- galaxy-dev - lists.galaxyproject.org

How to remove a broken toolshed install
by Clare Sloggett 30 Oct '12

30 Oct '12

Hi all, I managed to break a toolshed-installed tool by fiddling with the files under shed_tools. This led to a situation in which the Galaxy admin interface claims the tool is still installed, but can't find any files for it. I manually put the repository files where I think they should go, but this didn't fix the situation, so what I really want to do is just get rid of it altogether and reinstall cleanly. I'm not certain that the tool was working properly before I fiddled with it, either. Galaxy won't let me uninstall, deactivate or update it (because it can't find it properly) and it won't let me install it (because it thinks it's installed). It also seems (judging by the last of the errors below) to be unable to find some config information that it expects, but I don't really understand what's going on there. So my question is: given a messy, screwed up install, how can I completely remove it and start from scratch? What are the different components and config files I need to remove it from and are they all manually accessible? Thanks in advance for any help! If it's relevant to my question, here are some of the behaviours I see currently: The tool appears as "Installed" under Admin -> Manage installed tool shed repositories, but doesn't show up in the tools panel. If I try Repository Actions -> Get repository updates , I get the error: The directory containing the installed repository named 'bcftools_view' cannot be found. But if I try Repository Actions -> Reset repository metadata , it apparently works, I get Metadata has been reset on repository bcftools_view. And, if I try to 'Deactivate or uninstall' the apparently-installed repository, I get: URL: http://galaxy-tut.genome.edu.au/admin_toolshed/deactivate_or_uninstall_repo… Module paste.exceptions.errormiddleware:144 in __call__ >> app_iter = self.application(environ, sr_checker) Module paste.debug.prints:106 in __call__ >> environ, self.app) Module paste.wsgilib:543 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:84 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ >> body = method( trans, **kwargs ) Module galaxy.web.framework:205 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:452 in deactivate_or_uninstall_repository >> remove_from_tool_panel( trans, tool_shed_repository, shed_tool_conf, uninstall=remove_from_disk_checked ) Module galaxy.util.shed_util:1781 in remove_from_tool_panel >> tool_panel_dict = generate_tool_panel_dict_from_shed_tool_conf_entries( trans, repository ) Module galaxy.util.shed_util:942 in generate_tool_panel_dict_from_shed_tool_conf_entries >> tree = util.parse_xml( shed_tool_conf ) Module galaxy.util:135 in parse_xml >> tree = ElementTree.parse(fname) Module elementtree.ElementTree:859 in parse Module elementtree.ElementTree:576 in parse TypeError: coercing to Unicode: need string or buffer, NoneType found Thanks, Clare -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759

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Error while uploading data from local directory
by Luciano Cosme 29 Oct '12

29 Oct '12

Howdy, I installed galaxy in a new server that I build and I am getting the following error when I try to upload the files from a local directory. Error attempting to display contents of library (A.aegypti_mRNA): (OperationalError) no such column: True u'SELECT dataset_permissions.id AS dataset_permissions_id, dataset_permissions.create_time AS dataset_permissions_create_time, dataset_permissions.update_time AS dataset_permissions_update_time, dataset_permissions.action AS dataset_permissions_action, dataset_permissions.dataset_id AS dataset_permissions_dataset_id, dataset_permissions.role_id AS dataset_permissions_role_id XnFROM dataset_permissions XnWHERE True AND dataset_permissions.action = ?' ['access']. My raw data is stored in a different hard drive and I am just linking them to Galaxy. I also changed the permissions recursively in the folder where the data is (777). Any help will be appreciated. Thank you. Luciano -- *Luciano Cosme* --------------------------------------------- PhD Candidate Texas A&M Entomology Vector Biology Research Group www.lcosme.com 979 845 1885 cosme(a)tamu.edu ---------------------------------------------

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Re: [galaxy-dev] How are jobs managed on single machine?
by Hans-Rudolf Hotz 29 Oct '12

29 Oct '12

On 10/29/2012 11:33 AM, James Vincent wrote: > Thanks very much. Sorry for the double post - my first was rejected > due to wroneg email, but I guess it made it through. > > Do you happen to know if one can query the number of jobs queued and > running? I'd like to put status monitor somewhere for regular users. I > think this will cut down on the number of emails back to me asking why > jobs are not running. :) > use the 'report tool', see: reports_wsgi.ini and run_reports.sh Hans-Rudolf > Jim > > On Mon, Oct 29, 2012 at 4:09 AM, Hans-Rudolf Hotz <hrh(a)fmi.ch> wrote: >> Hi Jim >> >> If using a standalone server, Galaxy is using its own queuing system, which >> you can modify by changing (in universe_wsgi.ini): >> >> local_job_queue_workers >> user_job_limit >> >> but the system is not aware of the memory size and number of cores. In your >> "specific example", running out of memory is probably the bigger issue..... >> >> >> Hope this helps, >> Hans-Rudolf >> >> >> On 10/26/2012 01:41 PM, James Vincent wrote: >>> >>> Hello, >>> >>> I cannot seem to find the details on how jobs are managed when Galaxy >>> is run on a standalone server. Are jobs managed in a queue of some >>> sort? Does Galaxy determine resources available in some way and >>> moderate jobs that are run? >>> >>> As a specific example, we have a 40 core machine with 1TB of memory. >>> If 10 users each submit 10 jobs each, say for a bowtie job that has >>> been set to use 8 cores, will Galaxy sort this all out and only run >>> jobs to fill the 40 cores? Are there settings to control this behavior >>> without installing an external job manager like SGE? >>> >>> Thanks, >>> Jim >>> ___________________________________________________________ >>> 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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How are jobs managed on single machine?
by James Vincent 29 Oct '12

29 Oct '12

Hello, I cannot seem to find the details on how jobs are managed when Galaxy is run on a standalone server. Are jobs managed in a queue of some sort? Does Galaxy determine resources available in some way and moderate jobs that are run? As a specific example, we have a 40 core machine with 1TB of memory. If 10 users each submit 10 jobs each, say for a bowtie job that has been set to use 8 cores, will Galaxy sort this all out and only run jobs to fill the 40 cores? Are there settings to control this behavior without installing an external job manager like SGE? Thanks, Jim

2 1

Fwd: MACS failed because of lambdaset options
by Hans-Rudolf Hotz 29 Oct '12

29 Oct '12

...moved to dalaxy-dev, since it is about your local Galaxy instances: Hi Philippe Your galaxy wrapper for MACS expects version 1.3, where the option "--lambdaset" is present. (see https://github.com/taoliu/MACS/blob/macs_v1/ChangeLog) Regards, Hans-Rudolf -------- Original Message -------- Subject: [galaxy-user] MACS failed because of lambdaset options Date: Mon, 29 Oct 2012 11:40:28 +1100 From: Philipe Moncuquet <philippe.mcqt(a)gmail.com> To: <galaxy-user(a)lists.bx.psu.edu> Hi, I am trying to use MACS and I get the following error when the job fails : Usage: macs <-t tfile> [-n name] [-g genomesize] [options] Example: macs -t ChIP.bam -c Control.bam -f BAM -g h -n test -w --call-subpeaks macs: error: no such option: --lambdaset I am not really familiar to MACS so I checked the documentation and it seems Galaxy is rigth to complain because there is no such option as --lambdaset (http://liulab.dfci.harvard.edu/MACS/README.html) I went back to the xml wrapper and there is this ( <paramname="lambdaset"type="text" ....) parameters that corresponds to the text box 3 levels of regions around the peak region to calculate the maximum lambda as local lambda: Does anyone face the same problem ? Any clue on what I should try, should I modify the wrapper ? Cheers, Philippe

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Fwd: Failed to run display.py
by Tom Hait 26 Oct '12

26 Oct '12

---------- Forwarded message ---------- From: Tom Hait <sthait(a)gmail.com> Date: Wed, Oct 24, 2012 at 10:48 AM Subject: Re: [galaxy-dev] Failed to run display.py To: Scott McManus <scottmcmanus(a)gatech.edu> Hi Scott, Thanks for the reply. I'm still having that problem and I also asked our system for help and they coulsn't help me. for that request the output is: HTTP Error 503: Service Unavailable <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" " http://www.w3.org/TR/html4/loose.dtd"> <HTML><HEAD><META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1"> <TITLE>ERROR: The requested URL could not be retrieved</TITLE> <STYLE type="text/css"></STYLE> </HEAD><BODY> <H1>ERROR</H1> <H2>The requested URL could not be retrieved</H2> <HR noshade size="1px"> <P> While trying to retrieve the URL: <A HREF=" http://localhost:8080/api/libraries?key=ff76834f42d18414b4aaed577466ef35"> http://localhost:8080/api/libraries?key=ff76834f42d18414b4aaed577466ef35</A> <P> The following error was encountered: <UL> <LI> <STRONG> Connection to *.*.*.* Failed </STRONG> </UL> <P> The system returned: <PRE><I> (111) Connection refused</I></PRE> <P> The remote host or network may be down. Please try the request again. <P>Your cache administrator is <A HREF="mailto:root">root</A>. <BR clear="all"> <HR nos instead of *.*.*.* this is my localhost. in the console of run.sh i see: r, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,160 Loaded label: Filtration galaxy.tools DEBUG 2012-10-24 10:43:34,160 Loaded tool id: gatk_variant_filtration, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,160 Loaded tool id: gatk_variant_select, version: 0.0.2 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,160 Loaded label: Variant Quality Score Recalibration galaxy.tools DEBUG 2012-10-24 10:43:34,161 Loaded tool id: gatk_variant_recalibrator, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,161 Loaded tool id: gatk_variant_apply_recalibration, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,161 Loaded label: Variant Utilities galaxy.tools DEBUG 2012-10-24 10:43:34,161 Loaded tool id: gatk_validate_variants, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,161 Loaded tool id: gatk_variant_eval, version: 0.0.8 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,161 Loaded tool id: gatk_variant_combine, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,161 Loading section: NGS: Peak Calling galaxy.tools DEBUG 2012-10-24 10:43:34,161 Loaded tool id: peakcalling_macs, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,161 Loaded tool id: peakcalling_sicer, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,161 Loaded tool id: peakcalling_ccat, version: 0.0.1 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,162 Loaded tool id: bed2genetrack, version: 1.0.1 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,162 Loaded tool id: predict2genetrack, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,162 Loading section: NGS: Simulation galaxy.tools DEBUG 2012-10-24 10:43:34,162 Loaded tool id: ngs_simulation, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,162 Loading section: SNP/WGA: Data; Filters galaxy.tools DEBUG 2012-10-24 10:43:34,162 Loaded label: Data: Import and upload galaxy.tools DEBUG 2012-10-24 10:43:34,162 Loaded tool id: upload1, version: 1.1.3 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,162 Loaded tool id: library_access1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,162 Loaded label: Data: Filter and Clean galaxy.tools DEBUG 2012-10-24 10:43:34,162 Loaded tool id: rgClean1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,163 Loaded tool id: rgPedSub1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,163 Loaded tool id: rgLDIndep1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,163 Loaded label: Simulate galaxy.tools DEBUG 2012-10-24 10:43:34,163 Loaded tool id: fakePhe1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,163 Loaded tool id: rgfakePed1, version: 0.02 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,163 Loading section: SNP/WGA: QC; LD; Plots galaxy.tools DEBUG 2012-10-24 10:43:34,163 Loaded label: QC; Eigenstrat galaxy.tools DEBUG 2012-10-24 10:43:34,163 Loaded tool id: rgQC1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,163 Loaded tool id: rgEigPCA1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,163 Loaded label: LD; Manhattan/QQ; GRR galaxy.tools DEBUG 2012-10-24 10:43:34,163 Loaded tool id: rgHaploView1, version: 0.3 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,164 Loaded tool id: rgManQQ1, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,164 Loaded tool id: rgGRR1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,164 Loading section: SNP/WGA: Statistical Models galaxy.tools DEBUG 2012-10-24 10:43:34,164 Loaded tool id: rgCaCo1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,164 Loaded tool id: rgTDT1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,164 Loaded tool id: rgGLM1, version: 0.2 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,164 Loaded tool id: rgManQQ1, version: 1.0.3 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,164 Loading section: Phenotype Association galaxy.tools DEBUG 2012-10-24 10:43:34,164 Loaded tool id: hgv_codingSnps, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,165 Loaded tool id: hgv_add_scores, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,165 Loaded tool id: hgv_sift, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,165 Loaded tool id: hgv_linkToGProfile, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,165 Loaded tool id: hgv_david, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,165 Loaded tool id: ctdBatch_1, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,165 Loaded tool id: hgv_funDo, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,165 Loaded tool id: hgv_snpFreq, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,165 Loaded tool id: hgv_ldtools, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,165 Loaded tool id: hgv_pass, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,165 Loaded tool id: hgv_gpass, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,166 Loaded tool id: hgv_beam, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,166 Loaded tool id: hgv_lps, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,166 Loaded tool id: hgv_hilbertvis, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,166 Loaded tool id: freebayes_wrapper, version: 0.5.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,166 Loaded tool id: hgv_master2pgSnp, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,166 Loaded tool id: vcf2pgSnp, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,166 Loaded tool id: dividePgSnp, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,166 Loading section: VCF Tools galaxy.tools DEBUG 2012-10-24 10:43:34,166 Loaded tool id: vcf_intersect, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,166 Loaded tool id: vcf_annotate, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,166 Loaded tool id: vcf_filter, version: 1.0.0 into tool panel. galaxy.tools DEBUG 2012-10-24 10:43:34,167 Loaded tool id: vcf_extract, version: 1.0.0 into tool panel. galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,323 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,327 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,331 Loaded display application 'igv_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,333 Loaded display application 'igb_bam' for datatype 'bam', inherit=False. galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,334 Loaded display application 'genetrack_interval' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,336 Loaded display application 'igb_bed' for datatype 'bed', inherit=False. galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,340 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,341 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False. galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,345 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,347 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False. galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,354 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True. galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,355 Loaded display application 'genetrack_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,363 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,372 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,375 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True. galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,378 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False. galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,383 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,386 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False. galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,388 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True. galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,390 Loaded display application 'igb_wig' for datatype 'wig', inherit=False. galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,393 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False. galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,393 Adding inherited display application 'ensembl_gff' to datatype 'gtf' galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,393 Adding inherited display application 'genetrack_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,394 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,394 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,394 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict' galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,394 Adding inherited display application 'genetrack_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,394 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,394 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,394 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph' galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,395 Adding inherited display application 'genetrack_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,395 Adding inherited display application 'ensembl_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,395 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,395 Adding inherited display application 'rviewer_interval' to datatype 'bed12' galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,396 Adding inherited display application 'ensembl_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,396 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed' galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,396 Adding inherited display application 'rviewer_interval' to datatype 'bed' galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,396 Adding inherited display application 'ensembl_gff' to datatype 'gff3' galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,396 Adding inherited display application 'genetrack_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,396 Adding inherited display application 'ensembl_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,396 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,396 Adding inherited display application 'rviewer_interval' to datatype 'bed6' galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,397 Adding inherited display application 'genetrack_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,397 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,397 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,397 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak' galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,406 Loaded converter: CONVERTER_Bam_Bai_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,415 Loaded converter: CONVERTER_bam_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,428 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,436 Loaded converter: CONVERTER_interval_to_coverage_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,445 Loaded converter: CONVERTER_bed_to_bgzip_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,453 Loaded converter: CONVERTER_bed_to_tabix_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,462 Loaded converter: CONVERTER_bed_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,471 Loaded converter: CONVERTER_bed_to_fli_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,480 Loaded converter: CONVERTER_bedgraph_to_bigwig galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,488 Loaded converter: CONVERTER_bed_to_genetrack_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,497 Loaded converter: CONVERTER_len_to_linecount galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,506 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,514 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,527 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,535 Loaded converter: CONVERTER_fasta_to_2bit galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,544 Loaded converter: CONVERTER_fasta_to_len galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,552 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,561 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,570 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,578 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,585 Loaded converter: CONVERTER_fastq_to_fqtoc0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,593 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,602 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,610 Loaded converter: CONVERTER_gff_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,624 Loaded converter: CONVERTER_gff_to_fli_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,633 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,642 Loaded converter: CONVERTER_gff_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,650 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,660 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,668 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,676 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,685 Loaded converter: CONVERTER_interval_to_bgzip_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,694 Loaded converter: CONVERTER_interval_to_tabix_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,702 Loaded converter: CONVERTER_interval_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,711 Loaded converter: CONVERTER_picard_interval_list_to_bed6 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,720 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,731 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,740 Loaded converter: CONVERTER_encodepeak_to_tabix_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,749 Loaded converter: CONVERTER_encodepeak_to_bgzip_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,762 Loaded converter: CONVERTER_encodepeak_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,772 Loaded converter: CONVERTER_sam_to_bam galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,783 Loaded converter: CONVERTER_sam_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,793 Loaded converter: CONVERTER_vcf_to_bgzip_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,801 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,812 Loaded converter: CONVERTER_vcf_to_tabix_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,822 Loaded converter: CONVERTER_vcf_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,831 Loaded converter: CONVERTER_wig_to_bigwig galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,833 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,842 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0 galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,856 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,865 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,874 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,885 Loaded converter: pbed2ldindepconvert galaxy.datatypes.registry DEBUG 2012-10-24 10:43:34,889 Loaded external metadata tool: __SET_METADATA__ galaxy.tools.imp_exp DEBUG 2012-10-24 10:43:34,893 Loaded history export tool: __EXPORT_HISTORY__ galaxy.tools.imp_exp DEBUG 2012-10-24 10:43:34,895 Loaded history import tool: __IMPORT_HISTORY__ galaxy.tools.genome_index DEBUG 2012-10-24 10:43:34,899 Loaded genome index tool: __GENOME_INDEX__ galaxy.jobs.runners.local INFO 2012-10-24 10:43:34,913 starting workers galaxy.jobs.runners.local DEBUG 2012-10-24 10:43:34,914 5 workers ready galaxy.jobs.handler DEBUG 2012-10-24 10:43:34,914 Loaded job runner: galaxy.jobs.runners.local:LocalJobRunner galaxy.jobs.runners.lwr INFO 2012-10-24 10:43:34,921 starting workers galaxy.jobs.runners.lwr DEBUG 2012-10-24 10:43:34,922 5 workers ready galaxy.jobs.handler DEBUG 2012-10-24 10:43:34,922 Loaded job runner: galaxy.jobs.runners.lwr:LwrJobRunner galaxy.jobs.handler DEBUG 2012-10-24 10:43:34,922 Job runners: local:lwr galaxy.jobs.handler INFO 2012-10-24 10:43:34,922 job handler stop queue started galaxy.jobs.manager INFO 2012-10-24 10:43:34,928 job manager queue started galaxy.jobs.manager INFO 2012-10-24 10:43:34,929 job manager stop queue started galaxy.jobs.handler INFO 2012-10-24 10:43:34,933 job handler queue started galaxy.sample_tracking.external_service_types DEBUG 2012-10-24 10:43:34,936 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2012-10-24 10:43:34,939 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 >>> /specific/fprivate/gaga/tomhait/galaxy-dist/lib/galaxy/webapps/galaxy/controllers ['/specific/fprivate/gaga/tomhait/galaxy-dist/lib/galaxy/webapps/galaxy/controllers'] galaxy.webapps.galaxy.controllers admin galaxy.webapps.galaxy.controllers.admin galaxy.web.framework.base DEBUG 2012-10-24 10:43:34,966 Enabling 'admin' controller, class: AdminGalaxy galaxy.webapps.galaxy.controllers admin_toolshed galaxy.webapps.galaxy.controllers.admin_toolshed galaxy.web.framework.base DEBUG 2012-10-24 10:43:34,984 Enabling 'admin_toolshed' controller, class: AdminGalaxy galaxy.web.framework.base DEBUG 2012-10-24 10:43:34,984 Enabling 'admin_toolshed' controller, class: AdminToolshed galaxy.webapps.galaxy.controllers async galaxy.webapps.galaxy.controllers.async galaxy.web.framework.base DEBUG 2012-10-24 10:43:34,988 Enabling 'async' controller, class: ASync galaxy.webapps.galaxy.controllers cloudlaunch galaxy.webapps.galaxy.controllers.cloudlaunch galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,042 Enabling 'cloudlaunch' controller, class: CloudController galaxy.webapps.galaxy.controllers data_admin galaxy.webapps.galaxy.controllers.data_admin galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,073 Enabling 'data_admin' controller, class: DataAdmin galaxy.webapps.galaxy.controllers dataset galaxy.webapps.galaxy.controllers.dataset galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,089 Enabling 'dataset' controller, class: DatasetInterface galaxy.webapps.galaxy.controllers error galaxy.webapps.galaxy.controllers.error galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,091 Enabling 'error' controller, class: Error galaxy.webapps.galaxy.controllers external_service galaxy.webapps.galaxy.controllers.external_service galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,097 Enabling 'external_service' controller, class: ExternalService galaxy.webapps.galaxy.controllers external_services galaxy.webapps.galaxy.controllers.external_services galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,100 Enabling 'external_services' controller, class: ExternalServiceController galaxy.webapps.galaxy.controllers forms galaxy.webapps.galaxy.controllers.forms galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,105 Enabling 'forms' controller, class: Forms galaxy.webapps.galaxy.controllers history galaxy.webapps.galaxy.controllers.history galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,114 Enabling 'history' controller, class: HistoryController galaxy.webapps.galaxy.controllers library galaxy.webapps.galaxy.controllers.library galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,119 Enabling 'library' controller, class: Library galaxy.webapps.galaxy.controllers library_admin galaxy.webapps.galaxy.controllers.library_admin galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,121 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.webapps.galaxy.controllers library_common galaxy.webapps.galaxy.controllers.library_common galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,122 Enabling 'library_common' controller, class: LibraryCommon galaxy.webapps.galaxy.controllers mobile galaxy.webapps.galaxy.controllers.mobile galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,124 Enabling 'mobile' controller, class: Mobile galaxy.webapps.galaxy.controllers page galaxy.webapps.galaxy.controllers.page galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,128 Enabling 'page' controller, class: PageController galaxy.webapps.galaxy.controllers phyloviz galaxy.webapps.galaxy.controllers.phyloviz galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,147 Enabling 'phyloviz' controller, class: PhyloVizController galaxy.webapps.galaxy.controllers request_type galaxy.webapps.galaxy.controllers.request_type galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,149 Enabling 'request_type' controller, class: RequestType galaxy.webapps.galaxy.controllers requests galaxy.webapps.galaxy.controllers.requests galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,152 Enabling 'requests' controller, class: Requests galaxy.webapps.galaxy.controllers requests_admin galaxy.webapps.galaxy.controllers.requests_admin galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,188 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.webapps.galaxy.controllers requests_common galaxy.webapps.galaxy.controllers.requests_common galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,189 Enabling 'requests_common' controller, class: RequestsCommon galaxy.webapps.galaxy.controllers root galaxy.webapps.galaxy.controllers.root galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,192 Enabling 'root' controller, class: RootController galaxy.webapps.galaxy.controllers tag galaxy.webapps.galaxy.controllers.tag galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,194 Enabling 'tag' controller, class: TagsController galaxy.webapps.galaxy.controllers tool_runner galaxy.webapps.galaxy.controllers.tool_runner galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,197 Enabling 'tool_runner' controller, class: ToolRunner galaxy.webapps.galaxy.controllers ucsc_proxy galaxy.webapps.galaxy.controllers.ucsc_proxy galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,199 Enabling 'ucsc_proxy' controller, class: UCSCProxy galaxy.webapps.galaxy.controllers user galaxy.webapps.galaxy.controllers.user galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,202 Enabling 'user' controller, class: User galaxy.webapps.galaxy.controllers visualization galaxy.webapps.galaxy.controllers.visualization galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,208 Enabling 'visualization' controller, class: VisualizationController galaxy.webapps.galaxy.controllers workflow galaxy.webapps.galaxy.controllers.workflow galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,304 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,316 Enabling 'datasets' API controller, class: DatasetsController galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,319 Enabling 'forms' API controller, class: FormDefinitionAPIController galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,320 Enabling 'genomes' API controller, class: GenomesController galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,322 Enabling 'group_roles' API controller, class: GroupRolesAPIController galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,324 Enabling 'group_users' API controller, class: GroupUsersAPIController galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,325 Enabling 'groups' API controller, class: GroupAPIController galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,327 Enabling 'histories' API controller, class: HistoriesController galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,338 Enabling 'history_contents' API controller, class: HistoryContentsController galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,340 Enabling 'libraries' API controller, class: LibrariesController galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,343 Enabling 'library_contents' API controller, class: LibraryContentsController galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,345 Enabling 'permissions' API controller, class: PermissionsController galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,347 Enabling 'quotas' API controller, class: QuotaAPIController galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,351 Enabling 'request_types' API controller, class: RequestTypeAPIController galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,352 Enabling 'requests' API controller, class: RequestsAPIController galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,354 Enabling 'roles' API controller, class: RoleAPIController galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,356 Enabling 'samples' API controller, class: SamplesAPIController galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,358 Enabling 'tools' API controller, class: ToolsController galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,360 Enabling 'users' API controller, class: UserAPIController galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,362 Enabling 'visualizations' API controller, class: VisualizationsController galaxy.web.framework.base DEBUG 2012-10-24 10:43:35,364 Enabling 'workflows' API controller, class: WorkflowsAPIController galaxy.webapps.galaxy.buildapp DEBUG 2012-10-24 10:43:35,535 Enabling 'httpexceptions' middleware galaxy.webapps.galaxy.buildapp DEBUG 2012-10-24 10:43:35,537 Enabling 'recursive' middleware galaxy.webapps.galaxy.buildapp DEBUG 2012-10-24 10:43:35,548 Enabling 'print debug' middleware galaxy.webapps.galaxy.buildapp DEBUG 2012-10-24 10:43:35,739 Enabling 'eval exceptions' middleware galaxy.webapps.galaxy.buildapp DEBUG 2012-10-24 10:43:35,744 Enabling 'trans logger' middleware galaxy.webapps.galaxy.buildapp DEBUG 2012-10-24 10:43:35,744 Enabling 'config' middleware galaxy.webapps.galaxy.buildapp DEBUG 2012-10-24 10:43:35,746 Enabling 'x-forwarded-host' middleware Starting server in PID 24919. serving on http://localhost:8080 Thanks for any help, Tom. On Tue, Oct 23, 2012 at 7:29 PM, Scott McManus <scottmcmanus(a)gatech.edu>wrote: > > Hi Tom- > > Are you still having this problem? If so, then could you try your request > again and return what > you're seeing from the console's logging output for that request? If not, > then anything that you may > have done to get around this problem would be appreciated. > > -Scott > > ------------------------------ > > > Hi Dannon, > > Thanks for the reply. > Galaxy is running - I just typed http://localhost:8080 on the browser and > I get the galaxy with the line: *Hello world! It's running...* > * > * > *Tom. > * > On Sun, Oct 21, 2012 at 3:55 PM, Dannon Baker <dannonbaker(a)me.com> wrote: > >> On Oct 21, 2012, at 6:11 AM, Tom Hait <sthait(a)gmail.com> wrote: >> > so I tried to change the URL to: http://localhost:8080, >> http://127.0.0.1:8080 ... >> > It also didn't work. >> > >> > Any Ideas about could go wrong? >> >> First thing I'd check would be to verify that your galaxy server is >> currently running, and on localhost:8080. >> >> -Dannon >> >> > > ___________________________________________________________ > 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/ > > >

1 0

Output file naming
by Darin 26 Oct '12

26 Oct '12

Hello, I'm new to Galaxy, and I've been asked to tweak some tools so that output file names are related to input file names. For example, an input file of myData.abc might lead to an output file named myData_afterMyTool.xyz. I think the user is really just interested in the labels showing up in the history panel, so that gives me some flexibility. In my development environment, I've changed one tool's xml file's output tag to this: <outputs> <data name="out_file1" format="bed" label="${input1}_afterTool.xyz"/> </outputs> ... and that seems to work, but it's using an internal file name, instead of the label for the input file. So - does anyone know if there's an easy way to get the label from the input file into the output label, instead of the path/dataset_n.dat file format for this name? If there's a better way to approach this, I'd love any suggestions on that, too. Thanks, Darin

5 4

How to move a history item to a data library through the API
by Anthonius deBoer 26 Oct '12

26 Oct '12

Hi, I am trying to automatically move certain outputs from my workflow into a particular folder of a particular library THROUGH THE API. I can find how to do the reverse, but can't find an example of how to do this... Is there an equivalent of passing the history ID, like you can pass the Library ID using data['from_ld_id']. I tried the 'from_hd_id' but there is nothing in the lib/galaxy/web/api*.py that looks for that, so I guess that would not work. And looking in library_content.py it is not obvious either... Thanks! Regards, Thon de Boer, Ph.D. Bioinformatics Guru +1-650-799-6839 thondeboer(a)me.com LinkedIn Profile

1 1

Creating new instance
by Scooter Willis 26 Oct '12

26 Oct '12

Following the instructions at http://wiki.g2.bx.psu.edu/CloudMan?action=show&redirect=Admin%2FCloud Setup an instance using the latest AMI and did configure it to use a password AMI: galaxy-cloudman-2012-05-10 (ami-78a00411) Waited 10+ minutes after instance is running and going to http://ec2-54-242-2-243.compute-1.amazonaws.com/ Or http://ec2-54-242-2-243.compute-1.amazonaws.com/cloud Gets a Unable to Connect message. I am able to ssh into the instance but don't have any clue where to look for error messages or what is expected to be running. >From the ssh client if I do a wget localhost I get a connection refused message. ubuntu@ip-10-80-199-13:~$ wget localhost --2012-10-26 18:05:07-- http://localhost/ Resolving localhost (localhost)... 127.0.0.1 Connecting to localhost (localhost)|127.0.0.1|:80... failed: Connection refused. I have been using Amazon EC2 for years so familiar with everything. I know just enough linux to cause more problems then I can solve!!! Any suggestions?

2 1

Tools Always Failing? (repost from gal-users)
by Yilk, Todd A 26 Oct '12

26 Oct '12

Hello all, I'm using a local install of Galaxy connected to a UGE cluster and Python 2.6.7. Most of my tools are reporting failures in the history with messages like: An error occurred running this job: (34) Job output not returned from cluster; exit status = "0" With the relevant lines from Galaxy's log file looking like: galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:31:26,586 job 34 working directory is /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34 galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:31:26,636 job 34 input = [["/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_48.dat", "fastq", "5230830"]] galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:31:26,671 (34) submitting file /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/uge/galaxy_34.sh galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:31:26,672 (34) command is: memtimepro -q -o /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/34.drmmt perl /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/tools/lanl/readMapping/fastqSplitter/separate_paired_end_reads.pl -i /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_48.dat -l /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_53.dat -r /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_54.dat ; cd /opt/galaxy/dev/Galaxy-JGI_galaxy-dev; /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/set_metadata.sh ./database/files /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34 . /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/universe_wsgi.ini /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/tmp/tmp831aRx /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/galaxy.json /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_in_HistoryDatasetAssociation_59_fpBxRp,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_kwds_HistoryDatasetAssociation_59_MLg1Aw,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_out_HistoryDatasetAssociation_59_ZVYBIT,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_results_HistoryDatasetAssociation_59_q4FpIq,,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_override_HistoryDatasetAssociation_59_3HXPLq /opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_in_HistoryDatasetAssociation_60_Qw0GpA,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_kwds_HistoryDatasetAssociation_60_ZF6Zk_,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_out_HistoryDatasetAssociation_60_eEItGr,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_results_HistoryDatasetAssociation_60_bMa6HN,,/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/job_working_directory/000/34/metadata_override_HistoryDatasetAssociation_60_X1El1z galaxy.jobs.runners.drmaa INFO 2012-10-25 10:31:26,720 (34) queued as 553774 galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:31:28,947 (34/553774) state change: job is running -- snip -- galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:32:29,411 (34/553774) state change: job finished normally 128.165.72.57 - - [25/Oct/2012:10:32:31 -0600] "POST /root/history_item_updates HTTP/1.0" 200 - "http://galaxy-dev.lanl.gov/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:15.0) Gecko/20100101 Firefox/15.0.1" galaxy.jobs.runners.drmaa DEBUG 2012-10-25 10:32:31,241 (34) Job output not returned from cluster; exit status = "0 " galaxy.jobs DEBUG 2012-10-25 10:32:31,285 The tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG 2012-10-25 10:32:31,427 setting dataset state to ERROR galaxy.jobs DEBUG 2012-10-25 10:32:31,471 setting dataset state to ERROR galaxy.jobs DEBUG 2012-10-25 10:32:31,728 job 34 ended galaxy.datatypes.metadata DEBUG 2012-10-25 10:32:31,729 Cleaning up external metadata files And yet, for this example, the tool did actually run successfully with the expected output files where they should be in the galaxy/database/files directory. Further, the 34.drmec file has just the exit code 0, the 34.drmout file is empty and the 34.drmmt file is: { "program": "perl", "arguments": [ "/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/tools/lanl/readMapping/fastqSplitter/separate_paired_end_reads.pl", "-i", "/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_48.dat", "-l", "/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_53.dat", "-r", "/opt/galaxy/dev/Galaxy-JGI_galaxy-dev/database/files/000/dataset_54.dat" ], "exit_status": 0, "start_time": 1351182686, "wall_time": 0.223, "usage": { "utime": 0.04, "stime": 0.08, "max_vmem_kb": 11920, "max_rss_kb": 156, "start_time": 1351182686, "wall_time": 0.223 } } So everything looks good to me but Galaxy is reporting a failed run. What piece am I missing? Thanks!

1 0