Hi Dave,

I was able to get galaxy back up by doing a fresh install, moving the old database folder in the new install, reconfiguring universe and job_conf, and leaving tool_conf and all shed related items to default. I also truncated the tables 'tool_dependency', tool_shed_repository and tool_version associates. Finally I removed in tool_version all entries that had a tool_shed_repository_id !== NULL.


Now I'm installing all my toolsheds again, and it's still working it seems.

If you want, I can try to make my database dump (post-error, but before truncating) available to you.

Best,

Geert

On 02/11/2014 10:56 PM, Dave Bouvier wrote:
Geert,

I have not yet been able to reproduce that error in my local Galaxy installation running on the release_2014.02.10 tag, but I am continuing to investigate. Are you able to determine which repository last succeeded in the migration script output?

   --Dave B.

On 02/11/2014 10:29 AM, Geert Vandeweyer wrote:
This message is also returned when I try to start the server without the
migrate tools script (but after the initial error).

Can I safely revert to a previous rel

Best,

Geert

On 02/11/2014 03:18 PM, Geert Vandeweyer wrote:
Hi,

I'm having problems upgrading Galaxy to the latest release. The
migrate tools script gives the following error.

No handlers could be found for logger "galaxy.tools"
Traceback (most recent call last):
  File "./scripts/migrate_tools/migrate_tools.py", line 21, in <module>
    app = MigrateToolsApplication( sys.argv[ 1 ] )
  File
"/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/migrate/common.py",
line 45, in __init__
    self.installed_repository_manager =
installed_repository_manager.InstalledRepositoryManager( self )
  File
"/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/installed_repository_manager.py",
line 66, in __init__
    self.load_dependency_relationships()
  File
"/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/installed_repository_manager.py",
line 269, in load_dependency_relationships
self.add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies(
tool_dependency )
  File
"/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/installed_repository_manager.py",
line 147, in
add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies
tool_dependency_util.get_runtime_dependent_tool_dependency_tuples(
self.app, tool_dependency, status=None )
  File
"/galaxy/galaxy-dist/lib/tool_shed/util/tool_dependency_util.py", line
323, in get_runtime_dependent_tool_dependency_tuples
    env_shell_file_path = td.get_env_shell_file_path( app )
  File
"/galaxy/galaxy-dist/lib/galaxy/model/tool_shed_install/__init__.py",
line 533, in get_env_shell_file_path
    installation_directory = self.installation_directory( app )
  File
"/galaxy/galaxy-dist/lib/galaxy/model/tool_shed_install/__init__.py",
line 548, in installation_directory
    self.tool_shed_repository.owner,
AttributeError: 'NoneType' object has no attribute 'owner'

Any help on how to resolve this?

The 0009_tools.xml content is :


<?xml version="1.0"?>
<toolshed name="toolshed.g2.bx.psu.edu">
    <repository owner="devteam" changeset_revision="96d2e31a3938"
name="bowtie2" description="Bowtie2">
        <tool id="bowtie2" version="0.2" file="bowtie2_wrapper.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="a0c8dc671a23"
name="ccat" description="Control-based ChIP-seq Analysis Tool">
        <tool id="peakcalling_ccat" version="0.0.1"
file="ccat_wrapper.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="7cc64024fe92"
name="clustalw" description="ClustalW multiple sequence alignment
program for DNA or proteins">
        <tool id="clustalw" version="0.1" file="rgClustalw.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="6708501767b6"
name="dwt_cor_ava_perclass" description="Compute P-values and
Correlation Coefficients for Feature Occurrences">
        <tool
id="compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom"
version="1.0.0" file="execute_dwt_cor_aVa_perClass.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="0f2eda4ea8dc"
name="dwt_cor_avb_all" description="Compute P-values and Correlation
Coefficients for Occurrences of Two Set of Features">
        <tool
id="compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom"
version="1.0.0" file="execute_dwt_cor_aVb_all.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="0b89b03ad760"
name="dwt_ivc_all" description="Compute P-values and Second Moments
for Feature Occurrences">
        <tool
id="compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom"
version="1.0.0" file="execute_dwt_IvC_all.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="cb422b6f49d2"
name="dwt_var_perclass" description="Compute P-values and Max
Variances for Feature Occurrences">
        <tool
id="compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom"
version="1.0.0" file="execute_dwt_var_perClass.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="d56c5d2e1a29"
name="dwt_var_perfeature" description="Wavelet variance using Discrete
Wavelet Transfoms">
        <tool id="dwt_var1" version="1.0.0"
file="execute_dwt_var_perFeature.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="7b0708761d05"
name="express" description="Quantify the abundances of a set of target
sequences from sampled subsequences">
<tool id="express" version="1.1.1" file="express_wrapper.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="e28c965eeed4"
name="fastqc" description="Read QC reports using FastQC">
        <tool id="fastqc" version="1.0.0" file="rgFastQC.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="94306bdd58f7"
name="fastq_combiner" description="Combine FASTA and QUAL into FASTQ.">
        <tool id="fastq_combiner" version="1.0.1"
file="fastq_combiner.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="30d9ece6c752"
name="fastq_filter" description="Filter FASTQ reads by quality score
and length">
        <tool id="fastq_filter" version="1.0.0"
file="fastq_filter.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="1298445c852b"
name="fastq_groomer" description="Convert between various FASTQ
quality formats.">
        <tool id="fastq_groomer" version="1.0.4"
file="fastq_groomer.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="5d1e9e13e8db"
name="fastq_manipulation" description="Manipulate FASTQ reads on
various attributes.">
        <tool id="fastq_manipulation" version="1.0.1"
file="fastq_manipulation.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="5a7b5751617b"
name="fastq_masker_by_quality" description="FASTQ Masker by quality
score">
        <tool id="fastq_masker_by_quality" version="1.0.0"
file="fastq_masker_by_quality.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="f0949bc49926"
name="fastq_paired_end_deinterlacer" description="FASTQ de-interlacer
on paired end reads.">
        <tool id="fastq_paired_end_deinterlacer" version="1.1"
file="fastq_paired_end_deinterlacer.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="b89bdf6acb6c"
name="fastq_paired_end_interlacer" description="FASTQ interlacer on
paired end reads">
        <tool id="fastq_paired_end_interlacer" version="1.1"
file="fastq_paired_end_interlacer.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="2793d1d765b9"
name="fastq_paired_end_joiner" description="FASTQ joiner on paired end
reads">
        <tool id="fastq_paired_end_joiner" version="1.0.0"
file="fastq_paired_end_joiner.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="c549e99026db"
name="fastq_paired_end_splitter" description="FASTQ splitter on joined
paired end reads">
        <tool id="fastq_paired_end_splitter" version="1.0.0"
file="fastq_paired_end_splitter.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="9b7b4e0ca9db"
name="fastq_stats" description="FASTQ Summary Statistics by column">
<tool id="fastq_stats" version="1.0.0" file="fastq_stats.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="3571553aeb20"
name="fastqtofasta" description="FASTQ to FASTA converter">
        <tool id="fastq_to_fasta_python" version="1.0.0"
file="fastq_to_fasta.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="bc9269529e88"
name="fastq_to_tabular" description="FASTQ to Tabular converter">
        <tool id="fastq_to_tabular" version="1.1.0"
file="fastq_to_tabular.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="0b9feb0ed628"
name="fastq_trimmer" description="FASTQ Trimmer by quality">
        <tool id="fastq_trimmer" version="1.0.0"
file="fastq_trimmer.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="1cdcaf5fc1da"
name="fastq_trimmer_by_quality" description="FASTQ Quality Trimmer by
sliding window">
        <tool id="fastq_quality_trimmer" version="1.0.0"
file="fastq_trimmer_by_quality.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="31154ff9f5e1"
name="filter_transcripts_via_tracking" description="Filter Combined
Transcripts">
        <tool id="filter_combined_via_tracking" version="0.1"
file="filter_transcripts_via_tracking.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="acf51ff24c7d"
name="find_diag_hits" description="Identify sequence reads
corresponding to a particular taxonomic group">
        <tool id="find_diag_hits" version="1.0.0"
file="find_diag_hits.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="33a0e6aca936"
name="freebayes_wrapper" description="Call SNPS with Freebayes">
        <tool id="freebayes_wrapper" version="0.5.0"
file="freebayes.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="7b1b03c4465d"
name="gi2taxonomy" description="Fetch taxonomic representation">
        <tool id="Fetch Taxonomic Ranks" version="1.1.0"
file="gi2taxonomy.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="2cd5ee197ec7"
name="gmaj" description="GMAJ Multiple Alignment Viewer">
        <tool id="gmaj_1" version="2.0.1" file="GMAJ.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="33e8ed5a4601"
name="lca_wrapper" description="Find lowest diagnostic rank">
        <tool id="lca1" version="1.0.1" file="lca.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="ae2ec275332a"
name="macs" description="Model-based Analysis of ChIP-Seq">
        <tool id="peakcalling_macs" version="1.0.1"
file="macs_wrapper.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="8cd5945559b8"
name="poisson2test" description="Poisson two-sample test">
        <tool id="poisson2test" version="1.0.0"
file="poisson2test.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="82a8234e03f2"
name="sicer" description="Statistical approach for the Identification
of ChIP-Enriched Regions">
        <tool id="peakcalling_sicer" version="0.0.1"
file="sicer_wrapper.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="9e2b9ca7f33a"
name="t2ps" description="Draw phylogeny">
        <tool id="Draw_phylogram" version="1.0.0"
file="t2ps_wrapper.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="592acb9505fc"
name="t2t_report" description="Summarize taxonomy">
        <tool id="t2t_report" version="1.0.0" file="t2t_report.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="b334cd1095ea"
name="tabular_to_fastq" description="Tabular to FASTQ converter">
        <tool id="tabular_to_fastq" version="1.0.0"
file="tabular_to_fastq.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="1030acbecce6"
name="tophat" description="Find splice junctions using RNA-seq data">
        <tool id="tophat" version="1.5.0" file="tophat_wrapper.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="ffa30bedbee3"
name="tophat2" description="Gapped-read mapper for RNA-seq data">
        <tool id="tophat2" version="0.6" file="tophat2_wrapper.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="b001b50f2009"
name="vcf_annotate" description="Annotate a VCF file (dbSNP, hapmap)">
        <tool id="vcf_annotate" version="1.0.0" file="annotate.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="76ad0b7865b9"
name="vcf_extract" description="Extract reads from a specified region">
        <tool id="vcf_extract" version="1.0.0" file="extract.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="da1a6f33b504"
name="vcf_filter" description="Filter a VCF file">
        <tool id="vcf_filter" version="1.0.0" file="filter.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="9d162bde4113"
name="vcf_intersect" description="Generate the intersection of two VCF
files">
        <tool id="vcf_intersect" version="1.0.0"
file="vcf_tools/intersect.xml" />
    </repository>
    <repository owner="devteam" changeset_revision="66253fc0a69b"
name="weblogo3" description="Sequence Logo generator for fasta (eg
Clustal alignments)">
        <tool id="rgweblogo3" version="0.4" file="rgWebLogo3.xml" />
    </repository>
</toolshed>


Best,

Geert





--

Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandewe...@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer

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