---------- Forwarded message ---------- From: Tom Hait <sthait@gmail.com> Date: Wed, Oct 24, 2012 at 10:48 AM Subject: Re: [galaxy-dev] Failed to run display.py To: Scott McManus <scottmcmanus@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"><!--BODY{background-color:#ffffff;font-family:verdana,sans-serif}PRE{font-family:sans-serif}--></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@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@me.com> wrote:
On Oct 21, 2012, at 6:11 AM, Tom Hait <sthait@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
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