migrate_tools error with latest release (hg update release_2014.02.10 ) - galaxy-dev

11 Feb 2014

      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.vandeweyer@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer