Thanks!

I didn't get output before the error, so I think no tools were migrated 
successfully. I tried to strip down the XML to only hold the first tool, but 
that gave the same error. 

I hope to try a fresh install today keeping the database and all settings not 
related to toolshed ( ie copy them from the old install.) could I then 
reinstall all shed tools, or will there be conflicts from info in the MySQL 
database?

Best

Geert
________________________________________
Van: Dave Bouvier [d...@bx.psu.edu]
Verzonden: dinsdag 11 februari 2014 22:56
Aan: Vandeweyer Geert; galaxy-dev@lists.bx.psu.edu
Onderwerp: Re: [galaxy-dev] migrate_tools error with latest release (hg update 
release_2014.02.10 )

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 release somehow?
>
> 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
>>
>
>

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