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lastz on local galaxy failing
by Andreas Kuntzagk 27 Nov '12

27 Nov '12

Hi, when I start a lastz job it submits a job to GridEngine. But this job seems to hang. The process running is python /data/galaxy/galaxy-dist/tools/sr_mapping/lastz_wrapper.py --ref_source= ... This wrapper seems to not start a lastz but lastz is in the path. After 2 days then Galaxy shows "Job did not produce output" Here is the paster.log from the start of the job. galaxy.jobs DEBUG 2012-11-15 09:03:07,539 (254) Working directory for job is: /data/galaxy/galaxy-dist/database/job_working_directory/000/254 galaxy.jobs.handler DEBUG 2012-11-15 09:03:07,540 dispatching job 254 to drmaa runner galaxy.jobs.handler INFO 2012-11-15 09:03:07,688 (254) Job dispatched galaxy.tools DEBUG 2012-11-15 09:03:07,980 Building dependency shell command for dependency 'lastz' galaxy.tools WARNING 2012-11-15 09:03:07,981 Failed to resolve dependency on 'lastz', ignoring galaxy.jobs.runners.drmaa DEBUG 2012-11-15 09:03:08,669 (254) submitting file /data/galaxy/galaxy-dist/database/pbs/galaxy_254.sh galaxy.jobs.runners.drmaa DEBUG 2012-11-15 09:03:08,670 (254) command is: python /data/galaxy/galaxy-dist/tools/sr_mapping/lastz_wrapper.py --ref_source=cached --source_select=pre_set --out_format=sam --input2=/data/galaxy/galaxy-dist/database/files/027/dataset_27795.dat --input1="/data/galaxy/galaxy-dist/tool-data/shared/ucsc/hg18/seq/hg18.2bit" --ref_sequences="None" --pre_set_options=yasra98 --identity_min=0 --identity_max=100 --coverage=0 --output=/data/galaxy/galaxy-dist/database/job_working_directory/000/254/galaxy_dataset_27800.dat --unmask=yes --lastzSeqsFileDir=/data/galaxy/galaxy-dist/tool-data; cd /data/galaxy/galaxy-dist; /data/galaxy/galaxy-dist/set_metadata.sh ./database/files /data/galaxy/galaxy-dist/database/job_working_directory/000/254 . /data/galaxy/galaxy-dist/universe_wsgi.ini /data/galaxy/galaxy-dist/database/tmp/tmpL4MMJV /data/galaxy/galaxy-dist/database/job_working_directory/000/254/galaxy.json /data/galaxy/galaxy-dist/database/job_working_directory/000/254/metadata_in_HistoryDatasetAssociation_288_9ynzEN,/data/galaxy/galaxy-dist/database/job_working_directory/000/254/metadata_kwds_HistoryDatasetAssociation_288_AEIseO,/data/galaxy/galaxy-dist/database/job_working_directory/000/254/metadata_out_HistoryDatasetAssociation_288_RhsufT,/data/galaxy/galaxy-dist/database/job_working_directory/000/254/metadata_results_HistoryDatasetAssociation_288_86DYsR,/data/galaxy/galaxy-dist/database/job_working_directory/000/254/galaxy_dataset_27800.dat,/data/galaxy/galaxy-dist/database/job_working_directory/000/254/metadata_override_HistoryDatasetAssociation_288_HMRNEG galaxy.jobs.runners.drmaa DEBUG 2012-11-15 09:03:08,676 run as user ['kuntzagk', '600'] galaxy.jobs DEBUG 2012-11-15 09:03:08,676 (254) Changing ownership of working directory with: /usr/bin/sudo -E scripts/external_chown_script.py /data/galaxy/galaxy-dist/database/job_working_directory/000/254 kuntzagk 600 galaxy.jobs.runners.drmaa DEBUG 2012-11-15 09:03:09,148 (254) Job script for external submission is: /data/galaxy/galaxy-dist/database/pbs/254.jt_json 141.80.188.178 - - [15/Nov/2012:09:03:10 +0200] "POST /galaxy/root/history_item_updates HTTP/1.1" 200 - "http://bbc.mdc-berlin.de/galaxy/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:16.0) Gecko/20100101 Firefox/16.0" galaxy.jobs.runners.drmaa INFO 2012-11-15 09:03:11,553 (254) queued as 1282605 galaxy.jobs.runners.drmaa DEBUG 2012-11-15 09:03:11,767 (254/1282605) state change: job is running -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich

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How to delete a toolshed tool completely or change category
by Andreas Kuntzagk 27 Nov '12

27 Nov '12

Hi, In the past I installed bwa_wrapper from the toolshed. Unfortunately I must have choosen a wrong category. Currently it is not part of any tool section. According to integrated_tool_panel.xml it's supposed to be part of this section: <section id="ngs:_assembly" name="NGS: Assembly" version=""> while it contains another section with the same name and a different id: <section id="ngs_assembly" name="NGS: Assembly" version=""> I tried to rectify this by deleting and reinstalling but unfortunately there is no way to really reinstall and it always ends up with the same problem again. Is there a way to really uninstall? regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich

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Occasionally, commandline tools are not found
by Joachim Jacob 27 Nov '12

27 Nov '12

Hi all, This is a strange error, still lingering around on our Galaxy. From time to time, some tools fail, with the same error: job stderr: /bin/sh: fastx_clipper: command not found So I log in as the user Galaxy, and run the tools successfully on the commandline. The solution is to restart the complete machine. I run CentOS6.3 with Galaxy distro 12fcd068b12e (Okt 23 release). Apparently, the PATH of the Galaxy session gets corrupted during running Galaxy, and I don't know where or how. Anybody a hint? Perhaps somebody knows how to reset the PATH of the current sessions where Galaxy is running as? Thanks, Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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No output from IGVtools tile
by Sytchev, Ilya 27 Nov '12

27 Nov '12

Hi, I'm running IGVtools (http://toolshed.g2.bx.psu.edu/repos/jjohnson/igvtools) tile tool in Galaxy on a WIG file but it's failing with exit code 1 and producing no output file. On the other hand, IGVtools count and sort run successfully in Galaxy on their respective inputs. Also, IGVtools tile tool runs successfully by itself from the command line on the same input WIG file from the same user account that runs this Galaxy instance. Standard out and error from running tile in Galaxy are below. I was wondering if anyone had a similar problem with IGVtools in their Galaxy instance. Thanks, Ilya stdout: Tile. File = input_file.wig Max zoom = 7 Probe file = None Window functions: mean IGV directory: /n/galaxy/home/galaxy_scc/igv INFO [2012-11-27 00:14:07,942] [GenomeManager.java:118] [main] Genome loaded Processing chromosome chr19 .........10.0% .........20.0% .........30.0% .........40.0% .........50.0% ..INFO [2012-11-27 00:14:12,778] [Preprocessor.java:179] [main] Ignoring data from non-existent locus. Probe = null Locus = chr19:61342442-61342477. chr19 length = 61342430 Group idx: 1 100.0% stderr: cp: cannot stat `/n/galaxy/www/galaxy_scc_dev/galaxy-central-hbc-20121101220520/database/jo b_working_directory/000/100/output.tdf': No such file or directory

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how to get annotation files for rna-seq
by Dr. Mira A. Bisso 26 Nov '12

26 Nov '12

Dear help; How to get the human annotation file for RNAseq analysis, for mapping by BWA and for RNAseq analysis, on Cufflinks and cuffdiff tools on galaxy? Mira Thanks [image001] Mira Bosso, M.Sc, B.D.S Research associate Pancreatic Islet Biology and Transplantation Unit P.O.Box 1180, Dasman 15462, Kuwait Phone: +965 2224 2999 Ext.2803 Mob: +96599500197 Email: mira.bisso(a)dasmaninstitute.org<mailto:mira.bisso@dasmaninstitute.org>

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Folder permissions after cluster run
by Sajoscha Sauer 26 Nov '12

26 Nov '12

Hi, We are running galaxy on the cluster with the 'real user' submission. It all works fine, but at the end of the run we found something unexpected. All the .dat files in the file_path folder are owned by the user running Galaxy, but all the folders (e.g. dataset_25808_files) are still owned by the user that was running the tool on the cluster. Is this the expected outcome or is there something wrong? Thanks for your help, Sajoscha

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Can't edit galaxy workflow
by Sanjarbek Hudaiberdiev 26 Nov '12

26 Nov '12

I tried to reply to similar posts, but couldn't figure out how to do it. So posting again: Galaxy giving this error when editing workflow, just after creating workflow from existing history: URL:http://localhost/galaxy/workflow/load_workflow?id=df7a1f0c02a5b08e&_=1352817462148 Moduleweberror.evalexception.middleware:*364*in|respond| |>> <http://localhost/galaxy/workflow/editor?id=df7a1f0c02a5b08e#>app_iter*=*self*.*application*(*environ*,*detect_start_response*)*| Modulepaste.debug.prints:*98*in|__call__| |>> <http://localhost/galaxy/workflow/editor?id=df7a1f0c02a5b08e#>environ*,*self*.*app*)*| Modulepaste.wsgilib:*539*in|intercept_output| |>> <http://localhost/galaxy/workflow/editor?id=df7a1f0c02a5b08e#>app_iter*=*application*(*environ*,*replacement_start_response*)*| Modulepaste.recursive:*80*in|__call__| |>> <http://localhost/galaxy/workflow/editor?id=df7a1f0c02a5b08e#>*return*self*.*application*(*environ*,*start_response*)*| Modulepaste.httpexceptions:*632*in|__call__| |>> <http://localhost/galaxy/workflow/editor?id=df7a1f0c02a5b08e#>*return*self*.*application*(*environ*,*start_response*)*| Modulegalaxy.web.framework.base:*160*in|__call__| |>> <http://localhost/galaxy/workflow/editor?id=df7a1f0c02a5b08e#>body*=*method*(*trans*,*****kwargs*)*| Modulegalaxy.web.framework:*73*in|decorator| |>> <http://localhost/galaxy/workflow/editor?id=df7a1f0c02a5b08e#>*return*simplejson*.*dumps*(*func*(*self*,*trans*,****args*,*****kwargs*)**)*| Modulegalaxy.webapps.galaxy.controllers.workflow:*733*in|load_workflow| |>> <http://localhost/galaxy/workflow/editor?id=df7a1f0c02a5b08e#>'tooltip'*:*module*.*get_tooltip*(*static_path*=*url_for*(*'/static'*)**)**,*| Modulegalaxy.workflow.modules:*258*in|get_tooltip| |>> <http://localhost/galaxy/workflow/editor?id=df7a1f0c02a5b08e#>*return*self*.*tool*.*help*.*render*(*static_path*=*static_path*)*| *AttributeError: 'NoneType' object has no attribute 'render'* Could anyone help me to solve this problem? Thanks, Sanjar.

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WebDAV
by Adhemar 26 Nov '12

26 Nov '12

Hi folks, I've just set a WebDAV directory in order to let users upload files as an alternative to the good old FTP. Since it might be useful, here are the steps. I hope you enjoy! Adhemar *Configuring WebDAV* In order to provide a drag and drop interface to upload files to galaxy, one can choose WebDAV. To make it available, you'll need to install the following: # These modules are responsible for enabling the DAV protocol through the apache webserver mod_dav mod_dav_fs # This package is necessary in order to set galaxy uid/gid (AssignUserId) rather than the default apache user httpd-itk.x86_64 : MPM Itk for Apache HTTP Server # First, install httpd-itk (http://www.webtatic.com/packages/httpd-itk/) yum install httpd-itk # Then edit /etc/sysconfig/httpd and add the following line: HTTPD=/usr/sbin/httpd.itk # The galaxy user must have write permission in the directory containing the DavLockDB files otherwise: [error] [client 127.0.0.1] The locks could not be queried for verification against a possible "If:" header. [500, #0] [error] [client 127.0.0.1] Could not open the lock database. [500, #400] [error] [client 127.0.0.1] (13)Permission denied: Could not open property database. [500, #1] # Here's an example of apache's virtual host configuration, assuming ftp_upload_dir = /home/galaxy/database/ftp in the Galaxy config file: # include 'REMOTE_USER' in the directory path in order to limit users to their own directories RewriteRule ^/repository(.*) /home/galaxy/database/ftp/%{LA-U:REMOTE_USER}$1 <Directory /var/webdav> Options Indexes FollowSymlinks MultiViews AllowOverride None Order Allow,Deny Allow from all # set the galaxy user and group for your vhosts to use AssignUserId galaxy galaxy # here follows the PAM authentication in order to allow users registered in the server itself # can be changed to ldap, htpasswd file, ... AuthType Basic AuthName Repository AuthPAM_Enabled on Require valid-user # activate mod_dav Dav On </Directory> # It's necessary to create each user directory with the correct galaxy user permissions!!! # After that you can use a webdav client (cadaver) or map the network directory in a filemanager (nautilus, konqueror, orca) to view/edit/transfer files. cadaver http://hostname/repository

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XGRID and Galaxy
by James Boocock 26 Nov '12

26 Nov '12

Hi Galaxy Dev Team. We are looking to put xgrid into the galaxy api as part of a summer project. We are hoping to add this functionality directly into galaxy so that all users can benefit. We are curious where to start investigating how galaxy interfaces with grids. We hope to integrate the functionality into galaxy so that a user can specify xgrid in the config file and galaxy will deal with the rest of the interfacing with xgrid. This would of course only be avaliable to MACOSX galaxy installs. Cheers James. Research Assistant Department of Biochemistry University Of Otago

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FW: Re. RNA-Seq
by Songyan Liu 23 Nov '12

23 Nov '12

My account emailis soliu(a)cc.umanitoba.ca From: Songyan Liu [mailto:mfgc@cc.umanitoba.ca] Sent: Friday, November 23, 2012 1:41 PM To: 'galaxy-dev(a)lists.bx.psu.edu' Subject: Re. RNA-Seq I was using Cufflinks to analyze Clip-Seq data. The results as 'gene expression' and 'transcript expression' gave me almost same results (No. of genes ? No. of transcripts). I guess the number of genes should be relatively smaller than that in transcripts. I wonder if I need to get a special format for the annotation? I used '62: UCSC Main on Human: refGene (genome)'. Thanks, Songyan Liu

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