---------- 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.


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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