# Notebook from AndreasSko/planemo
Path: docs/notebooks/cwl.ipynb

<code>
!pip install planemoYou are using pip version 6.1.1, however version 7.1.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Requirement already satisfied (use --upgrade to upgrade): planemo in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages/planemo-0.18.2.dev0-py2.7.egg
Requirement already satisfied (use --upgrade to upgrade): Click in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from planemo)
Requirement already satisfied (use --upgrade to upgrade): six in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from planemo)
Requirement already satisfied (use --upgrade to upgrade): pyyaml in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from planemo)
Requirement already satisfied (use --upgrade to upgrade): jinja2 in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from planemo)
Requirement already satisfied (use --upgrade to upgrade): docutils in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from planemo)
Requirement already satisfied (use --upgrade to upgrade): PyGithub in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages/PyGithub-1.25.2-py2.7.egg (from planemo)
Requirement already satisfied (use --upgrade to upgrade): bioblend in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from planemo)
Requirement already satisfied (use --upgrade to upgrade): glob2 in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from planemo)
Requirement already satisfied (use --upgrade to upgrade): cwltool in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages/cwltool-1.0.20151026181844-py2.7.egg (from planemo)
Requirement already satisfied (use --upgrade to upgrade): markupsafe in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from jinja2->planemo)
Requirement already satisfied (use --upgrade to upgrade): requests>=1.1.0 in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from bioblend->planemo)
Requirement already satisfied (use --upgrade to upgrade): poster in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from bioblend->planemo)
Requirement already satisfied (use --upgrade to upgrade): boto>=2.9.7 in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from bioblend->planemo)
Requirement already satisfied (use --upgrade to upgrade): rdflib>=4.2.0 in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from cwltool->planemo)
Requirement already satisfied (use --upgrade to upgrade): rdflib-jsonld>=0.3.0 in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages/rdflib_jsonld-0.3-py2.7.egg (from cwltool->planemo)
Requirement already satisfied (use --upgrade to upgrade): shellescape in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages/shellescape-3.4.1-py2.7.egg (from cwltool->planemo)
Requirement already satisfied (use --upgrade to upgrade): schema-salad>=1.0.4 in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages/schema_salad-1.0.4-py2.7.egg (from cwltool->planemo)
Requirement already satisfied (use --upgrade to upgrade): isodate in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from rdflib>=4.2.0->cwltool->planemo)
Requirement already satisfied (use --upgrade to upgrade): pyparsing in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from rdflib>=4.2.0->cwltool->planemo)
Requirement already satisfied (use --upgrade to upgrade): SPARQLWrapper in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from rdflib>=4.2.0->cwltool->planemo)
Requirement already satisfied (use --upgrade to upgrade): html5lib in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from rdflib>=4.2.0->cwltool->planemo)
Requirement already satisfied (use --upgrade to upgrade): avro in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from schema-salad>=1.0.4->cwltool->planemo)
Requirement already satisfied (use --upgrade to upgrade): mistune in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages/mistune-0.7.1-py2.7.egg (from schema-salad>=1.0.4->cwltool->planemo)
!planemo project_init --template cwl_draft2_specwget -q --recursive -O - 'https://codeload.github.com/galaxyproject/planemo/tar.gz/master' | tar  -C /tmp/tmpnesC3S -zxf - --strip-components=2
ls '/tmp/tmpnesC3S'
appliance.rst
bioblend.py
bootstrap_history.py
bwa
categories.py
cli.py
commands
commands.rst
commands_to_rst.py
commit_version.py
conduct.rst
config.py
configuration.rst
conf.py
contributing.rst
cwl
cwl2script
cwl_draft2_spec
cwl-runner
data
demo
developing.rst
galaxy
galaxy_config.py
galaxy_run.py
galaxy_serve.py
galaxy_test
github_util.py
git.py
glob.py
history.rst
images
index.rst
__init__.py
installation.rst
io.py
linters
lint.py
make.bat
Makefile
modules.rst
network_util.py
new_version.py
notebooks
options.py
organization.rst
other_docs.rst
package_bwa_0_7_7
package_samtools_0.1.16
package_seqtk_1_0_r75
planemo.commands.rst
planemo.cwl.rst
planemo_ext.cwl2script.rst
planemo_ext.galaxy.jobs.metrics.collectl.rst
planemo_ext.galaxy.jobs.metrics.instrumenters.rst
planemo_ext.galaxy.jobs.metrics.rst
planemo_ext.galaxy.jobs.rst
planemo_ext.galaxy.objectstore.rst
planemo_ext.galaxy.rst
planemo_ext.galaxy.tools.deps.resolvers.rst
planemo_ext.galaxy.tools.deps.rst
planemo_ext.galaxy.tools.linters.rst
planemo_ext.galaxy.tools.rst
planemo_ext.galaxy.util.rst
planemo_ext.rst
planemo.galaxy_test.rst
planemo.linters.rst
planemo_logo.png
planemo.reports.rst
planemo.rst
planemo.shed2tap.rst
planemo.shed.rst
planemo.xml.rst
pre-commit-lint
pre-commit-lint-and-test
publishing.rst
README
readme.rst
reports
repository_dependencies_shed.xml
repository_dependencies.xml
scripts
setup.py
shed
shed2tap
shed_app.py
shed_app_test_utils.py
shed_lint.py
templates.py
test_build_and_lint.py
test_cmd_serve.py
test_cmd_shed_serve.py
test_config_init.py
test_cwl_run.py
test_dependency_script.py
test_galaxy_serve.py
test_galaxy_test.py
test_git.py
test_init_and_test.py
test_lint.py
test_normalize.py
test_planemo.py
test_shed_create.py
test_shed_diff.py
test_shed_diff_xml.py
test_shed_download.py
test_shed_expansion.py
test_shed_init.py
test_shed_lint.py
test_shed_operations.py
test_shed.py
test_shed_test.py
test_shed_upload.py
test_utils.py
test_validation.py
test_xml_diff.py
tool_builder.py
tool_dependencies_good_1.xml
tool_dependencies_good_2.xml
tool_factory_2
tool_lint.py
tools.py
travis_test.sh
update_extern.sh
update_planemo_recipe.bash
update_report_assets.sh
Vagrantfile
writing
writing_advanced.rst
writing_appliance.rst
_writing_collections.rst
_writing_conclusion.rst
writing_how_do_i.rst
_writing_intro.rst
_writing_parameters.rst
_writing_publish_intro.rst
writing.rst
_writing_scripts.rst
writing_standalone.rst
_writing_suites.rst
_writing_test_and_serve_appliance.rst
_writing_test_and_serve.rst
_writing_testing.rst
xml
xml_bad_1.xml
xml_good_1.xml
xml_good_2.xml
xsd_command.xsd
xsd_schema_1.xsd
mv '/tmp/tmpnesC3S/cwl_draft2_spec'/* '/home/john/workspace/planemo/docs/notebooks'
mv '/tmp/tmpnesC3S/cwl_draft2_spec'/.* '/home/john/workspace/planemo/docs/notebooks'
mv: cannot move ‘/tmp/tmpnesC3S/cwl_draft2_spec/.’ to ‘/home/john/workspace/planemo/docs/notebooks/.’: Device or resource busy
mv: cannot move ‘/tmp/tmpnesC3S/cwl_draft2_spec/..’ to ‘/home/john/workspace/planemo/docs/notebooks/..’: Device or resource busy
lsadd-lines-wf.cwl*      count-lines8-wf.cwl*  scatter-job2.json
basics.ipynb           count-lines9-wf.cwl*  scatter-wf1.cwl
binding-test.cwl*      cwl.ipynb             scatter-wf2.cwl
bwa-mem-job.json       echo-tool.cwl         scatter-wf3.cwl
bwa-mem-tool.cwl*      empty.json            scatter-wf4.cwl
cat1-tool.cwl*         env-job.json          search.cwl
cat2-tool.cwl*         env-tool1.cwl         search-job.json
cat3-tool.cwl*         env-tool2.cwl         search.py*
cat4-tool.cwl*         env-wf1.cwl           seqtk_seq.xml
cat5-tool.cwl*         env-wf2.cwl           sorttool.cwl
cat-job.json           hello.txt             template-tool.cwl*
cat-n-job.json         index.py*             test-data/
count-lines1-wf.cwl*   node-engine.cwl       tmap-job.json
count-lines2-wf.cwl*   number.txt            tmap-tool.cwl*
count-lines3-job.json  parseInt-job.json     underscore.js
count-lines3-wf.cwl*   parseInt-tool.cwl*    wc2-tool.cwl*
count-lines4-job.json  rename.cwl            wc3-tool.cwl
count-lines4-wf.cwl*   rename-job.json       wc-job.json
count-lines5-wf.cwl*   revsort.cwl           wc-tool.cwl*
count-lines6-job.json  revsort-job.json      whale.txt
count-lines6-wf.cwl*   revtool.cwl
count-lines7-wf.cwl*   scatter-job1.json
!planemo serve --cwl cat3-tool.cwlStarting galaxy with command [/home/john/workspace/galaxy/run.sh --server-name 'planemo18130' --reload]
Activating virtualenv at /home/john/workspace/galaxy/.venv
Ignoring indexes: https://pypi.python.org/simple
/home/john/workspace/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:90: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
  InsecurePlatformWarning
Requirement already up-to-date: pip in ./.venv/lib/python2.7/site-packages
Requirement already satisfied (use --upgrade to upgrade): Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2))
Requirement already satisfied (use --upgrade to upgrade): bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3))
Requirement already satisfied (use --upgrade to upgrade): MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4))
Requirement already satisfied (use --upgrade to upgrade): PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5))
Requirement already satisfied (use --upgrade to upgrade): SQLAlchemy==1.0.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 6))
Requirement already satisfied (use --upgrade to upgrade): mercurial==3.5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7))
Requirement already satisfied (use --upgrade to upgrade): numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8))
Requirement already satisfied (use --upgrade to upgrade): pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9))
Requirement already satisfied (use --upgrade to upgrade): python-lzo==1.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 10))
Requirement already satisfied (use --upgrade to upgrade): pysam==0.8.3+gx1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 13))
Requirement already satisfied (use --upgrade to upgrade): Paste==1.7.5.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16))
Requirement already satisfied (use --upgrade to upgrade): PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17))
Requirement already satisfied (use --upgrade to upgrade): docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18))
Requirement already satisfied (use --upgrade to upgrade): wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19))
Requirement already satisfied (use --upgrade to upgrade): repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20))
Requirement already satisfied (use --upgrade to upgrade): Routes==2.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21))
Requirement already satisfied (use --upgrade to upgrade): WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22))
Requirement already satisfied (use --upgrade to upgrade): WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23))
Requirement already satisfied (use --upgrade to upgrade): Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24))
Requirement already satisfied (use --upgrade to upgrade): pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25))
Requirement already satisfied (use --upgrade to upgrade): Babel==2.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26))
Requirement already satisfied (use --upgrade to upgrade): Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27))
Requirement already satisfied (use --upgrade to upgrade): bioblend==0.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30))
Requirement already satisfied (use --upgrade to upgrade): boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31))
Requirement already satisfied (use --upgrade to upgrade): requests==2.8.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 32))
Requirement already satisfied (use --upgrade to upgrade): WebError==0.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35))
Requirement already satisfied (use --upgrade to upgrade): Pygments==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36))
Requirement already satisfied (use --upgrade to upgrade): kombu==3.0.26 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 39))
Requirement already satisfied (use --upgrade to upgrade): amqp==1.4.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40))
Requirement already satisfied (use --upgrade to upgrade): anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41))
Requirement already satisfied (use --upgrade to upgrade): sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 44))
Requirement already satisfied (use --upgrade to upgrade): decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45))
Requirement already satisfied (use --upgrade to upgrade): Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 46))
Requirement already satisfied (use --upgrade to upgrade): sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 47))
Requirement already satisfied (use --upgrade to upgrade): pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48))
Requirement already satisfied (use --upgrade to upgrade): six==1.9.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49))
Requirement already satisfied (use --upgrade to upgrade): Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 50))
Requirement already satisfied (use --upgrade to upgrade): nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51))
Requirement already satisfied (use --upgrade to upgrade): SVGFig==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 52))
Requirement already satisfied (use --upgrade to upgrade): Fabric==1.10.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 55))
Requirement already satisfied (use --upgrade to upgrade): paramiko==1.15.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 56))
Requirement already satisfied (use --upgrade to upgrade): ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 57))
Requirement already satisfied (use --upgrade to upgrade): Whoosh==2.4.1+gx1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 64))
Requirement already satisfied (use --upgrade to upgrade): Markdown>=2.0.1 in ./.venv/lib/python2.7/site-packages (from Cheetah==2.4.4->-r requirements.txt (line 2))
Requirement already satisfied (use --upgrade to upgrade): requests-toolbelt in ./.venv/lib/python2.7/site-packages (from bioblend==0.6.1->-r requirements.txt (line 30))
Activating virtualenv at /home/john/workspace/galaxy/.venv
Starting subprocess with file monitor
python path is: /home/john/workspace/galaxy/lib, /home/john/workspace/galaxy/.venv/lib/python2.7, /home/john/workspace/galaxy/.venv/lib/python2.7/plat-x86_64-linux-gnu, /home/john/workspace/galaxy/.venv/lib/python2.7/lib-tk, /home/john/workspace/galaxy/.venv/lib/python2.7/lib-old, /home/john/workspace/galaxy/.venv/lib/python2.7/lib-dynload, /usr/lib/python2.7, /usr/lib/python2.7/plat-x86_64-linux-gnu, /usr/lib/python2.7/lib-tk, /home/john/workspace/galaxy/.venv/local/lib/python2.7/site-packages
No handlers could be found for logger "galaxy.config"
galaxy.queue_worker INFO 2015-11-03 11:17:35,619 Initalizing main Galaxy Queue Worker on sqlalchemy+sqlite://
tool_shed.tool_shed_registry DEBUG 2015-11-03 11:17:35,664 Loading references to tool sheds from /tmp/tmpV60k0e/tool_sheds_conf.xml
tool_shed.tool_shed_registry DEBUG 2015-11-03 11:17:35,665 Loaded reference to tool shed: Target Shed
galaxy.app DEBUG 2015-11-03 11:17:35,667 Using "galaxy.ini" config file: /tmp/tmpV60k0e/galaxy.ini
migrate.versioning.repository DEBUG 2015-11-03 11:17:35,733 Loading repository lib/galaxy/model/migrate...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,735 Loading script lib/galaxy/model/migrate/versions/0001_initial_tables.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,735 Script lib/galaxy/model/migrate/versions/0001_initial_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,735 Loading script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,735 Script lib/galaxy/model/migrate/versions/0002_metadata_file_table.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,735 Loading script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,736 Script lib/galaxy/model/migrate/versions/0003_security_and_libraries.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,736 Loading script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,736 Script lib/galaxy/model/migrate/versions/0004_indexes_and_defaults.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,736 Loading script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,736 Script lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,736 Loading script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,736 Script lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,736 Loading script lib/galaxy/model/migrate/versions/0007_sharing_histories.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,737 Script lib/galaxy/model/migrate/versions/0007_sharing_histories.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,737 Loading script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,737 Script lib/galaxy/model/migrate/versions/0008_galaxy_forms.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,737 Loading script lib/galaxy/model/migrate/versions/0009_request_table.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,737 Script lib/galaxy/model/migrate/versions/0009_request_table.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,737 Loading script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,737 Script lib/galaxy/model/migrate/versions/0010_hda_display_at_authz_table.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,737 Loading script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,737 Script lib/galaxy/model/migrate/versions/0011_v0010_mysql_index_fix.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,738 Loading script lib/galaxy/model/migrate/versions/0012_user_address.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,738 Script lib/galaxy/model/migrate/versions/0012_user_address.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,738 Loading script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,738 Script lib/galaxy/model/migrate/versions/0013_change_lib_item_templates_to_forms.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,738 Loading script lib/galaxy/model/migrate/versions/0014_pages.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,738 Script lib/galaxy/model/migrate/versions/0014_pages.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,738 Loading script lib/galaxy/model/migrate/versions/0015_tagging.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,738 Script lib/galaxy/model/migrate/versions/0015_tagging.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,738 Loading script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,739 Script lib/galaxy/model/migrate/versions/0016_v0015_mysql_index_fix.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,739 Loading script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,739 Script lib/galaxy/model/migrate/versions/0017_library_item_indexes.py loaded successfully
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migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,757 Loading script lib/galaxy/model/migrate/versions/0093_add_job_params_col.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,757 Script lib/galaxy/model/migrate/versions/0093_add_job_params_col.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,757 Loading script lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,757 Script lib/galaxy/model/migrate/versions/0094_add_job_handler_col.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,758 Loading script lib/galaxy/model/migrate/versions/0095_hda_subsets.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,758 Script lib/galaxy/model/migrate/versions/0095_hda_subsets.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,758 Loading script lib/galaxy/model/migrate/versions/0096_openid_provider.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,758 Script lib/galaxy/model/migrate/versions/0096_openid_provider.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,758 Loading script lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,758 Script lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,758 Loading script lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,758 Script lib/galaxy/model/migrate/versions/0098_genome_index_tool_data_table.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,759 Loading script lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,759 Script lib/galaxy/model/migrate/versions/0099_add_tool_dependency_table.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,759 Loading script lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,759 Script lib/galaxy/model/migrate/versions/0100_alter_tool_dependency_table_version_column.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,759 Loading script lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,759 Script lib/galaxy/model/migrate/versions/0101_drop_installed_changeset_revision_column.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,759 Loading script lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,759 Script lib/galaxy/model/migrate/versions/0102_add_tool_dependency_status_columns.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,759 Loading script lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,760 Script lib/galaxy/model/migrate/versions/0103_add_tool_shed_repository_status_columns.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,760 Loading script lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,760 Script lib/galaxy/model/migrate/versions/0104_update_genome_downloader_job_parameters.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,760 Loading script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,760 Script lib/galaxy/model/migrate/versions/0105_add_cleanup_event_table.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,760 Loading script lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,760 Script lib/galaxy/model/migrate/versions/0106_add_missing_indexes.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,760 Loading script lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,760 Script lib/galaxy/model/migrate/versions/0107_add_exit_code_to_job_and_task.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,761 Loading script lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,761 Script lib/galaxy/model/migrate/versions/0108_add_extended_metadata.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,761 Loading script lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,761 Script lib/galaxy/model/migrate/versions/0109_add_repository_dependency_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,761 Loading script lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,761 Script lib/galaxy/model/migrate/versions/0110_add_dataset_uuid.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,761 Loading script lib/galaxy/model/migrate/versions/0111_add_job_destinations.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,761 Script lib/galaxy/model/migrate/versions/0111_add_job_destinations.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,762 Loading script lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,762 Script lib/galaxy/model/migrate/versions/0112_add_data_manager_history_association_and_data_manager_job_association_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,762 Loading script lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,762 Script lib/galaxy/model/migrate/versions/0113_update_migrate_tools_table.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,762 Loading script lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,762 Script lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,762 Loading script lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,762 Script lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,762 Loading script lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,763 Script lib/galaxy/model/migrate/versions/0116_drop_update_available_col_add_tool_shed_status_col.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,763 Loading script lib/galaxy/model/migrate/versions/0117_add_user_activation.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,763 Script lib/galaxy/model/migrate/versions/0117_add_user_activation.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,763 Loading script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,763 Script lib/galaxy/model/migrate/versions/0118_add_hda_extended_metadata.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,763 Loading script lib/galaxy/model/migrate/versions/0119_job_metrics.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,763 Script lib/galaxy/model/migrate/versions/0119_job_metrics.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,764 Loading script lib/galaxy/model/migrate/versions/0120_dataset_collections.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,764 Script lib/galaxy/model/migrate/versions/0120_dataset_collections.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,764 Loading script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,764 Script lib/galaxy/model/migrate/versions/0121_workflow_uuids.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,764 Loading script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,764 Script lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,764 Loading script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,764 Script lib/galaxy/model/migrate/versions/0123_add_workflow_request_tables.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,764 Loading script lib/galaxy/model/migrate/versions/0124_job_state_history.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,765 Script lib/galaxy/model/migrate/versions/0124_job_state_history.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,765 Loading script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,765 Script lib/galaxy/model/migrate/versions/0125_workflow_step_tracking.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,765 Loading script lib/galaxy/model/migrate/versions/0126_password_reset.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,765 Script lib/galaxy/model/migrate/versions/0126_password_reset.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,765 Loading script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,765 Script lib/galaxy/model/migrate/versions/0127_output_collection_adjustments.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,765 Loading script lib/galaxy/model/migrate/versions/0128_session_timeout.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,765 Script lib/galaxy/model/migrate/versions/0128_session_timeout.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,766 Loading script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,766 Script lib/galaxy/model/migrate/versions/0129_job_external_output_metadata_validity.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,766 Loading script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,766 Script lib/galaxy/model/migrate/versions/0130_change_pref_datatype.py loaded successfully
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,766 Loading script lib/galaxy/model/migrate/versions/0131_initial_cwl_state.py...
migrate.versioning.script.base DEBUG 2015-11-03 11:17:35,766 Script lib/galaxy/model/migrate/versions/0131_initial_cwl_state.py loaded successfully
migrate.versioning.repository DEBUG 2015-11-03 11:17:35,766 Repository lib/galaxy/model/migrate loaded successfully
migrate.versioning.repository DEBUG 2015-11-03 11:17:35,766 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'Galaxy'), ('version_table', 'migrate_version'), ('required_dbs', '[]')]))])
galaxy.model.migrate.check INFO 2015-11-03 11:17:35,833 Migrating 127 -> 128...
galaxy.model.migrate.check INFO 2015-11-03 11:17:36,619
galaxy.model.migrate.check INFO 2015-11-03 11:17:36,620 Migration script to add session update time (used for timeouts)
galaxy.model.migrate.check INFO 2015-11-03 11:17:36,620
galaxy.model.migrate.check INFO 2015-11-03 11:17:36,620
galaxy.model.migrate.check INFO 2015-11-03 11:17:36,620 Migrating 128 -> 129...
galaxy.model.migrate.check INFO 2015-11-03 11:17:37,493
galaxy.model.migrate.check INFO 2015-11-03 11:17:37,493 Migration script to allow invalidation of job external output metadata temp files
galaxy.model.migrate.check INFO 2015-11-03 11:17:37,493
galaxy.model.migrate.check INFO 2015-11-03 11:17:37,493
galaxy.model.migrate.check INFO 2015-11-03 11:17:37,493 Migrating 129 -> 130...
galaxy.model.migrate.check INFO 2015-11-03 11:17:38,527
galaxy.model.migrate.check INFO 2015-11-03 11:17:38,527 Migration script to change the value column of user_preference from varchar to text.
galaxy.model.migrate.check INFO 2015-11-03 11:17:38,527
galaxy.model.migrate.check INFO 2015-11-03 11:17:38,527
galaxy.model.migrate.check INFO 2015-11-03 11:17:38,528 Migrating 130 -> 131...
galaxy.model.migrate.check INFO 2015-11-03 11:17:39,837
galaxy.model.migrate.check INFO 2015-11-03 11:17:39,838 Migration script to allow invalidation of job external output metadata temp files
galaxy.model.migrate.check INFO 2015-11-03 11:17:39,838
galaxy.model.migrate.check INFO 2015-11-03 11:17:39,838
galaxy.config INFO 2015-11-03 11:17:39,903 Install database targetting Galaxy's database configuration.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,089 Loading datatypes from ./config/datatypes_conf.xml
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,090 Retrieved datatype module galaxy.datatypes.oxli:Count from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,090 Retrieved datatype module galaxy.datatypes.oxli:Presence from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,091 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,091 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,093 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,093 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,093 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,093 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,093 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,094 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,094 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,094 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,094 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,095 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,095 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,096 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,096 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,096 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,096 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,096 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,097 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,098 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,098 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,099 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,099 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,099 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,099 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,099 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,100 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,100 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,100 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,100 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,100 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,101 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,101 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,101 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,101 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,101 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,102 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,102 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,102 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,102 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,102 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,103 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,103 Retrieved datatype module galaxy.datatypes.images:Html from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,104 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,104 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,105 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,105 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,105 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,106 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,107 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,107 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,107 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,108 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,108 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,109 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,109 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,109 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,110 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,110 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,110 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,110 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,111 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,111 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,111 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,112 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,112 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,112 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,113 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,113 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,113 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,114 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,114 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,115 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,115 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,115 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,116 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,116 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,116 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,117 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,117 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,117 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,117 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,118 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,118 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,118 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,118 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,119 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,119 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,119 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,120 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,120 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,120 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,121 Retrieved datatype module galaxy.datatypes.images:Image from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,121 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,121 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,122 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,122 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,122 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,123 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,123 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,123 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,124 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,124 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,124 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,125 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,125 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,125 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,126 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,126 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,126 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,127 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,127 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,128 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,131 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,146 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,147 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,148 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,148 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,151 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,152 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,152 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,152 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,153 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,153 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,154 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,154 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,154 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,155 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,155 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,157 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,157 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,157 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,158 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,165 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,166 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,166 Retrieved datatype module galaxy.datatypes.graph:Rdf from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,166 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,166 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,167 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,167 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,168 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,168 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,169 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,169 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,170 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,170 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,171 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,173 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,173 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,174 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,174 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,176 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,176 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,180 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,180 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,181 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,182 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,182 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,182 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,183 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,183 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,186 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,188 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,190 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,191 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,191 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,192 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,192 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,193 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,195 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,197 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,197 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,197 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,198 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,199 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,200 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,204 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,204 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,204 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,205 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,205 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,206 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,206 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,207 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,207 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,209 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,210 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,210 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,211 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,213 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,213 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,220 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,220 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,221 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,221 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,222 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,222 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,222 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,223 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,223 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,224 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,224 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,224 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,225 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,225 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,226 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,226 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,227 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,227 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,227 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,231 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,232 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,232 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,233 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,233 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,234 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,234 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,234 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,238 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,246 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,247 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,247 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,248 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,248 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,249 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,249 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,250 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,250 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,251 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,251 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,253 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,253 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,254 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,259 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,260 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,261 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,261 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,261 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,262 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,262 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,262 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,262 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,262 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,267 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,269 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,270 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,270 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,271 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,271 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,271 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,271 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,272 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,272 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,272 Loaded sniffer for datatype 'galaxy.datatypes.images:Html'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,272 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,272 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,273 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,273 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,277 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,278 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,278 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,278 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,278 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,279 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,279 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,279 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,279 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,280 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,280 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,280 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,280 Loaded sniffer for datatype 'galaxy.datatypes.text:Json'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,280 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,281 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,281 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,281 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,281 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,282 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,282 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,282 Loaded sniffer for datatype 'galaxy.datatypes.images:Png'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,282 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,282 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,283 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,283 Loaded sniffer for datatype 'galaxy.datatypes.images:Im'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,283 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,283 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,283 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,284 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,284 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,284 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,284 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,285 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,285 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,285 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,285 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,289 Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt with display sites: main,test,archaea,ucla
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,290 Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,290 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,290 Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,290 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,290 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt
galaxy.tools.data DEBUG 2015-11-03 11:17:40,334 Loaded tool data table 'ccat_configurations'
galaxy.tools.data DEBUG 2015-11-03 11:17:40,335 Loaded tool data table 'all_fasta'
galaxy.tools.data DEBUG 2015-11-03 11:17:40,336 Loaded tool data table 'blastdb'
galaxy.tools.data DEBUG 2015-11-03 11:17:40,336 Loaded tool data table 'blastdb_p'
galaxy.tools.data DEBUG 2015-11-03 11:17:40,337 Loaded tool data table 'blastdb_d'
galaxy.jobs WARNING 2015-11-03 11:17:40,588 Job configuration "./job_conf.xml" does not exist, using legacy job configuration from Galaxy config file "/tmp/tmpV60k0e/galaxy.ini" instead
galaxy.jobs DEBUG 2015-11-03 11:17:40,588 Loading job configuration from /tmp/tmpV60k0e/galaxy.ini
galaxy.jobs DEBUG 2015-11-03 11:17:40,588 Done loading job configuration
beaker.container DEBUG 2015-11-03 11:17:40,608 data file /tmp/tmpV60k0e/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache
galaxy.tools.toolbox.watcher INFO 2015-11-03 11:17:40,609 Failed to load ToolWatcher (watchdog is likely unavailable) - proceeding without tool monitoring.
galaxy.tools.toolbox.base INFO 2015-11-03 11:17:40,609 Parsing the tool configuration /tmp/tmpV60k0e/tool_conf.xml
galaxy.tools.toolbox.base DEBUG 2015-11-03 11:17:40,623 Loaded tool id: upload1, version: 1.1.4 into tool panel..
galaxy.tools.parser.factory INFO 2015-11-03 11:17:40,624 Loading CWL tool - this is experimental - tool likely will not function in future at least in same way.
galaxy.tools.parser.cwl WARNING 2015-11-03 11:17:42,797 TOOL ID is cat3-tool
galaxy.tools.toolbox.base DEBUG 2015-11-03 11:17:42,798 Loaded tool id: cat3-tool, version: 0.0.1 into tool panel..
galaxy.tools.toolbox.base INFO 2015-11-03 11:17:42,798 Parsing the tool configuration /tmp/tmpV60k0e/shed_tool_conf.xml
galaxy.tools.toolbox.base INFO 2015-11-03 11:17:42,798 Parsing the tool configuration /tmp/tmpV60k0e/empty_tool_conf.xml
galaxy.tools.deps WARNING 2015-11-03 11:17:42,799 Path '/tmp/tmpV60k0e/deps' does not exist, ignoring
galaxy.tools.deps WARNING 2015-11-03 11:17:42,799 Path '/tmp/tmpV60k0e/deps' is not directory, ignoring
galaxy.tools.deps DEBUG 2015-11-03 11:17:42,800 Unable to find config file './dependency_resolvers_conf.xml'
galaxy.tools.search DEBUG 2015-11-03 11:17:42,892 Starting to build toolbox index.
galaxy.tools.search DEBUG 2015-11-03 11:17:43,127 Toolbox index finished.
galaxy.tools.data_manager.manager WARNING 2015-11-03 11:17:43,143 Could not determine tool shed repository from database. This should only ever happen when running tests.
galaxy.tools.data_manager.manager DEBUG 2015-11-03 11:17:43,153 Loaded Data Manager: toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/data_manager/fetch_genome_all_fasta/0.0.1
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,158 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,160 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.display_applications.application ERROR 2015-11-03 11:17:43,163 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes".
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,163 Loaded display application 'igv_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,164 Loaded display application 'igb_bam' for datatype 'bam', inherit=False.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,165 Loaded display application 'igb_bed' for datatype 'bed', inherit=False.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,166 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,170 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,171 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,175 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,176 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,186 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True.
galaxy.datatypes.display_applications.application ERROR 2015-11-03 11:17:43,188 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes".
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,189 Loaded display application 'igv_gff' for datatype 'gff', inherit=True.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,190 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,200 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,215 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,217 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True.
galaxy.datatypes.display_applications.application ERROR 2015-11-03 11:17:43,219 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes".
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,220 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,223 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,228 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False.
galaxy.datatypes.display_applications.application ERROR 2015-11-03 11:17:43,231 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes".
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,231 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,233 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,234 Loaded display application 'igb_wig' for datatype 'wig', inherit=False.
galaxy.datatypes.display_applications.application ERROR 2015-11-03 11:17:43,237 Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes".
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,237 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False.
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,238 Adding inherited display application 'ensembl_gff' to datatype 'gtf'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,238 Adding inherited display application 'igv_gff' to datatype 'gtf'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,238 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,238 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,238 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,239 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,240 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,240 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,240 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,240 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,240 Adding inherited display application 'ensembl_interval' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,240 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,241 Adding inherited display application 'rviewer_interval' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,241 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,242 Adding inherited display application 'ensembl_interval' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,242 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,242 Adding inherited display application 'rviewer_interval' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,242 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,244 Adding inherited display application 'ensembl_interval' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,244 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,244 Adding inherited display application 'rviewer_interval' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,244 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,245 Adding inherited display application 'ensembl_gff' to datatype 'gff3'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,245 Adding inherited display application 'igv_gff' to datatype 'gff3'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,246 Adding inherited display application 'ensembl_interval' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,246 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,247 Adding inherited display application 'rviewer_interval' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,247 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,247 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,247 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,247 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,247 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,250 Loaded converter: CONVERTER_Bam_Bai_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,252 Loaded converter: CONVERTER_bam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,254 Loaded converter: CONVERTER_bed_to_gff_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,256 Loaded converter: CONVERTER_bed_to_bgzip_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,259 Loaded converter: CONVERTER_bed_to_tabix_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,261 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,264 Loaded converter: CONVERTER_bed_to_fli_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,266 Loaded converter: CONVERTER_bedgraph_to_bigwig
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,269 Loaded converter: CONVERTER_len_to_linecount
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,271 Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,273 Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,275 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,277 Loaded converter: CONVERTER_fasta_to_tabular
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,280 Loaded converter: CONVERTER_fasta_to_bowtie_base_index
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,282 Loaded converter: CONVERTER_fasta_to_bowtie_color_index
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,285 Loaded converter: CONVERTER_fasta_to_2bit
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,287 Loaded converter: CONVERTER_fasta_to_len
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,289 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,291 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,293 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,295 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,298 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,300 Loaded converter: CONVERTER_gff_to_bed_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,301 Loaded converter: CONVERTER_gff_to_interval_index_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,304 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,306 Loaded converter: CONVERTER_gff_to_fli_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,307 Loaded converter: CONVERTER_gff_to_interval_index_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,310 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,312 Loaded converter: CONVERTER_interval_to_bed_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,315 Loaded converter: CONVERTER_interval_to_bedstrict_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,317 Loaded converter: CONVERTER_interval_to_bed6_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,319 Loaded converter: CONVERTER_interval_to_bed12_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,321 Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,324 Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,326 Loaded converter: CONVERTER_interval_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,328 Loaded converter: CONVERTER_picard_interval_list_to_bed6
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,331 Loaded converter: CONVERTER_maf_to_fasta_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,333 Loaded converter: CONVERTER_maf_to_interval_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,335 Loaded converter: CONVERTER_encodepeak_to_tabix_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,337 Loaded converter: CONVERTER_encodepeak_to_bgzip_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,339 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,340 Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,342 Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,346 Loaded converter: CONVERTER_sam_to_bam
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,349 Loaded converter: CONVERTER_sam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,351 Loaded converter: tabular_to_dbnsfp
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,352 Loaded converter: CONVERTER_vcf_to_bgzip_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,354 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,356 Loaded converter: CONVERTER_vcf_to_tabix_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,358 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,360 Loaded converter: CONVERTER_wig_to_bigwig
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,362 Loaded converter: CONVERTER_wiggle_to_interval_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,364 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,366 Loaded converter: lped2fpedconvert
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,369 Loaded converter: lped2pbedconvert
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,370 Loaded converter: pbed2lpedconvert
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,372 Loaded converter: pbed2ldindepconvert
galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,375 Loaded external metadata tool: __SET_METADATA__
galaxy.tools.imp_exp DEBUG 2015-11-03 11:17:43,377 Loaded history export tool: __EXPORT_HISTORY__
galaxy.tools.imp_exp DEBUG 2015-11-03 11:17:43,379 Loaded history import tool: __IMPORT_HISTORY__
galaxy.web.base.pluginframework INFO 2015-11-03 11:17:43,382 VisualizationsRegistry, loaded plugin: charts
galaxy.visualization.plugins.config_parser INFO 2015-11-03 11:17:43,383 Visualizations plugin disabled: Circster. Skipping...
galaxy.web.base.pluginframework INFO 2015-11-03 11:17:43,385 VisualizationsRegistry, loaded plugin: graphview
galaxy.visualization.plugins.config_parser INFO 2015-11-03 11:17:43,386 template syntax is deprecated: use entry_point instead
galaxy.web.base.pluginframework INFO 2015-11-03 11:17:43,386 VisualizationsRegistry, loaded plugin: graphviz
galaxy.web.base.pluginframework INFO 2015-11-03 11:17:43,388 VisualizationsRegistry, loaded plugin: phyloviz
galaxy.web.base.pluginframework INFO 2015-11-03 11:17:43,390 VisualizationsRegistry, loaded plugin: scatterplot
galaxy.visualization.plugins.config_parser INFO 2015-11-03 11:17:43,391 Visualizations plugin disabled: Sweepster. Skipping...
galaxy.web.base.pluginframework INFO 2015-11-03 11:17:43,393 VisualizationsRegistry, loaded plugin: trackster
galaxy.jobs.manager DEBUG 2015-11-03 11:17:43,398 Starting job handler
galaxy.jobs INFO 2015-11-03 11:17:43,398 Handler 'main' will load all configured runner plugins
galaxy.jobs.runners.state_handler_factory DEBUG 2015-11-03 11:17:43,400 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit
galaxy.jobs.runners DEBUG 2015-11-03 11:17:43,400 Starting 5 LocalRunner workers
galaxy.jobs DEBUG 2015-11-03 11:17:43,401 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local'
galaxy.jobs DEBUG 2015-11-03 11:17:43,402 Legacy destination with id 'local:///', url 'local:///' converted, got params:
galaxy.jobs.handler DEBUG 2015-11-03 11:17:43,402 Loaded job runners plugins: local
galaxy.jobs.handler INFO 2015-11-03 11:17:43,402 job handler stop queue started
galaxy.jobs.handler INFO 2015-11-03 11:17:43,436 job handler queue started
galaxy.sample_tracking.external_service_types DEBUG 2015-11-03 11:17:43,439 Loaded external_service_type: Simple unknown sequencer 1.0.0
galaxy.sample_tracking.external_service_types DEBUG 2015-11-03 11:17:43,442 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0
galaxy.workflow.scheduling_manager DEBUG 2015-11-03 11:17:43,453 Starting workflow schedulers
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,466 Enabling 'external_service' controller, class: ExternalService
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,466 Enabling 'requests_common' controller, class: RequestsCommon
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,487 Enabling 'library_common' controller, class: LibraryCommon
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,490 Enabling 'visualization' controller, class: VisualizationController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,492 Enabling 'page' controller, class: PageController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,493 Enabling 'async' controller, class: ASync
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,500 Enabling 'forms' controller, class: Forms
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,508 Enabling 'history' controller, class: HistoryController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,510 Enabling 'user' controller, class: User
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,516 Enabling 'library_admin' controller, class: LibraryAdmin
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,520 Enabling 'requests' controller, class: Requests
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,520 Enabling 'mobile' controller, class: Mobile
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,521 Enabling 'biostar' controller, class: BiostarController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,526 Enabling 'workflow' controller, class: WorkflowController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,582 Enabling 'admin_toolshed' controller, class: AdminGalaxy
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,583 Enabling 'admin_toolshed' controller, class: AdminToolshed
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,583 Enabling 'search' controller, class: SearchController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,583 Enabling 'library' controller, class: Library
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,585 Enabling 'requests_admin' controller, class: RequestsAdmin
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,586 Enabling 'data_manager' controller, class: DataManager
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,586 Enabling 'userskeys' controller, class: User
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,587 Enabling 'tag' controller, class: TagsController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,591 Enabling 'dataset' controller, class: DatasetInterface
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,592 Enabling 'root' controller, class: RootController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,593 Enabling 'tool_runner' controller, class: ToolRunner
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,594 Enabling 'request_type' controller, class: RequestType
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,594 Enabling 'error' controller, class: Error
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,594 Enabling 'external_services' controller, class: ExternalServiceController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,594 Enabling 'admin' controller, class: AdminGalaxy
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,597 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,597 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,598 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,598 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,599 Enabling 'visualizations' API controller, class: VisualizationsController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,599 Enabling 'jobs' API controller, class: JobController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,600 Enabling 'request_types' API controller, class: RequestTypeAPIController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,601 Enabling 'forms' API controller, class: FormDefinitionAPIController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,601 Enabling 'group_roles' API controller, class: GroupRolesAPIController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,602 Enabling 'authenticate' API controller, class: AuthenticationController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,602 Enabling 'group_users' API controller, class: GroupUsersAPIController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,603 Enabling 'roles' API controller, class: RoleAPIController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,603 Enabling 'pages' API controller, class: PagesController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,605 Enabling 'configuration' API controller, class: ConfigurationController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,606 Enabling 'workflows' API controller, class: WorkflowsAPIController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,607 Enabling 'samples' API controller, class: SamplesAPIController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,607 Enabling 'users' API controller, class: UserAPIController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,608 Enabling 'requests' API controller, class: RequestsAPIController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,609 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,609 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,609 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,610 Enabling 'genomes' API controller, class: GenomesController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,612 Enabling 'lda_datasets' API controller, class: LibraryDatasetsController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,612 Enabling 'folders' API controller, class: FoldersController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,613 Enabling 'job_files' API controller, class: JobFilesAPIController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,614 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,628 Enabling 'search' API controller, class: SearchController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,629 Enabling 'history_contents' API controller, class: HistoryContentsController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,630 Enabling 'page_revisions' API controller, class: PageRevisionsController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,631 Enabling 'library_contents' API controller, class: LibraryContentsController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,631 Enabling 'quotas' API controller, class: QuotaAPIController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,632 Enabling 'datatypes' API controller, class: DatatypesController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,632 Enabling 'datasets' API controller, class: DatasetsController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,633 Enabling 'groups' API controller, class: GroupAPIController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,633 Enabling 'folder_contents' API controller, class: FolderContentsController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,634 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,635 Enabling 'tools' API controller, class: ToolsController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,635 Enabling 'tool_data' API controller, class: ToolData
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,636 Enabling 'histories' API controller, class: HistoriesController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,637 Enabling 'libraries' API controller, class: LibrariesController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,638 Enabling 'metrics' API controller, class: MetricsController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,639 Enabling 'remote_files' API controller, class: RemoteFilesAPIController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,640 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,640 Enabling 'history_tags' API controller, class: HistoryTagsController
galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,640 Enabling 'workflow_tags' API controller, class: WorkflowTagsController
galaxy.webapps.galaxy.buildapp DEBUG 2015-11-03 11:17:44,276 Enabling 'httpexceptions' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2015-11-03 11:17:44,277 Enabling 'recursive' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2015-11-03 11:17:44,281 Enabling 'error' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2015-11-03 11:17:44,282 Enabling 'trans logger' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2015-11-03 11:17:44,283 Enabling 'x-forwarded-host' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2015-11-03 11:17:44,283 Enabling 'Request ID' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2015-11-03 11:17:44,290 added url, path to static middleware: /plugins/visualizations/charts/static, ./config/plugins/visualizations/charts/static
galaxy.webapps.galaxy.buildapp DEBUG 2015-11-03 11:17:44,290 added url, path to static middleware: /plugins/visualizations/graphview/static, ./config/plugins/visualizations/graphview/static
galaxy.webapps.galaxy.buildapp DEBUG 2015-11-03 11:17:44,290 added url, path to static middleware: /plugins/visualizations/graphviz/static, ./config/plugins/visualizations/graphviz/static
galaxy.webapps.galaxy.buildapp DEBUG 2015-11-03 11:17:44,290 added url, path to static middleware: /plugins/visualizations/scatterplot/static, ./config/plugins/visualizations/scatterplot/static
galaxy.queue_worker INFO 2015-11-03 11:17:44,291 Binding and starting galaxy control worker for main
Starting server in PID 7761.
serving on http://127.0.0.1:9991
/home/john/workspace/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:565: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage.
  'storage.' % (dialect.name, dialect.driver))
127.0.0.1 - - [03/Nov/2015:11:17:47 +0100] "GET / HTTP/1.1" 200 - "http://localhost:8889/notebooks/cwl.ipynb" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/42.0.2311.135 Safari/537.36"
127.0.0.1 - - [03/Nov/2015:11:17:48 +0100] "GET /root/welcome HTTP/1.1" 302 - "http://127.0.0.1:9991/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/42.0.2311.135 Safari/537.36"
127.0.0.1 - - [03/Nov/2015:11:17:48 +0100] "GET /api/genomes HTTP/1.1" 200 - "http://127.0.0.1:9991/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/42.0.2311.135 Safari/537.36"
127.0.0.1 - - [03/Nov/2015:11:17:48 +0100] "GET /api/datatypes?extension_only=False& HTTP/1.1" 200 - "http://127.0.0.1:9991/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/42.0.2311.135 Safari/537.36"
127.0.0.1 - - [03/Nov/2015:11:17:48 +0100] "GET /history/current_history_json HTTP/1.1" 200 - "http://127.0.0.1:9991/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/42.0.2311.135 Safari/537.36"
127.0.0.1 - - [03/Nov/2015:11:17:51 +0100] "GET /api/tools/cat3-tool/build HTTP/1.1" 200 - "http://127.0.0.1:9991/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/42.0.2311.135 Safari/537.36"
galaxy.tools.actions.upload_common INFO 2015-11-03 11:18:20,908 tool upload1 created job id 1
galaxy.tools.execute DEBUG 2015-11-03 11:18:21,060 Tool [upload1] created job [1] (670.783 ms)
127.0.0.1 - - [03/Nov/2015:11:18:20 +0100] "POST /api/tools HTTP/1.1" 200 - "http://127.0.0.1:9991/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/42.0.2311.135 Safari/537.36"
127.0.0.1 - - [03/Nov/2015:11:18:21 +0100] "GET /api/histories/2891970512fa2d5a/contents HTTP/1.1" 200 - "http://127.0.0.1:9991/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/42.0.2311.135 Safari/537.36"
galaxy.jobs DEBUG 2015-11-03 11:18:21,736 (1) Working directory for job is: /tmp/tmpV60k0e/job_working_directory/000/1
galaxy.jobs.handler DEBUG 2015-11-03 11:18:21,743 (1) Dispatching to local runner
galaxy.jobs DEBUG 2015-11-03 11:18:21,951 (1) Persisting job destination (destination id: local:///)
galaxy.jobs.runners DEBUG 2015-11-03 11:18:22,024 Job [1] queued (280.634 ms)
galaxy.jobs.handler INFO 2015-11-03 11:18:22,037 (1) Job dispatched
galaxy.tools.deps DEBUG 2015-11-03 11:18:22,382 Building dependency shell command for dependency 'samtools'
galaxy.tools.deps WARNING 2015-11-03 11:18:22,386 Failed to resolve dependency on 'samtools', ignoring
galaxy.jobs.runners DEBUG 2015-11-03 11:18:22,678 (1) command is: python /home/john/workspace/galaxy/tools/data_source/upload.py /home/john/workspace/galaxy /tmp/tmpV60k0e/tmp/tmpMIgT_R /tmp/tmpV60k0e/tmp/tmpsEkU9y 1:/tmp/tmpV60k0e/job_working_directory/000/1/dataset_1_files:/tmp/tmpV60k0e/files/000/dataset_1.dat; return_code=$?; python "/tmp/tmpV60k0e/job_working_directory/000/1/set_metadata_bXNElE.py" "/tmp/tmpV60k0e/tmp/tmpMIgT_R" "/tmp/tmpV60k0e/job_working_directory/000/1/galaxy.json" "/tmp/tmpV60k0e/job_working_directory/000/1/metadata_in_HistoryDatasetAssociation_1_Z9ZGn_,/tmp/tmpV60k0e/job_working_directory/000/1/metadata_kwds_HistoryDatasetAssociation_1_PjqGQ0,/tmp/tmpV60k0e/job_working_directory/000/1/metadata_out_HistoryDatasetAssociation_1_xDEMpC,/tmp/tmpV60k0e/job_working_directory/000/1/metadata_results_HistoryDatasetAssociation_1_2jF5l3,/tmp/tmpV60k0e/files/000/dataset_1.dat,/tmp/tmpV60k0e/job_working_directory/000/1/metadata_override_HistoryDatasetAssociation_1_OwuHPJ" 5242880; sh -c "exit $return_code"
galaxy.jobs.runners.local DEBUG 2015-11-03 11:18:22,699 (1) executing job script: /tmp/tmpV60k0e/job_working_directory/000/1/galaxy_1.sh
galaxy.jobs DEBUG 2015-11-03 11:18:22,757 (1) Persisting job destination (destination id: local:///)
127.0.0.1 - - [03/Nov/2015:11:18:25 +0100] "GET /api/histories/2891970512fa2d5a/contents HTTP/1.1" 200 - "http://127.0.0.1:9991/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/42.0.2311.135 Safari/537.36"
galaxy.jobs.runners.local DEBUG 2015-11-03 11:18:25,626 execution finished: /tmp/tmpV60k0e/job_working_directory/000/1/galaxy_1.sh
galaxy.datatypes.metadata DEBUG 2015-11-03 11:18:25,983 loading metadata from file for: HistoryDatasetAssociation 1
galaxy.jobs DEBUG 2015-11-03 11:18:26,411 job 1 ended (finish() executed in (785.504 ms))
127.0.0.1 - - [03/Nov/2015:11:18:29 +0100] "GET /api/histories/2891970512fa2d5a/contents HTTP/1.1" 200 - "http://127.0.0.1:9991/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/42.0.2311.135 Safari/537.36"
127.0.0.1 - - [03/Nov/2015:11:18:29 +0100] "GET /api/histories/2891970512fa2d5a HTTP/1.1" 200 - "http://127.0.0.1:9991/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/42.0.2311.135 Safari/537.36"
127.0.0.1 - - [03/Nov/2015:11:18:40 +0100] "GET /api/tools/cat3-tool/build HTTP/1.1" 200 - "http://127.0.0.1:9991/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/42.0.2311.135 Safari/537.36"
galaxy.tools.actions INFO 2015-11-03 11:18:41,590 Handled output (285.044 ms)
galaxy.tools.actions INFO 2015-11-03 11:18:41,859 Verified access to datasets (13.535 ms)
galaxy.tools.execute DEBUG 2015-11-03 11:18:41,942 Tool [cat3-tool] created job [2] (649.957 ms)
127.0.0.1 - - [03/Nov/2015:11:18:41 +0100] "POST /api/tools HTTP/1.1" 200 - "http://127.0.0.1:9991/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/42.0.2311.135 Safari/537.36"
127.0.0.1 - - [03/Nov/2015:11:18:42 +0100] "GET /api/histories/2891970512fa2d5a/contents HTTP/1.1" 200 - "http://127.0.0.1:9991/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/42.0.2311.135 Safari/537.36"
galaxy.jobs DEBUG 2015-11-03 11:18:42,686 (2) Working directory for job is: /tmp/tmpV60k0e/job_working_directory/000/2
galaxy.jobs.handler DEBUG 2015-11-03 11:18:42,693 (2) Dispatching to local runner
galaxy.jobs DEBUG 2015-11-03 11:18:42,916 (2) Persisting job destination (destination id: local:///)
galaxy.jobs.runners DEBUG 2015-11-03 11:18:42,971 Job [2] queued (277.979 ms)
galaxy.jobs.handler INFO 2015-11-03 11:18:43,011 (2) Job dispatched
galaxy.tools INFO 2015-11-03 11:18:43,368 exec_before_job for CWL tool
galaxy.tools INFO 2015-11-03 11:18:43,370 CwlTool.exec_before_job() generated command_line cat /tmp/tmpV60k0e/files/000/dataset_1.dat> "output.txt"
galaxy.jobs.runners DEBUG 2015-11-03 11:18:43,653 (2) command is: cat /tmp/tmpV60k0e/files/000/dataset_1.dat> "output.txt"; return_code=$?; python /tmp/tmpV60k0e/job_working_directory/000/2/relocate_dynamic_outputs_WZDe1X.py; if [ -f /tmp/tmpV60k0e/job_working_directory/000/2/__cwl_output_output_file ] ; then cp /tmp/tmpV60k0e/job_working_directory/000/2/__cwl_output_output_file /tmp/tmpV60k0e/files/000/dataset_2.dat ; fi; python "/tmp/tmpV60k0e/job_working_directory/000/2/set_metadata_C2_lE7.py" "/tmp/tmpV60k0e/tmp/tmpMIgT_R" "/tmp/tmpV60k0e/job_working_directory/000/2/galaxy.json" "/tmp/tmpV60k0e/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_cgadyy,/tmp/tmpV60k0e/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_3g4bLI,/tmp/tmpV60k0e/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_fKUEBl,/tmp/tmpV60k0e/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_X7G32P,/tmp/tmpV60k0e/files/000/dataset_2.dat,/tmp/tmpV60k0e/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_LGVdAs" 5242880; sh -c "exit $return_code"
galaxy.jobs.runners.local DEBUG 2015-11-03 11:18:43,667 (2) executing job script: /tmp/tmpV60k0e/job_working_directory/000/2/galaxy_2.sh
galaxy.jobs DEBUG 2015-11-03 11:18:43,733 (2) Persisting job destination (destination id: local:///)
127.0.0.1 - - [03/Nov/2015:11:18:46 +0100] "GET /api/histories/2891970512fa2d5a/contents HTTP/1.1" 200 - "http://127.0.0.1:9991/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/42.0.2311.135 Safari/537.36"
galaxy.jobs.runners.local DEBUG 2015-11-03 11:18:49,008 execution finished: /tmp/tmpV60k0e/job_working_directory/000/2/galaxy_2.sh
galaxy.datatypes.metadata DEBUG 2015-11-03 11:18:49,203 loading metadata from file for: HistoryDatasetAssociation 2
galaxy.jobs DEBUG 2015-11-03 11:18:49,530 job 2 ended (finish() executed in (522.083 ms))
127.0.0.1 - - [03/Nov/2015:11:18:50 +0100] "GET /api/histories/2891970512fa2d5a/contents HTTP/1.1" 200 - "http://127.0.0.1:9991/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/42.0.2311.135 Safari/537.36"
127.0.0.1 - - [03/Nov/2015:11:18:50 +0100] "GET /api/histories/2891970512fa2d5a HTTP/1.1" 200 - "http://127.0.0.1:9991/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/42.0.2311.135 Safari/537.36"
^C^C caught in monitor process

Aborted!

!planemo cwl_run cat3-tool.cwl cat-job.jsonStarting galaxy with command [/home/john/workspace/galaxy/run.sh --daemon --wait]
Activating virtualenv at /home/john/workspace/galaxy/.venv
Ignoring indexes: https://pypi.python.org/simple
/home/john/workspace/galaxy/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:90: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
  InsecurePlatformWarning
Requirement already up-to-date: pip in ./.venv/lib/python2.7/site-packages
Requirement already satisfied (use --upgrade to upgrade): Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2))
Requirement already satisfied (use --upgrade to upgrade): bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3))
Requirement already satisfied (use --upgrade to upgrade): MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4))
Requirement already satisfied (use --upgrade to upgrade): PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5))
Requirement already satisfied (use --upgrade to upgrade): SQLAlchemy==1.0.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 6))
Requirement already satisfied (use --upgrade to upgrade): mercurial==3.5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7))
Requirement already satisfied (use --upgrade to upgrade): numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8))
Requirement already satisfied (use --upgrade to upgrade): pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9))
Requirement already satisfied (use --upgrade to upgrade): python-lzo==1.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 10))
Requirement already satisfied (use --upgrade to upgrade): pysam==0.8.3+gx1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 13))
Requirement already satisfied (use --upgrade to upgrade): Paste==1.7.5.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16))
Requirement already satisfied (use --upgrade to upgrade): PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17))
Requirement already satisfied (use --upgrade to upgrade): docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18))
Requirement already satisfied (use --upgrade to upgrade): wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19))
Requirement already satisfied (use --upgrade to upgrade): repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20))
Requirement already satisfied (use --upgrade to upgrade): Routes==2.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21))
Requirement already satisfied (use --upgrade to upgrade): WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22))
Requirement already satisfied (use --upgrade to upgrade): WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23))
Requirement already satisfied (use --upgrade to upgrade): Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24))
Requirement already satisfied (use --upgrade to upgrade): pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25))
Requirement already satisfied (use --upgrade to upgrade): Babel==2.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26))
Requirement already satisfied (use --upgrade to upgrade): Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27))
Requirement already satisfied (use --upgrade to upgrade): bioblend==0.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30))
Requirement already satisfied (use --upgrade to upgrade): boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31))
Requirement already satisfied (use --upgrade to upgrade): requests==2.8.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 32))
Requirement already satisfied (use --upgrade to upgrade): WebError==0.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35))
Requirement already satisfied (use --upgrade to upgrade): Pygments==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36))
Requirement already satisfied (use --upgrade to upgrade): kombu==3.0.26 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 39))
Requirement already satisfied (use --upgrade to upgrade): amqp==1.4.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40))
Requirement already satisfied (use --upgrade to upgrade): anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41))
Requirement already satisfied (use --upgrade to upgrade): sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 44))
Requirement already satisfied (use --upgrade to upgrade): decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45))
Requirement already satisfied (use --upgrade to upgrade): Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 46))
Requirement already satisfied (use --upgrade to upgrade): sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 47))
Requirement already satisfied (use --upgrade to upgrade): pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48))
Requirement already satisfied (use --upgrade to upgrade): six==1.9.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49))
Requirement already satisfied (use --upgrade to upgrade): Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 50))
Requirement already satisfied (use --upgrade to upgrade): nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51))
Requirement already satisfied (use --upgrade to upgrade): SVGFig==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 52))
Requirement already satisfied (use --upgrade to upgrade): Fabric==1.10.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 55))
Requirement already satisfied (use --upgrade to upgrade): paramiko==1.15.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 56))
Requirement already satisfied (use --upgrade to upgrade): ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 57))
Requirement already satisfied (use --upgrade to upgrade): Whoosh==2.4.1+gx1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 64))
Requirement already satisfied (use --upgrade to upgrade): Markdown>=2.0.1 in ./.venv/lib/python2.7/site-packages (from Cheetah==2.4.4->-r requirements.txt (line 2))
Requirement already satisfied (use --upgrade to upgrade): requests-toolbelt in ./.venv/lib/python2.7/site-packages (from bioblend==0.6.1->-r requirements.txt (line 30))
Activating virtualenv at /home/john/workspace/galaxy/.venv
Entering daemon mode
.........
{u'stdin': None, u'command_line': [u'cat', u'/tmp/tmptEYGQR/files/000/dataset_1.dat'], u'stdout': u'output.txt'}

</code>