Hi, Marius,
I got ansible running and installed the tools on my local instance of Galaxy.
However, the tools are not shown on the tool panel on the web page. Wonder if
the tools has been installed in the wrong place, or something else is wrong.
Have been searching the Wiki and list without any resulst. Please point me to
the right directions.
Thanks,
Bill
From: Marius van den Beek [mailto:m.vandenb...@gmail.com]
Sent: Friday, March 4, 2016 12:27 PM
To: William Ge <w...@centrilliontech.com>
Cc: Dannon Baker <dannon.ba...@gmail.com>; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play
On 4 March 2016 at 20:47, William Ge
<w...@centrilliontech.com<mailto:w...@centrilliontech.com>> wrote:
Thanks a lot, Marius!
Sure, you're welcome!
I am a newbie to this complex system and want a quick clone/install locally. I
have spent over two weeks on the process. There are many configuration files
and environment variables or dependencies to sort out. I wish the sample
configuration files would include most of the options so that new installation
just needs to comment out or delete unwanted ones.
The galaxy team definitely aims for this, and usually you should (tm) be able
to clone galaxy and use run.sh to get going.
If you can tell us the steps where you were struggling we can try to update or
clarify the documentation (A lot of it is on the wiki).
Anyway, here is the error I got:
[galaxy@Pegasus ansible-galaxy-tools]$ python files/install_tool_shed_tools.py
-h
Traceback (most recent call last):
File "files/install_tool_shed_tools.py", line 49, in <module>
logging.captureWarnings(True) # Capture HTTPS warngings from urllib3
AttributeError: 'module' object has no attribute 'captureWarnings'
If I run this after activating the galaxy_env and install ensible, bioblend,
argparse and importlib, the same error came up. I guess this is Python 2.6
issue. Any solutions known?
PLAY [localhost] **************************************************************
TASK: [galaxy_tools | Copy the bootstrap user management script] **************
skipping: [localhost]
TASK: [galaxy_tools | Create Galaxy bootstrap user] ***************************
skipping: [localhost]
TASK: [galaxy_tools | Check/Set bootstrap user as Galaxy Admin if admin_users tag is already in the config file] ***
skipping: [localhost]
TASK: [galaxy_tools | Set bootstrap user as Galaxy Admin] *********************
skipping: [localhost]
TASK: [galaxy_tools | Delete Galaxy bootstrap user] ***************************
skipping: [localhost]
TASK: [galaxy_tools | Remove bootstrap user as Galaxy Admin if admin_users tag was already in the config file before bootstrap_user task] ***
skipping: [localhost]
TASK: [galaxy_tools | Remove bootstrap user as Galaxy Admin] ******************
skipping: [localhost]
TASK: [galaxy_tools | Check if Galaxy is managed by supervisor] ***************
skipping: [localhost]
TASK: [galaxy_tools | Restart Galaxy] *****************************************
skipping: [localhost]
TASK: [galaxy_tools | Stop Galaxy] ********************************************
skipping: [localhost]
TASK: [galaxy_tools | Wait for Galaxy to stop] ********************************
skipping: [localhost]
TASK: [galaxy_tools | Start Galaxy] *******************************************
skipping: [localhost]
TASK: [galaxy_tools | Wait for Galaxy to start] *******************************
skipping: [localhost]
TASK: [galaxy_tools | Remove the bootstrap user management script] ************
skipping: [localhost]
TASK: [galaxy_tools | set_fact galaxy_tools_api_key="{{ api_key.stdout_lines[0] }}"] ***
skipping: [localhost]
TASK: [galaxy_tools | Create/invoke script virtualenv] ************************
ok: [localhost] => (item=pyyaml)
ok: [localhost] => (item=bioblend)
TASK: [galaxy_tools | Place the tool management script] ***********************
changed: [localhost]
TASK: [galaxy_tools | get tool list] ******************************************
ok: [localhost]
TASK: [galaxy_tools | Install Tool Shed tools] ********************************
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'textutil', 'name': 'column_maker', 'revisions': ['08a01b2ce4cd']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'convert', 'name': 'tabular_to_fasta', 'revisions': ['0b4e36026794']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'convert', 'name': 'fasta_to_tabular', 'revisions': ['9d189d08f2ad']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'convert', 'name': 'fastqtofasta', 'revisions': ['3571553aeb20']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'filter', 'name': 'dna_filtering', 'revisions': ['a6f0d355b05f']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'group', 'name': 'subtract_query', 'revisions': ['5f6ebef89722']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastqc', 'revisions': ['8c650f7f76e9', 'e28c965eeed4']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'short_reads_trim_seq', 'revisions': ['f17a1585733b']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'short_reads_figure_score', 'revisions': ['b52b9c7aabd9']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_quality_boxplot', 'revisions': ['f95284aa2946']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_quality_converter', 'revisions': ['b87c74b61d81']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_quality_filter', 'revisions': ['57adb07cccfc']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastx_artifacts_filter', 'revisions': ['c8808979ba33']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastx_barcode_splitter', 'revisions': ['c46a5807f2b6']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastx_clipper', 'revisions': ['8192b4014977']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastx_collapser', 'revisions': ['13c2d9e8c6d5']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastx_nucleotides_distribution', 'revisions': ['9353010b95df']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastx_quality_statistics', 'revisions': ['c2af34024061']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastx_renamer', 'revisions': ['d7bce63e6e09']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastx_reverse_complement', 'revisions': ['5bd826723d61']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastx_trimmer', 'revisions': ['d77c9c6ecf68']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_combiner', 'revisions': ['94306bdd58f7']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_filter', 'revisions': ['30d9ece6c752']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_groomer', 'revisions': ['1298445c852b']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_manipulation', 'revisions': ['5d1e9e13e8db']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_masker_by_quality', 'revisions': ['5a7b5751617b']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_paired_end_joiner', 'revisions': ['270a8ed8a300']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_paired_end_splitter', 'revisions': ['c549e99026db']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_stats', 'revisions': ['9b7b4e0ca9db']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_to_tabular', 'revisions': ['bc9269529e88']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_trimmer', 'revisions': ['0b9feb0ed628']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_trimmer_by_quality', 'revisions': ['1cdcaf5fc1da']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'tabular_to_fastq', 'revisions': ['b334cd1095ea']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs_mapping', 'name': 'bowtie2', 'revisions': ['ceb6467e276c', 'c1ec08cb34f9', 'a54de7e658f7']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs_mapping', 'name': 'bwa', 'revisions': ['c71dd035971e', 'ac30bfd3e2a8']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs_mapping', 'name': 'megablast_xml_parser', 'revisions': ['03ca082aeb2e']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs_mapping', 'name': 'megablast_wrapper', 'revisions': ['dc7b4acb3fa6']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs_mapping', 'name': 'bwa_wrappers', 'revisions': ['b4427dbb6ced']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs_mapping', 'name': 'lastz', 'revisions': ['d054d95585b1']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_bam_tools', 'name': 'bamtools', 'revisions': ['76b2f1eee508']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_bam_tools', 'name': 'bamtools_filter', 'revisions': ['d64c7e752f4d']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_bam_tools', 'name': 'bamtools_split', 'revisions': ['71dd32fb0b0a']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_picard', 'name': 'picard', 'revisions': ['379fdf4c41ac']})
ok: [localhost] => (item={'owner': 'anton', 'tool_panel_section_id': 'ngs:_vcf_manipulation', 'name': 'vcfgeno2haplo', 'revisions': ['d6fd217a1f90']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_vcf_manipulation', 'name': 'vcfgeno2haplo', 'revisions': ['2bdb74ab3270']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_vcf_manipulation', 'name': 'vcfcombine', 'revisions': ['da419f5ed589']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_vcf_manipulation', 'name': 'vcffilter', 'revisions': ['34c3b846e0b6']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_vcf_manipulation', 'name': 'vcf2tsv', 'revisions': ['d6c944f1581a']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_vcf_manipulation', 'name': 'vcfallelicprimitives', 'revisions': ['3f4fefbc52c8']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_vcf_manipulation', 'name': 'vcfbreakcreatemulti', 'revisions': ['f0dae4ac267e']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_vcf_manipulation', 'name': 'vcfrandomsample', 'revisions': ['d9efe7842413']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_vcf_manipulation', 'name': 'vcfflatten', 'revisions': ['38d93ca9c0f0']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_vcf_manipulation', 'name': 'vcfselectsamples', 'revisions': ['88fd8ef7e4af']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_vcf_manipulation', 'name': 'vcfcheck', 'revisions': ['d7d4d88ae84d']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_vcf_manipulation', 'name': 'vcfgenotypes', 'revisions': ['1673e7848bf4']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_vcf_manipulation', 'name': 'vcfvcfintersect', 'revisions': ['b29dbe1270b5']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_vcf_manipulation', 'name': 'vcfhethom', 'revisions': ['586d614a4c2d']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_vcf_manipulation', 'name': 'vcfleftalign', 'revisions': ['3e3d0dffeb1f']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_vcf_manipulation', 'name': 'vcfaddinfo', 'revisions': ['4d4b16af67aa']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_vcf_manipulation', 'name': 'vcfsort', 'revisions': ['433d50620231']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_vcf_manipulation', 'name': 'vcfprimers', 'revisions': ['67a4da1a4df3']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_vcf_manipulation', 'name': 'vcfannotategenotypes', 'revisions': ['c6be83b8883d']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_vcf_manipulation', 'name': 'vcffixup', 'revisions': ['a03f346b6aae']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_vcf_manipulation', 'name': 'vcfbedintersect', 'revisions': ['8a482a9aa45d']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_vcf_manipulation', 'name': 'vcfdistance', 'revisions': ['6e0fc18309f4']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_vcf_manipulation', 'name': 'vcfcommonsamples', 'revisions': ['f27d6187d808']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'bxops', 'name': 'annotation_profiler', 'revisions': ['3b33da018e74']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'bxops', 'name': 'merge', 'revisions': ['1bc76ceffa7f']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'bxops', 'name': 'flanking_features', 'revisions': ['90100b587723']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'bxops', 'name': 'concat', 'revisions': ['855580142a12']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'bxops', 'name': 'get_flanks', 'revisions': ['4b14d0e3a837']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'bxops', 'name': 'coverage', 'revisions': ['16b62a897aac']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'bxops', 'name': 'cluster', 'revisions': ['520de69b107a']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'bxops', 'name': 'basecoverage', 'revisions': ['b8a9e718caa3']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'bxops', 'name': 'join', 'revisions': ['de21bdbb8d28']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'bxops', 'name': 'annotation_profiler', 'revisions': ['3b33da018e74']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'bxops', 'name': 'subtract', 'revisions': ['c19a2a29c561']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'bxops', 'name': 'intersect', 'revisions': ['77641d5731c8']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'bxops', 'name': 'complement', 'revisions': ['2221cf5f59aa']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'stats', 'name': 'plot_from_lda', 'revisions': ['c5ab37076128']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'stats', 'name': 'lda_analysis', 'revisions': ['f38763b52f33']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'stats', 'name': 'generate_pc_lda_matrix', 'revisions': ['04cdbd00dcec']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'stats', 'name': 'correlation', 'revisions': ['24e01abf9e34']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'plots', 'name': 'ucsc_custom_track', 'revisions': ['618e56c3109b']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'plots', 'name': 'scatterplot', 'revisions': ['c12b0759203b']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'plots', 'name': 'histogram', 'revisions': ['6ff47de059a0']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'plots', 'name': 'xy_plot', 'revisions': ['1a73a2406edc']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'plots', 'name': 'gmaj', 'revisions': ['2cd5ee197ec7']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'hgv', 'name': 'vcf2pgsnp', 'revisions': ['5fca46616675']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'hgv', 'name': 'snpfreq', 'revisions': ['72ea0d13dd66']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'hgv', 'name': 'ctd_batch', 'revisions': ['4a32700dcaa2']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'hgv', 'name': 'divide_pg_snp', 'revisions': ['f74fdfc17143']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'hgv', 'name': 'hgv_fundo', 'revisions': ['64133669255f']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'hgv', 'name': 'hgv_hilbertvis', 'revisions': ['e1a9ad05dced']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'hgv', 'name': 'freebayes_wrapper', 'revisions': ['33a0e6aca936']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'hgv', 'name': 'dgidb_annotator', 'revisions': ['c5bb987015c5']})
ok: [localhost] => (item={'owner': 'pcingola', 'tool_panel_section_id': 'snpeff', 'name': 'snpeff', 'revisions': ['c052639fa666']})
ok: [localhost] => (item={'owner': 'gregory-minevich', 'tool_panel_section_id': 'snpeff', 'name': 'check_snpeff_candidates', 'revisions': ['f20585ccbf05']})
ok: [localhost] => (item={'owner': 'aaronquinlan', 'tool_panel_section_id': 'bedtools', 'name': 'bedtools', 'revisions': ['41bba3e648d1']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'EMBOSSLite', 'name': 'emboss_5', 'revisions': ['ce22ceec214a']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'regVar', 'name': 'linear_regression', 'revisions': ['cf431604ec3e']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'regVar', 'name': 'logistic_regression_vif', 'revisions': ['bd196d7c1ca9']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'regVar', 'name': 'partialr_square', 'revisions': ['88ef41de020d']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'regVar', 'name': 'rcve', 'revisions': ['7740956d197b']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'regVar', 'name': 'substitution_rates', 'revisions': ['d1b35bcdaacc']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'regVar', 'name': 'substitutions', 'revisions': ['c54f5d0bbb58']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'regVar', 'name': 'weightedaverage', 'revisions': ['90611e86a998']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'regVar', 'name': 'canonical_correlation_analysis', 'revisions': ['9bc0c48a027f']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'regVar', 'name': 'kernel_canonical_correlation_analysis', 'revisions': ['7a092113eb8c']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'regVar', 'name': 'kernel_principal_component_analysis', 'revisions': ['e9ebd4bfbdfc']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'regVar', 'name': 'indels_3way', 'revisions': ['5ad24b81dd10']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'regVar', 'name': 'featurecounter', 'revisions': ['ac6218e2b686']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'regVar', 'name': 'getindelrates_3way', 'revisions': ['d427e5acb9ee']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'regVar', 'name': 'maf_cpg_filter', 'revisions': ['7f2a12cb047d']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'regVar', 'name': 'microsats_mutability', 'revisions': ['4aa1ee5d8510']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'regVar', 'name': 'best_regression_subsets', 'revisions': ['4f33ec73e445']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'regVar', 'name': 'getindels_2way', 'revisions': ['f1dc6f5fce6e']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'regVar', 'name': 'microsats_alignment_level', 'revisions': ['ad471b193191']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'regVar', 'name': 'windowsplitter', 'revisions': ['75abda2290cc']})
ok: [localhost] => (item={'owner': 'guru-ananda', 'tool_panel_section_id': 'regVar', 'name': 'karyotype_plot', 'revisions': ['d810aa84ee6a']})
ok: [localhost] => (item={'owner': 'guru-ananda', 'tool_panel_section_id': 'regVar', 'name': 'rhmm', 'revisions': ['38f5cd46ffd3']})
ok: [localhost] => (item={'owner': 'guru-ananda', 'tool_panel_section_id': 'regVar', 'name': 'heatmap', 'revisions': ['dbd447fcd3e4']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'fasta_manipulation', 'name': 'fasta_filter_by_length', 'revisions': ['16679a7f554a']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'fasta_manipulation', 'name': 'fasta_concatenate_by_species', 'revisions': ['717aee069681']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'fasta_manipulation', 'name': 'fasta_compute_length', 'revisions': ['1dbb5181c327']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'fasta_manipulation', 'name': 'fasta_formatter', 'revisions': ['1dbb5181c327']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'fasta_manipulation', 'name': 'fasta_nucleotide_changer', 'revisions': ['2f868bfbe9de']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'hyphy', 'name': 'mutate_snp_codon', 'revisions': ['8f0af7251167']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'clustal', 'name': 'clustalw', 'revisions': ['acf51ff24c7d']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'tax_manipulation', 'name': 'find_diag_hits', 'revisions': ['acf51ff24c7d']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'tax_manipulation', 'name': 'gi2taxonomy', 'revisions': ['7b1b03c4465d']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'tax_manipulation', 'name': 'lca_wrapper', 'revisions': ['33e8ed5a4601']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'tax_manipulation', 'name': 'poisson2test', 'revisions': ['8cd5945559b8']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'tax_manipulation', 'name': 't2ps', 'revisions': ['dee81096ec71']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'tax_manipulation', 'name': 't2t_report', 'revisions': ['592acb9505fc']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'motifs', 'name': 'weblogo3', 'revisions': ['a10f9ed463ae']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'samtools', 'name': 'bam_to_sam', 'revisions': ['af7c50162f0b', 'dc20f447c0e2']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'samtools', 'name': 'pileup_interval', 'revisions': ['a110f9d6ae24']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'samtools', 'name': 'pileup_parser', 'revisions': ['1670f0565000']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'samtools', 'name': 'sam2interval', 'revisions': ['8c737b8ddc45']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'samtools', 'name': 'sam_bitwise_flag_filter', 'revisions': ['0b2424a404d9']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'samtools', 'name': 'sam_merge', 'revisions': ['a7a49d31c5cf']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'samtools', 'name': 'sam_pileup', 'revisions': ['890d97772e2a', '95612c159681']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'samtools', 'name': 'sam_to_bam', 'revisions': ['d04d9f1c6791']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'samtools', 'name': 'samtools_flagstat', 'revisions': ['0072bf593791']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'samtools', 'name': 'samtools_mpileup', 'revisions': ['aa0ef6f0ee89', '44a18a94d7a9']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'samtools', 'name': 'samtools_rmdup', 'revisions': ['3735f950b2f5']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'samtools', 'name': 'samtool_filter2', 'revisions': ['2d4ae2f8231e']})
ok: [localhost] => (item={'owner': 'gregory-minevich', 'tool_panel_section_id': 'samtools', 'name': 'bcftools_view', 'revisions': ['6572c40a8505']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'samtools', 'name': 'samtools_slice_bam', 'revisions': ['2b474ebbfc7d', '68ba55e96489']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'samtools', 'name': 'sam_merge', 'revisions': ['1f18d80df2a5', 'a7a49d31c5cf']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'samtools', 'name': 'samtools_idxstats', 'revisions': ['87398ae795c7']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'samtools', 'name': 'samtools_bedcov', 'revisions': ['8c3472790020']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'samtools', 'name': 'samtools_calmd', 'revisions': ['1ebb4ecdc1ef']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'samtools', 'name': 'samtools_sort', 'revisions': ['a430da4f04cd']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'samtools', 'name': 'samtools_stats', 'revisions': ['0d71d9467847']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'samtools', 'name': 'samtools_split', 'revisions': ['57f3e32f809d']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'samtools', 'name': 'samtools_reheader', 'revisions': ['020e144b5f78']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'peak_calling', 'name': 'macs', 'revisions': ['ae2ec275332a']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'peak_calling', 'name': 'sicer', 'revisions': ['82a8234e03f2']})
ok: [localhost] => (item={'owner': 'blankenberg', 'tool_panel_section_id': 'variant_detection', 'name': 'naive_variant_caller', 'revisions': ['907b40517289']})
ok: [localhost] => (item={'owner': 'gregory-minevich', 'tool_panel_section_id': 'variant_detection', 'name': 'ems_variant_density_mapping', 'revisions': ['ddfef7773c2d']})
ok: [localhost] => (item={'owner': 'gregory-minevich', 'tool_panel_section_id': 'variant_detection', 'name': 'snp_mapping_using_wgs', 'revisions': ['7fb9d1e732a0']})
ok: [localhost] => (item={'owner': 'gregory-minevich', 'tool_panel_section_id': 'variant_detection', 'name': 'cloudmap_variant_discovery_mapping', 'revisions': ['c80c0aabc869']})
ok: [localhost] => (item={'owner': 'gregory-minevich', 'tool_panel_section_id': 'variant_detection', 'name': 'cloudmap_in_silico_complementation', 'revisions': ['5389dc5a0be3']})
ok: [localhost] => (item={'owner': 'nick', 'tool_panel_section_id': 'variant_detection', 'name': 'allele_counts', 'revisions': ['31361191d2d2']})
ok: [localhost] => (item={'owner': 'boris', 'tool_panel_section_id': 'variant_detection', 'name': 'getalleleseq', 'revisions': ['5a89151b5e82']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'variant_detection', 'name': 'varscan_version_2', 'revisions': ['6f8cead3dc93']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'variant_detection', 'name': 'table_annovar', 'revisions': ['091154194ce8']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'variant_detection', 'name': 'vcftools_annotate', 'revisions': ['57a6550df582']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'variant_detection', 'name': 'vcftools_slice', 'revisions': ['1363e5d4a8b8']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs-rna-tools', 'name': 'tophat2', 'revisions': ['5c5517d2a9e9', '6242cda7e278', 'ae06af1118dc']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs-rna-tools', 'name': 'cuffcompare', 'revisions': ['8e534225baa9', '8b22e9adae34', '7fb01ea4a641']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs-rna-tools', 'name': 'cufflinks', 'revisions': ['64698e16f4a6', '9aab29e159a7', '7498f5a8fe06']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs-rna-tools', 'name': 'cuffmerge', 'revisions': ['b6e3849293b1', '424d49834830', 'aa209d311ece']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs-rna-tools', 'name': 'filter_transcripts_via_tracking', 'revisions': ['31154ff9f5e1']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs-rna-tools', 'name': 'cuffdiff', 'revisions': ['4e6f043995ff', 'db57b46b05bf', '604fa75232a2', '2d6a90609943']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs-rna-tools', 'name': 'tophat_fusion_post', 'revisions': ['f83394a2c2da']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs-rna-tools', 'name': 'gffread', 'revisions': ['5f6e6582c01d']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs-rna-tools', 'name': 'cuffnorm', 'revisions': ['a26af05ac218']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs-rna-tools', 'name': 'cuffquant', 'revisions': ['5d8b9dcaf17d']})
ok: [localhost] => (item={'owner': 'iuc', 'tool_panel_section_id': 'ngs-rna-tools', 'name': 'stringtie', 'revisions': ['48b891c1c2aa']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'variants_validate', 'revisions': ['7e1ecaa64370']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'variant_select', 'revisions': ['135e8721ffc5']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'variant_recalibrator', 'revisions': ['cb7cf57397a7']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'variant_filtration', 'revisions': ['da6e2503c62d']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'variant_eval', 'revisions': ['fbca1c0956d2']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'variant_combine', 'revisions': ['1a6e16391727']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'variant_apply_recalibration', 'revisions': ['350a4d0d1678']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'variant_annotator', 'revisions': ['ae9d0a543e9b']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'unified_genotyper', 'revisions': ['66dd4d4c1743']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'realigner_target_creator', 'revisions': ['5b8eaae854da']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'print_reads', 'revisions': ['e768f4851646']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'indel_realigner', 'revisions': ['bb0beda6cf83']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'depth_of_coverage', 'revisions': ['c3f08370fc82']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'count_covariates', 'revisions': ['14e304b70425']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'analyze_covariates', 'revisions': ['738bc749f9a3']})
ok: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'table_recalibration', 'revisions': ['30e1dd77e99c']})
ok: [localhost] => (item={'owner': 'matt-shirley', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu', 'tool_panel_section_id': 'convert', 'name': 'ncbi_sra_toolkit'})
ok: [localhost] => (item={'owner': 'fubar', 'tool_shed_url': 'https://testtoolshed.g2.bx.psu.edu', 'tool_panel_section_id': 'ngs-rna-tools', 'name': 'htseq_bams_to_count_matrix'})
ok: [localhost] => (item={'owner': 'iuc', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu', 'name': 'data_manager_snpeff'})
ok: [localhost] => (item={'owner': 'devteam', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu', 'name': 'data_manager_bwa_index_builder'})
ok: [localhost] => (item={'owner': 'devteam', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu', 'name': 'data_manager_gatk_picard_index_builder'})
ok: [localhost] => (item={'owner': 'devteam', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu', 'name': 'data_manager_sam_fasta_index_builder'})
ok: [localhost] => (item={'owner': 'devteam', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu', 'name': 'data_manager_fetch_genome_dbkeys_all_fasta'})
ok: [localhost] => (item={'owner': 'devteam', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu', 'name': 'data_manager_fetch_genome_all_fasta'})
ok: [localhost] => (item={'owner': 'blankenberg', 'tool_shed_url': 'https://testtoolshed.g2.bx.psu.edu', 'name': 'data_manager_rsync_g2'})
ok: [localhost] => (item={'owner': 'devteam', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu', 'name': 'data_manager_bowtie2_index_builder'})
ok: [localhost] => (item={'owner': 'devteam', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu', 'name': 'data_manager_bwa_mem_index_builder'})
ok: [localhost] => (item={'owner': 'devteam', 'tool_shed_url': 'https://testtoolshed.g2.bx.psu.edu', 'name': 'data_manager_picard_index_builder'})
TASK: [galaxy_tools | Install Tool Shed tools] ********************************
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'textutil', 'name': 'column_maker', 'revisions': ['08a01b2ce4cd']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'convert', 'name': 'tabular_to_fasta', 'revisions': ['0b4e36026794']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'convert', 'name': 'fasta_to_tabular', 'revisions': ['9d189d08f2ad']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'convert', 'name': 'fastqtofasta', 'revisions': ['3571553aeb20']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'filter', 'name': 'dna_filtering', 'revisions': ['a6f0d355b05f']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'group', 'name': 'subtract_query', 'revisions': ['5f6ebef89722']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastqc', 'revisions': ['8c650f7f76e9', 'e28c965eeed4']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'short_reads_trim_seq', 'revisions': ['f17a1585733b']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'short_reads_figure_score', 'revisions': ['b52b9c7aabd9']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_quality_boxplot', 'revisions': ['f95284aa2946']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_quality_converter', 'revisions': ['b87c74b61d81']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_quality_filter', 'revisions': ['57adb07cccfc']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastx_artifacts_filter', 'revisions': ['c8808979ba33']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastx_barcode_splitter', 'revisions': ['c46a5807f2b6']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastx_clipper', 'revisions': ['8192b4014977']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastx_collapser', 'revisions': ['13c2d9e8c6d5']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastx_nucleotides_distribution', 'revisions': ['9353010b95df']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastx_quality_statistics', 'revisions': ['c2af34024061']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastx_renamer', 'revisions': ['d7bce63e6e09']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastx_reverse_complement', 'revisions': ['5bd826723d61']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastx_trimmer', 'revisions': ['d77c9c6ecf68']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_combiner', 'revisions': ['94306bdd58f7']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_filter', 'revisions': ['30d9ece6c752']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_groomer', 'revisions': ['1298445c852b']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_manipulation', 'revisions': ['5d1e9e13e8db']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_masker_by_quality', 'revisions': ['5a7b5751617b']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_paired_end_joiner', 'revisions': ['270a8ed8a300']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_paired_end_splitter', 'revisions': ['c549e99026db']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_stats', 'revisions': ['9b7b4e0ca9db']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_to_tabular', 'revisions': ['bc9269529e88']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_trimmer', 'revisions': ['0b9feb0ed628']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'fastq_trimmer_by_quality', 'revisions': ['1cdcaf5fc1da']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'cshl_library_information', 'name': 'tabular_to_fastq', 'revisions': ['b334cd1095ea']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs_mapping', 'name': 'bowtie2', 'revisions': ['ceb6467e276c', 'c1ec08cb34f9', 'a54de7e658f7']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs_mapping', 'name': 'bwa', 'revisions': ['c71dd035971e', 'ac30bfd3e2a8']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs_mapping', 'name': 'megablast_xml_parser', 'revisions': ['03ca082aeb2e']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs_mapping', 'name': 'megablast_wrapper', 'revisions': ['dc7b4acb3fa6']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs_mapping', 'name': 'bwa_wrappers', 'revisions': ['b4427dbb6ced']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs_mapping', 'name': 'lastz', 'revisions': ['d054d95585b1']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_bam_tools', 'name': 'bamtools', 'revisions': ['76b2f1eee508']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_bam_tools', 'name': 'bamtools_filter', 'revisions': ['d64c7e752f4d']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_bam_tools', 'name': 'bamtools_split', 'revisions': ['71dd32fb0b0a']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs:_picard', 'name': 'picard', 'revisions': ['379fdf4c41ac']})
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skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs-rna-tools', 'name': 'tophat_fusion_post', 'revisions': ['f83394a2c2da']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs-rna-tools', 'name': 'gffread', 'revisions': ['5f6e6582c01d']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs-rna-tools', 'name': 'cuffnorm', 'revisions': ['a26af05ac218']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'ngs-rna-tools', 'name': 'cuffquant', 'revisions': ['5d8b9dcaf17d']})
skipping: [localhost] => (item={'owner': 'iuc', 'tool_panel_section_id': 'ngs-rna-tools', 'name': 'stringtie', 'revisions': ['48b891c1c2aa']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'variants_validate', 'revisions': ['7e1ecaa64370']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'variant_select', 'revisions': ['135e8721ffc5']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'variant_recalibrator', 'revisions': ['cb7cf57397a7']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'variant_filtration', 'revisions': ['da6e2503c62d']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'variant_eval', 'revisions': ['fbca1c0956d2']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'variant_combine', 'revisions': ['1a6e16391727']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'variant_apply_recalibration', 'revisions': ['350a4d0d1678']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'variant_annotator', 'revisions': ['ae9d0a543e9b']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'unified_genotyper', 'revisions': ['66dd4d4c1743']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'realigner_target_creator', 'revisions': ['5b8eaae854da']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'print_reads', 'revisions': ['e768f4851646']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'indel_realigner', 'revisions': ['bb0beda6cf83']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'depth_of_coverage', 'revisions': ['c3f08370fc82']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'count_covariates', 'revisions': ['14e304b70425']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'analyze_covariates', 'revisions': ['738bc749f9a3']})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_panel_section_id': 'gatk', 'name': 'table_recalibration', 'revisions': ['30e1dd77e99c']})
skipping: [localhost] => (item={'owner': 'matt-shirley', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu', 'tool_panel_section_id': 'convert', 'name': 'ncbi_sra_toolkit'})
skipping: [localhost] => (item={'owner': 'fubar', 'tool_shed_url': 'https://testtoolshed.g2.bx.psu.edu', 'tool_panel_section_id': 'ngs-rna-tools', 'name': 'htseq_bams_to_count_matrix'})
skipping: [localhost] => (item={'owner': 'iuc', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu', 'name': 'data_manager_snpeff'})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu', 'name': 'data_manager_bwa_index_builder'})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu', 'name': 'data_manager_gatk_picard_index_builder'})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu', 'name': 'data_manager_sam_fasta_index_builder'})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu', 'name': 'data_manager_fetch_genome_dbkeys_all_fasta'})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu', 'name': 'data_manager_fetch_genome_all_fasta'})
skipping: [localhost] => (item={'owner': 'blankenberg', 'tool_shed_url': 'https://testtoolshed.g2.bx.psu.edu', 'name': 'data_manager_rsync_g2'})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu', 'name': 'data_manager_bowtie2_index_builder'})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_shed_url': 'https://toolshed.g2.bx.psu.edu', 'name': 'data_manager_bwa_mem_index_builder'})
skipping: [localhost] => (item={'owner': 'devteam', 'tool_shed_url': 'https://testtoolshed.g2.bx.psu.edu', 'name': 'data_manager_picard_index_builder'})
TASK: [galaxy_tools | Remove tool management script] **************************
changed: [localhost]
TASK: [galaxy_tools | Create/invoke script virtualenv] ************************
skipping: [localhost] => (item=pyyaml)
skipping: [localhost] => (item=bioblend)
TASK: [galaxy_tools | Place the tool management script] ***********************
skipping: [localhost]
TASK: [galaxy_tools | Copy workflows] *****************************************
skipping: [localhost]
TASK: [galaxy_tools | Install workflows] **************************************
skipping: [localhost]
TASK: [galaxy_tools | Remove workflow script] *********************************
skipping: [localhost]
TASK: [galaxy_tools | Copy the bootstrap user management script] **************
skipping: [localhost]
TASK: [galaxy_tools | Create Galaxy bootstrap user] ***************************
skipping: [localhost]
TASK: [galaxy_tools | Check/Set bootstrap user as Galaxy Admin if admin_users tag is already in the config file] ***
skipping: [localhost]
TASK: [galaxy_tools | Set bootstrap user as Galaxy Admin] *********************
skipping: [localhost]
TASK: [galaxy_tools | Delete Galaxy bootstrap user] ***************************
skipping: [localhost]
TASK: [galaxy_tools | Remove bootstrap user as Galaxy Admin if admin_users tag was already in the config file before bootstrap_user task] ***
skipping: [localhost]
TASK: [galaxy_tools | Remove bootstrap user as Galaxy Admin] ******************
skipping: [localhost]
TASK: [galaxy_tools | Check if Galaxy is managed by supervisor] ***************
skipping: [localhost]
TASK: [galaxy_tools | Restart Galaxy] *****************************************
skipping: [localhost]
TASK: [galaxy_tools | Stop Galaxy] ********************************************
skipping: [localhost]
TASK: [galaxy_tools | Wait for Galaxy to stop] ********************************
skipping: [localhost]
TASK: [galaxy_tools | Start Galaxy] *******************************************
skipping: [localhost]
TASK: [galaxy_tools | Wait for Galaxy to start] *******************************
skipping: [localhost]
TASK: [galaxy_tools | Remove the bootstrap user management script] ************
skipping: [localhost]
TASK: [galaxy_tools | set_fact galaxy_tools_api_key="{{ api_key.stdout_lines[0] }}"] ***
skipping: [localhost]
PLAY RECAP ********************************************************************
localhost : ok=7 changed=2 unreachable=0 failed=0
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