_template_mako return template.render( **data ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/database/compiled_templates/base.mako.py', line 42 in render_body __M_writer(unicode(next.body())) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/database/compiled_templates/dataset/edit_attributes.mako.py', line 95 in render_body __M_writer(filters.html_escape(unicode(data.info ))) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 31: ordinal not in range(128)

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Re: [galaxy-dev] How to add to add hg16 index into the build-in index / reference gnome list?
by Jennifer Jackson 13 Dec '12

13 Dec '12

Hello Sachit, There are a few problems with the command line. If you want to install hg19, then hg16 should not be used. Also, the <reference_in> to the tool should be an uncompressed fasta file. This is described in the tool documentation. You will also need to use as the '<index_basename>' the same dbkey identifier for the genome as you are using to name the reference fasta file (minus the ".fasta" extension) and for the SAM index. This is also the same dbkey identifier as used in the $GALAXYROOT/tool-data/shared/ucsc/builds.txt file. Using simply "hg19" as the dbkey would be the simplest choice. The original link I sent you explains this, but perhaps you did not find the data integration wiki page linked from the top? It is important to know about, as it also covers the builds.txt file in the first section. It can be found here: http://wiki.galaxyproject.org/Admin/Data%20Integration You may find it helpful to rsync the current hg19 genome and indexes from our server to help you get started. These could be used as a base from where bowtie2 indexes could be added. Please note that some genomes, including hg19, have variants in our data archives and that this particular genome is very large with many indexes and related files (just a warning if space is a concern). The tool forms for the RNA-seq tools describe variant content, but in short, the "full" genome is the same as the original. It is important to follow the symbolic links to note which datasets are associated with which indexes and to follow the same conventions when adding new data. Or take what you need and reorganize is as it makes the most sense for your own use. This is not overly complicated - you will be able to see which are associated by browsing the contained data. The second section on the data integration wiki page above describes how to rsync, if you choose to do this. To use the data, even rsync data, the loc files must still be set up. You only have to set up the ones that you plan to use. The original wiki link and the one above have information about .loc files, as do the sample .loc files themselves. Hopefully this helps, Jen Galaxy team On 12/12/12 9:56 PM, Sachit Adhikari wrote: > I need to install hg19 not hg16. > > On Thu, Dec 13, 2012 at 4:26 AM, Sachit Adhikari > <sachit.technerves(a)gmail.com <mailto:sachit.technerves@gmail.com>> wrote: > > Hello Jen, > > Thanks for your reply. I have installed bowtie2 and tophat2. I am > trying to use this command to build the index: > bowtie2-build [options]* <reference_in> <index_basename> > > My file name is Homo_sapiens_UCSC_hg19.tar.gz. Thus I used > bowtie2-build -f Homo_sapiens_UCSC_hg19.tar.gz hg16 > > But it doesn't work. What am I doing wrong? Thanks > > On Wed, Dec 12, 2012 at 9:23 PM, Jennifer Jackson <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu>> wrote: > > Hello Sachit, > > Instructions for setting up local indexes are in our wiki here: > http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup > > Bowtie2 is not specifically listed, but the instructions for > Bowtie and Bowtie2 are nearly identical. The same indexes are > used for Bowtie2 and Tophat2. When building the index, you > simply replace "bowtie-build" with "bowtie2-build" in the > command string and create/modify the bowtie2_index.loc file > the same as you would the bowtie_index.loc file. > > The Tophat2 manual has some more details about getting set up > here: > http://tophat.cbcb.umd.edu/manual.html > > Next time, for questions about local installs, using just the > galaxy-dev(a)bx.psu.edu <mailto:galaxy-dev@bx.psu.edu> list is > best (no need to post to multiple lists). If your question has > been misunderstood, please send more details to clarify. > > Best, > > Jen > Galaxy team > > > > On 12/12/12 3:46 AM, Sachit Adhikari wrote: >> How do I add hg16 into the build-in index? >> >> >> ___________________________________________________________ >> 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/ > > -- > Jennifer Jackson > http://galaxyproject.org > > > -- Jennifer Jackson http://galaxyproject.org

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Doesn't have enable_beta_job_managers options in configuration file
by Sachit Adhikari 12 Dec '12

12 Dec '12

My Galaxy Doesn't have enable_beta_job_managers option in universe_conf.ini file.

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tools imported from toolshed stay in "waiting to run status"
by Philipe Moncuquet 12 Dec '12

12 Dec '12

Hi dev, We are running a local instance of Galaxy, last update was the November release (7148:17d57db9a7c0 I think). We are facing problem when trying to run tools that were imported via the toolshed. The never start and the status stays on "waiting to run". Other tools work fine, and this generic to all tools from toolshed. Any suggestions on where should I look to fix this ? Philippe

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