Re: [galaxy-dev] lastz on local galaxy failing
Hi, I just noticed that this was another case of a tool that needs more then the 1GB memory that is default on our cluster. After adjusting the job_runner settings everything seems fine. regards, Andreas On 15.11.2012 09:08, Andreas Kuntzagk wrote: 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 ___ 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/
[galaxy-dev] multithreaded tools
Hi, I'm wandering how galaxy supports tools that are multithreaded or multi-process. When working with lastz I noticed that it starts 4 parallel processes. Is that always so? Can this be adjusted? What other tools also are multi-process? 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 ___ 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/
Re: [galaxy-dev] multithreaded tools
Andreas, Yes this is possible. You can also have a look at the ncbi blast+ tools written by Peter. The same is true. Usually the tool wrappers (xml) have an option preconfigured how many threads can be used... You can adjust these directly in the xml OR as we did we added the option to be adjustable by a parameter directly in galaxy. Default low number of cores, but advanced users (login email bound) can select higher thread numbers. No experience on cluster/grid tools. Hope this helps, Alex -Oorspronkelijk bericht- Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Andreas Kuntzagk Verzonden: maandag 26 november 2012 9:58 Aan: galaxy-dev@lists.bx.psu.edu Onderwerp: [galaxy-dev] multithreaded tools Hi, I'm wandering how galaxy supports tools that are multithreaded or multi-process. When working with lastz I noticed that it starts 4 parallel processes. Is that always so? Can this be adjusted? What other tools also are multi-process? 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 ___ 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/ ___ 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/
[galaxy-dev] how to get annotation files for rna-seq
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.bi...@dasmaninstitute.orgmailto:mira.bi...@dasmaninstitute.org inline: image001.png___ 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/
Re: [galaxy-dev] how to get annotation files for rna-seq
You can use 'Get data' -- 'UCSC Main' to fetch an GTF (gene transfer format) format of your species of interest, Human in this case. I tend to use the Ensembl genes track (from the Genes and gene prediction tracks). Make sure you use GTF as output, and send to Galaxy! Cheers, 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 On 11/26/2012 01:07 PM, Dr. Mira A. Bisso wrote: 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.bi...@dasmaninstitute.org mailto:mira.bi...@dasmaninstitute.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/ ___ 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/
Re: [galaxy-dev] XGRID and Galaxy
XGrid is a dead-end technology. It has been removed from OS X starting with Mountain Lion (10.8). -- Glen L. Beane Senior Software Engineer The Jackson Laboratory (207) 288-6153 On 11/22/12 9:47 PM, James Boocock smilefreak2...@gmail.com wrote: 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 ___ 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/ The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. ___ 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/
[galaxy-dev] help
Dear Galaxy help-centre I want to use Tophat and Clifflinks to do an expression analysis. However, the reference genome for Heterobasidion annosum (it is available at JGI) is not listed. You have posted on your website that we can contact you if 'your genome of interest' is not listed. Is it possible that you can included the H. annosum genome on the list? Thank you very much Magriet ___ 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/
[galaxy-dev] 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 ___ 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/
[galaxy-dev] FW: Re. RNA-Seq
My account emailis so...@cc.umanitoba.ca From: Songyan Liu [mailto:m...@cc.umanitoba.ca] Sent: Friday, November 23, 2012 1:41 PM To: 'galaxy-dev@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 ___ 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/
Re: [galaxy-dev] how to get annotation files for rna-seq
Can we also fetch virus file from some sources like this? Thanks Kanwar On Mon, Nov 26, 2012 at 4:25 AM, Joachim Jacob joachim.ja...@vib.be wrote: You can use 'Get data' -- 'UCSC Main' to fetch an GTF (gene transfer format) format of your species of interest, Human in this case. I tend to use the Ensembl genes track (from the Genes and gene prediction tracks). Make sure you use GTF as output, and send to Galaxy! Cheers, 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 On 11/26/2012 01:07 PM, Dr. Mira A. Bisso wrote: 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.bi...@dasmaninstitute.org mailto:mira.bisso@** dasmaninstitute.org mira.bi...@dasmaninstitute.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/ __**_ 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/ ___ 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/
Re: [galaxy-dev] Can't edit galaxy workflow
Hi, Can you please send the entire link to access this changeset? I keep searching for 5013377e0bf7 but can not find it. Thanks in advance, Liisa From: Dannon Baker dannonba...@me.com To: Sanjarbek Hudaiberdiev hudai...@icgeb.org Cc: galaxy-...@bx.psu.edu Date: 13/11/2012 12:34 PM Subject:Re: [galaxy-dev] Can't edit galaxy workflow Sent by:galaxy-dev-boun...@lists.bx.psu.edu Sanjar, This is fixed as of 5013377e0bf7. This may not be in the next distribution, but will be in the one after that. Of course, you can manually pull the change from galaxy-central at any time. -Dannon On Nov 13, 2012, at 9:45 AM, Sanjarbek Hudaiberdiev hudai...@icgeb.org wrote: 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 Module weberror.evalexception.middleware:364 in respond app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ environ, self.app) Module paste.wsgilib:539 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ body = method( trans, **kwargs ) Module galaxy.web.framework:73 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ) ) Module galaxy.webapps.galaxy.controllers.workflow:733 in load_workflow 'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ), Module galaxy.workflow.modules:258 in get_tooltip 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. ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] lastz on local galaxy failing
Howdy, Andreas, Lastz memory requirements are dependent on the size of the input sequences (mainly on the size of reference sequence) and, to a lesser extent, the genome's repeat content. I'm a little confused/concerned by how this failure was indicated. When run from a console, if lastz has a memory allocation failure, a message is written to stderr (e.g. call to realloc failed to allocate 1,000,000,000 bytes) and the program exits to the shell with the status EXIT_FAILURE (an ISO C definition which I presume corresponds to a standard shell error code). Usually, if lastz isn't going to have enough memory, an allocation failure will occur early in the run as all the long term data structures are being built. This would normally be within the first five minutes. A later failure would (probably) mean that the long term structures were close to the memory limit and then alignments for one of the query sequences required enough additional memory to push us over the limit. I assume galaxy's Job did not produce output message must be based on a lack of any output to stdout. What is strange is that fact that it took 2 days to get this message. Lack of output to stdout suggests that the failure occurred before any queries were processed (strictly speaking, before any alignments were output). This should have occurred in the first few minutes of the run. Would it be possible for you to point me at the input sequences for this run, so that I can try running this via the console, and see if there's something happening in lastz that I don't understand? Bob H On Nov 26, 2012, at 3:35 AM, Andreas Kuntzagk wrote: Hi, I just noticed that this was another case of a tool that needs more then the 1GB memory that is default on our cluster. After adjusting the job_runner settings everything seems fine. regards, Andreas On 15.11.2012 09:08, Andreas Kuntzagk wrote: 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
Re: [galaxy-dev] multithreaded tools
Howdy, Andreas, The four processes started for a galaxy lastz job must involve post- processing the lastz output through some other shell tool. Lastz by itself doesn't support multiple threads or processes. Bob H On Nov 26, 2012, at 3:58 AM, Andreas Kuntzagk wrote: Hi, I'm wandering how galaxy supports tools that are multithreaded or multi-process. When working with lastz I noticed that it starts 4 parallel processes. Is that always so? Can this be adjusted? What other tools also are multi-process? 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 ___ 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/ ___ 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/
Re: [galaxy-dev] Can't edit galaxy workflow
Bitbucket will only show the first 7 characters when browsing through commits. Try this: https://bitbucket.org/galaxy/galaxy-central/changeset/5013377e0bf7a656ea593098f1d1b38f3d6928c6 -Scott - Original Message - Hi, Can you please send the entire link to access this changeset? I keep searching for 5013377e0bf7 but can not find it. Thanks in advance, Liisa From: Dannon Baker dannonba...@me.com To: Sanjarbek Hudaiberdiev hudai...@icgeb.org Cc: galaxy-...@bx.psu.edu Date: 13/11/2012 12:34 PM Subject: Re: [galaxy-dev] Can't edit galaxy workflow Sent by: galaxy-dev-boun...@lists.bx.psu.edu Sanjar, This is fixed as of 5013377e0bf7. This may not be in the next distribution, but will be in the one after that. Of course, you can manually pull the change from galaxy-central at any time. -Dannon On Nov 13, 2012, at 9:45 AM, Sanjarbek Hudaiberdiev hudai...@icgeb.org wrote: 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 Module weberror.evalexception.middleware:364 in respond app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ environ, self.app) Module paste.wsgilib:539 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ body = method( trans, **kwargs ) Module galaxy.web.framework:73 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ) ) Module galaxy.webapps.galaxy.controllers.workflow:733 in load_workflow 'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ), Module galaxy.workflow.modules:258 in get_tooltip 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. ___ 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/ ___ 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/ ___ 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/___ 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/
Re: [galaxy-dev] Galaxy IGV display error
Hi Joan, For IGV and most external displays that work on BAM and other larger seekable file formats (bigwig, bigbed, etc.) you'll need to use and configure a proxy server for your local Galaxy instance that provides byte-range request capabilities, such as nginx (http://wiki.galaxyproject.org/Admin/Config/Performance/nginx%20Proxy) or apache (http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy). Thanks for using Galaxy, Dan On Nov 26, 2012, at 6:11 AM, prota...@clinic.ub.es prota...@clinic.ub.es wrote: Hi all, I’m having problems when I click to visualize one BAM file from galaxy to IGV version 2.1.24. I’ve tried the local and also the web display options but I have the same problem. I have tried also to download first the bam file from galaxy and then loading into IGV manually and it works. I also have tried to modify the .jnlp generated but it does not work. IGV shows the next error message: ERROR [2012-11-26 11:44:54,591] [IGV.java:1555] [pool-1-thread-1] net.sf.samtools.util.RuntimeEOFException: Premature EOF; BinaryCodec in readmode; streamed file (filename not available) ERROR [2012-11-26 11:44:54,592] [IGV.java:1494] [pool-1-thread-1] Error loading tracks org.broad.igv.exceptions.DataLoadException: An error occurred while accessing: http://172.21.104.21:8080/display_application/9e23127bd2c9a880/igv_bam/web_link_main/8d9bcc17f9fede63/data/galaxy_9e23127bd2c9a880.bambrPremature EOF; BinaryCodec in readmode; streamed file (filename not available) Thanks for your help. Joan Protasio, Bioinformatician Software Engineer Bioinformatics Platform August Pi i Sunyer Biomedical Research Institute (IDIBAPS) C/ Rosselló 153, Barcelona http://bioinformatics.fcrb.es +34 93 227 54 00 ext. 4522 ___ 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/ ___ 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/
Re: [galaxy-dev] Folder permissions after cluster run
On Nov 19, 2012, at 10:26 AM, Sajoscha Sauer wrote: 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? Hi Sajoscha, Are your tools writing to the directory specified by the output's 'extra_files_path' attribute, or by its 'files_path' attribute? 'extra_files_path' always refers to the directory underneath the files/ directory, but 'files_path' refers to the temporary path under the job's working directory. You'll need to use 'files_path' to have the outputs collected and ownership changed after completion. --nate Thanks for your help, Sajoscha ___ 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/ ___ 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/
Re: [galaxy-dev] Problem with Active Directory/LDAP authentication
On Nov 19, 2012, at 12:49 PM, Harris Shapiro wrote:
Hello,
I'm writing because I've been trying for the past few days to configure
Galaxy to use Apache-based LDAP authentication, but have reached a point
where I'm basically stuck. The system in a virtual machine running:
- CentOS 5.8
- Apache 2.2.3
I'm trying to configure a Galaxy instance at localhost:8080, with Active
Directory authentication.
I started with the admin page documentation:
http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy
and also worked through the troubleshooting examples found at:
a)
http://user.list.galaxyproject.org/Galaxy-Apache-External-Authentication-tt4131493.html#a4131495
b) http://gmod.827538.n3.nabble.com/galaxy-dev-ldap-integration-td839409.html
c) http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-January/001676.html
Following the debugging steps suggested by URL (a), I'm able to verify that:
1) The authentication clause I have works, without rewrite rules and without
a proxy.
2) Without rewrite rules and a proxy, the Apache environment has the
AUTHENTICATE_SAMACCOUNTNAME and REMOTE_USER environment variables set.
Unfortunately, when I turn on the proxy (setting use_remote_user and
remote_user_maildomain in universe_wsgi.ini accordingly), I get the
following error message when I try accessing the localhost:8080 URL, the
following error message appears:
Access to Galaxy is denied
Galaxy is configured to authenticate users via an external method (such as
HTTP authentication in Apache), but a username was not provided by the
upstream (proxy) server. This is generally due to a misconfiguration in the
upstream server.
Please contact your local Galaxy administrator.
As suggested by URLs (a) and (c), I modified
./lib/galaxy/web/framework/middleware/remoteuser.py to print the environment
seen by that script. None of the remote user information seems to be making
to the script, either from AUTHENTICATE_SAMACCOUNTNAME or REMOTE_USER, no
matter which of the suggested combinations of RewriteCond, RewriteRule,
and RequestHeader options I tried. In addition, the troubleshooting
suggestions to force a REMOTE_USER value to be set via a directive like:
RequestHeader add REMOTE_USER [user name]
also failed to pass REMOTE_USER to the remoteuser.py script.
I've included below an extract from the Apache configuration file that I've
been trying. Any advice or assistance that people might be able to provide
would be greatly appreciated, and please let me know if you'd need any
additional information from me.
Hi Harris,
Have you tried upping the logging level for mod_rewrite as suggested by Assaf
in (a)? This should tell you exactly what is and is not being matched as
Apache processes requests through those directives.
--nate
Sincerely,
Harris Shapiro
Genomic Health, Inc.
Extract from Apache configuration file:
Note: I've also tried a variant where I replaced REMOTE_USER with
AUTHENTICATE_SAMACCOUNTNAME in the various RewriteCond RequestHeader
directives. That variant produced the same error message.
Proxy http://localhost:8080
Order deny,allow
Allow from all
/Proxy
RewriteEngine on
Location /
AuthType Basic
AuthName Please log in with your Windows account
AuthBasicProvider ldap
AuthLDAPURL [Verified LDAP connection information]
AuthzLDAPAuthoritative off
AuthLDAPBindDN [Verified DN]
AuthLDAPBindPassword [Verified password]
Require valid-user
RewriteCond %{IS_SUBREQ} ^false$
RewriteCond %{LA-U:REMOTE_USER} (.+)
RewriteRule . - [E=RU:%1]
RequestHeader set REMOTE_USER %{RU}e
/Location
RewriteRule ^/static/style/(.*)
/home/hshapiro/software/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L]
RewriteRule ^/static/scripts/(.*)
/home/hshapiro/software/galaxy/galaxy-dist/static/scripts/packed/$1 [L]
RewriteRule ^/static/(.*)
/home/hshapiro/software/galaxy/galaxy-dist/static/$1 [L]
RewriteRule ^/favicon.ico
/home/hshapiro/software/galaxy/galaxy-dist/static/favicon.ico [L]
RewriteRule ^/robots.txt
/home/hshapiro/software/galaxy/galaxy-dist/static/robots.txt [L]
RewriteRule ^(.*) http://localhost:8080$1 [P]
___
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/
___
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/
Re: [galaxy-dev] how to get annotation files for rna-seq
Thanks Jeremy, Are there any resources linked with Galaxy for viral genome seq annotation ? I'm not aware of any viral genome annotations resources integrated into Galaxy, but NCBI (and others) have virus gene annotations that you upload into Galaxy and use. Best, J. ___ 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/
[galaxy-dev] No output from IGVtools tile
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 ___ 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/
