docs/notebooks/cwl.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[33mYou are using pip version 6.1.1, however version 7.1.2 is available.\n",
      "You should consider upgrading via the 'pip install --upgrade pip' command.\u001b[0m\n",
      "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\n",
      "Requirement already satisfied (use --upgrade to upgrade): Click in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from planemo)\n",
      "Requirement already satisfied (use --upgrade to upgrade): six in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from planemo)\n",
      "Requirement already satisfied (use --upgrade to upgrade): pyyaml in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from planemo)\n",
      "Requirement already satisfied (use --upgrade to upgrade): jinja2 in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from planemo)\n",
      "Requirement already satisfied (use --upgrade to upgrade): docutils in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from planemo)\n",
      "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)\n",
      "Requirement already satisfied (use --upgrade to upgrade): bioblend in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from planemo)\n",
      "Requirement already satisfied (use --upgrade to upgrade): glob2 in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from planemo)\n",
      "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)\n",
      "Requirement already satisfied (use --upgrade to upgrade): markupsafe in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from jinja2->planemo)\n",
      "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)\n",
      "Requirement already satisfied (use --upgrade to upgrade): poster in /home/john/workspace/planemo/.venv/lib/python2.7/site-packages (from bioblend->planemo)\n",
      "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)\n",
      "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)\n",
      "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)\n",
      "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)\n",
      "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)\n",
      "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)\n",
      "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)\n",
      "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)\n",
      "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)\n",
      "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)\n",
      "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)\n"
     ]
    }
   ],
   "source": [
    "!pip install planemo"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[32m\u001b[1mwget -q --recursive -O - 'https://codeload.github.com/galaxyproject/planemo/tar.gz/master' | tar  -C /tmp/tmpnesC3S -zxf - --strip-components=2\u001b[0m\n",
      "\u001b[32m\u001b[1mls '/tmp/tmpnesC3S'\u001b[0m\n",
      "appliance.rst\n",
      "bioblend.py\n",
      "bootstrap_history.py\n",
      "bwa\n",
      "categories.py\n",
      "cli.py\n",
      "commands\n",
      "commands.rst\n",
      "commands_to_rst.py\n",
      "commit_version.py\n",
      "conduct.rst\n",
      "config.py\n",
      "configuration.rst\n",
      "conf.py\n",
      "contributing.rst\n",
      "cwl\n",
      "cwl2script\n",
      "cwl_draft2_spec\n",
      "cwl-runner\n",
      "data\n",
      "demo\n",
      "developing.rst\n",
      "galaxy\n",
      "galaxy_config.py\n",
      "galaxy_run.py\n",
      "galaxy_serve.py\n",
      "galaxy_test\n",
      "github_util.py\n",
      "git.py\n",
      "glob.py\n",
      "history.rst\n",
      "images\n",
      "index.rst\n",
      "__init__.py\n",
      "installation.rst\n",
      "io.py\n",
      "linters\n",
      "lint.py\n",
      "make.bat\n",
      "Makefile\n",
      "modules.rst\n",
      "network_util.py\n",
      "new_version.py\n",
      "notebooks\n",
      "options.py\n",
      "organization.rst\n",
      "other_docs.rst\n",
      "package_bwa_0_7_7\n",
      "package_samtools_0.1.16\n",
      "package_seqtk_1_0_r75\n",
      "planemo.commands.rst\n",
      "planemo.cwl.rst\n",
      "planemo_ext.cwl2script.rst\n",
      "planemo_ext.galaxy.jobs.metrics.collectl.rst\n",
      "planemo_ext.galaxy.jobs.metrics.instrumenters.rst\n",
      "planemo_ext.galaxy.jobs.metrics.rst\n",
      "planemo_ext.galaxy.jobs.rst\n",
      "planemo_ext.galaxy.objectstore.rst\n",
      "planemo_ext.galaxy.rst\n",
      "planemo_ext.galaxy.tools.deps.resolvers.rst\n",
      "planemo_ext.galaxy.tools.deps.rst\n",
      "planemo_ext.galaxy.tools.linters.rst\n",
      "planemo_ext.galaxy.tools.rst\n",
      "planemo_ext.galaxy.util.rst\n",
      "planemo_ext.rst\n",
      "planemo.galaxy_test.rst\n",
      "planemo.linters.rst\n",
      "planemo_logo.png\n",
      "planemo.reports.rst\n",
      "planemo.rst\n",
      "planemo.shed2tap.rst\n",
      "planemo.shed.rst\n",
      "planemo.xml.rst\n",
      "pre-commit-lint\n",
      "pre-commit-lint-and-test\n",
      "publishing.rst\n",
      "README\n",
      "readme.rst\n",
      "reports\n",
      "repository_dependencies_shed.xml\n",
      "repository_dependencies.xml\n",
      "scripts\n",
      "setup.py\n",
      "shed\n",
      "shed2tap\n",
      "shed_app.py\n",
      "shed_app_test_utils.py\n",
      "shed_lint.py\n",
      "templates.py\n",
      "test_build_and_lint.py\n",
      "test_cmd_serve.py\n",
      "test_cmd_shed_serve.py\n",
      "test_config_init.py\n",
      "test_cwl_run.py\n",
      "test_dependency_script.py\n",
      "test_galaxy_serve.py\n",
      "test_galaxy_test.py\n",
      "test_git.py\n",
      "test_init_and_test.py\n",
      "test_lint.py\n",
      "test_normalize.py\n",
      "test_planemo.py\n",
      "test_shed_create.py\n",
      "test_shed_diff.py\n",
      "test_shed_diff_xml.py\n",
      "test_shed_download.py\n",
      "test_shed_expansion.py\n",
      "test_shed_init.py\n",
      "test_shed_lint.py\n",
      "test_shed_operations.py\n",
      "test_shed.py\n",
      "test_shed_test.py\n",
      "test_shed_upload.py\n",
      "test_utils.py\n",
      "test_validation.py\n",
      "test_xml_diff.py\n",
      "tool_builder.py\n",
      "tool_dependencies_good_1.xml\n",
      "tool_dependencies_good_2.xml\n",
      "tool_factory_2\n",
      "tool_lint.py\n",
      "tools.py\n",
      "travis_test.sh\n",
      "update_extern.sh\n",
      "update_planemo_recipe.bash\n",
      "update_report_assets.sh\n",
      "Vagrantfile\n",
      "writing\n",
      "writing_advanced.rst\n",
      "writing_appliance.rst\n",
      "_writing_collections.rst\n",
      "_writing_conclusion.rst\n",
      "writing_how_do_i.rst\n",
      "_writing_intro.rst\n",
      "_writing_parameters.rst\n",
      "_writing_publish_intro.rst\n",
      "writing.rst\n",
      "_writing_scripts.rst\n",
      "writing_standalone.rst\n",
      "_writing_suites.rst\n",
      "_writing_test_and_serve_appliance.rst\n",
      "_writing_test_and_serve.rst\n",
      "_writing_testing.rst\n",
      "xml\n",
      "xml_bad_1.xml\n",
      "xml_good_1.xml\n",
      "xml_good_2.xml\n",
      "xsd_command.xsd\n",
      "xsd_schema_1.xsd\n",
      "\u001b[32m\u001b[1mmv '/tmp/tmpnesC3S/cwl_draft2_spec'/* '/home/john/workspace/planemo/docs/notebooks'\u001b[0m\n",
      "\u001b[32m\u001b[1mmv '/tmp/tmpnesC3S/cwl_draft2_spec'/.* '/home/john/workspace/planemo/docs/notebooks'\u001b[0m\n",
      "mv: cannot move ‘/tmp/tmpnesC3S/cwl_draft2_spec/.’ to ‘/home/john/workspace/planemo/docs/notebooks/.’: Device or resource busy\n",
      "mv: cannot move ‘/tmp/tmpnesC3S/cwl_draft2_spec/..’ to ‘/home/john/workspace/planemo/docs/notebooks/..’: Device or resource busy\n"
     ]
    }
   ],
   "source": [
    "!planemo project_init --template cwl_draft2_spec"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[0m\u001b[01;32madd-lines-wf.cwl\u001b[0m*      \u001b[01;32mcount-lines8-wf.cwl\u001b[0m*  scatter-job2.json\r\n",
      "basics.ipynb           \u001b[01;32mcount-lines9-wf.cwl\u001b[0m*  scatter-wf1.cwl\r\n",
      "\u001b[01;32mbinding-test.cwl\u001b[0m*      cwl.ipynb             scatter-wf2.cwl\r\n",
      "bwa-mem-job.json       echo-tool.cwl         scatter-wf3.cwl\r\n",
      "\u001b[01;32mbwa-mem-tool.cwl\u001b[0m*      empty.json            scatter-wf4.cwl\r\n",
      "\u001b[01;32mcat1-tool.cwl\u001b[0m*         env-job.json          search.cwl\r\n",
      "\u001b[01;32mcat2-tool.cwl\u001b[0m*         env-tool1.cwl         search-job.json\r\n",
      "\u001b[01;32mcat3-tool.cwl\u001b[0m*         env-tool2.cwl         \u001b[01;32msearch.py\u001b[0m*\r\n",
      "\u001b[01;32mcat4-tool.cwl\u001b[0m*         env-wf1.cwl           seqtk_seq.xml\r\n",
      "\u001b[01;32mcat5-tool.cwl\u001b[0m*         env-wf2.cwl           sorttool.cwl\r\n",
      "cat-job.json           hello.txt             \u001b[01;32mtemplate-tool.cwl\u001b[0m*\r\n",
      "cat-n-job.json         \u001b[01;32mindex.py\u001b[0m*             \u001b[01;34mtest-data\u001b[0m/\r\n",
      "\u001b[01;32mcount-lines1-wf.cwl\u001b[0m*   node-engine.cwl       tmap-job.json\r\n",
      "\u001b[01;32mcount-lines2-wf.cwl\u001b[0m*   number.txt            \u001b[01;32mtmap-tool.cwl\u001b[0m*\r\n",
      "count-lines3-job.json  parseInt-job.json     underscore.js\r\n",
      "\u001b[01;32mcount-lines3-wf.cwl\u001b[0m*   \u001b[01;32mparseInt-tool.cwl\u001b[0m*    \u001b[01;32mwc2-tool.cwl\u001b[0m*\r\n",
      "count-lines4-job.json  rename.cwl            wc3-tool.cwl\r\n",
      "\u001b[01;32mcount-lines4-wf.cwl\u001b[0m*   rename-job.json       wc-job.json\r\n",
      "\u001b[01;32mcount-lines5-wf.cwl\u001b[0m*   revsort.cwl           \u001b[01;32mwc-tool.cwl\u001b[0m*\r\n",
      "count-lines6-job.json  revsort-job.json      whale.txt\r\n",
      "\u001b[01;32mcount-lines6-wf.cwl\u001b[0m*   revtool.cwl\r\n",
      "\u001b[01;32mcount-lines7-wf.cwl\u001b[0m*   scatter-job1.json\r\n"
     ]
    }
   ],
   "source": [
    "ls"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[32m\u001b[1mStarting galaxy with command [/home/john/workspace/galaxy/run.sh --server-name 'planemo18130' --reload]\u001b[0m\n",
      "Activating virtualenv at /home/john/workspace/galaxy/.venv\n",
      "Ignoring indexes: https://pypi.python.org/simple\n",
      "/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.\n",
      "  InsecurePlatformWarning\n",
      "Requirement already up-to-date: pip in ./.venv/lib/python2.7/site-packages\n",
      "Requirement already satisfied (use --upgrade to upgrade): Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2))\n",
      "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))\n",
      "Requirement already satisfied (use --upgrade to upgrade): MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4))\n",
      "Requirement already satisfied (use --upgrade to upgrade): PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5))\n",
      "Requirement already satisfied (use --upgrade to upgrade): SQLAlchemy==1.0.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 6))\n",
      "Requirement already satisfied (use --upgrade to upgrade): mercurial==3.5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7))\n",
      "Requirement already satisfied (use --upgrade to upgrade): numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8))\n",
      "Requirement already satisfied (use --upgrade to upgrade): pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9))\n",
      "Requirement already satisfied (use --upgrade to upgrade): python-lzo==1.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 10))\n",
      "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))\n",
      "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))\n",
      "Requirement already satisfied (use --upgrade to upgrade): PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17))\n",
      "Requirement already satisfied (use --upgrade to upgrade): docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18))\n",
      "Requirement already satisfied (use --upgrade to upgrade): wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19))\n",
      "Requirement already satisfied (use --upgrade to upgrade): repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20))\n",
      "Requirement already satisfied (use --upgrade to upgrade): Routes==2.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21))\n",
      "Requirement already satisfied (use --upgrade to upgrade): WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22))\n",
      "Requirement already satisfied (use --upgrade to upgrade): WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23))\n",
      "Requirement already satisfied (use --upgrade to upgrade): Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24))\n",
      "Requirement already satisfied (use --upgrade to upgrade): pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25))\n",
      "Requirement already satisfied (use --upgrade to upgrade): Babel==2.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26))\n",
      "Requirement already satisfied (use --upgrade to upgrade): Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27))\n",
      "Requirement already satisfied (use --upgrade to upgrade): bioblend==0.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30))\n",
      "Requirement already satisfied (use --upgrade to upgrade): boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31))\n",
      "Requirement already satisfied (use --upgrade to upgrade): requests==2.8.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 32))\n",
      "Requirement already satisfied (use --upgrade to upgrade): WebError==0.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35))\n",
      "Requirement already satisfied (use --upgrade to upgrade): Pygments==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36))\n",
      "Requirement already satisfied (use --upgrade to upgrade): kombu==3.0.26 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 39))\n",
      "Requirement already satisfied (use --upgrade to upgrade): amqp==1.4.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40))\n",
      "Requirement already satisfied (use --upgrade to upgrade): anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41))\n",
      "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))\n",
      "Requirement already satisfied (use --upgrade to upgrade): decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45))\n",
      "Requirement already satisfied (use --upgrade to upgrade): Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 46))\n",
      "Requirement already satisfied (use --upgrade to upgrade): sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 47))\n",
      "Requirement already satisfied (use --upgrade to upgrade): pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48))\n",
      "Requirement already satisfied (use --upgrade to upgrade): six==1.9.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49))\n",
      "Requirement already satisfied (use --upgrade to upgrade): Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 50))\n",
      "Requirement already satisfied (use --upgrade to upgrade): nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51))\n",
      "Requirement already satisfied (use --upgrade to upgrade): SVGFig==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 52))\n",
      "Requirement already satisfied (use --upgrade to upgrade): Fabric==1.10.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 55))\n",
      "Requirement already satisfied (use --upgrade to upgrade): paramiko==1.15.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 56))\n",
      "Requirement already satisfied (use --upgrade to upgrade): ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 57))\n",
      "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))\n",
      "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))\n",
      "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))\n",
      "Activating virtualenv at /home/john/workspace/galaxy/.venv\n",
      "Starting subprocess with file monitor\n",
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      "galaxy.model.migrate.check INFO 2015-11-03 11:17:37,493 \n",
      "galaxy.model.migrate.check INFO 2015-11-03 11:17:37,493 \n",
      "galaxy.model.migrate.check INFO 2015-11-03 11:17:37,493 Migrating 129 -> 130... \n",
      "galaxy.model.migrate.check INFO 2015-11-03 11:17:38,527 \n",
      "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.\n",
      "galaxy.model.migrate.check INFO 2015-11-03 11:17:38,527 \n",
      "galaxy.model.migrate.check INFO 2015-11-03 11:17:38,527 \n",
      "galaxy.model.migrate.check INFO 2015-11-03 11:17:38,528 Migrating 130 -> 131... \n",
      "galaxy.model.migrate.check INFO 2015-11-03 11:17:39,837 \n",
      "galaxy.model.migrate.check INFO 2015-11-03 11:17:39,838 Migration script to allow invalidation of job external output metadata temp files\n",
      "galaxy.model.migrate.check INFO 2015-11-03 11:17:39,838 \n",
      "galaxy.model.migrate.check INFO 2015-11-03 11:17:39,838 \n",
      "galaxy.config INFO 2015-11-03 11:17:39,903 Install database targetting Galaxy's database configuration.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,089 Loading datatypes from ./config/datatypes_conf.xml\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,090 Retrieved datatype module galaxy.datatypes.oxli:Count from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,090 Retrieved datatype module galaxy.datatypes.oxli:Presence from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,091 Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,091 Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,093 Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,093 Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,093 Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,093 Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,093 Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,094 Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,094 Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,094 Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,094 Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,095 Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,095 Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,096 Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,096 Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,096 Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,096 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,096 Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,097 Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,098 Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,098 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,099 Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,099 Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,099 Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,099 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,099 Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,100 Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,100 Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,100 Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,100 Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,100 Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,101 Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,101 Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,101 Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,101 Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,101 Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,102 Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,102 Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,102 Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,102 Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,102 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,103 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,103 Retrieved datatype module galaxy.datatypes.images:Html from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,104 Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,104 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,105 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,105 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,105 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,106 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,107 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,107 Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,107 Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,108 Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,108 Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,109 Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,109 Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,109 Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,110 Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,110 Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,110 Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,110 Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,111 Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,111 Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,111 Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,112 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,112 Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,112 Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,113 Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,113 Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,113 Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,114 Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,114 Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,115 Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,115 Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,115 Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,116 Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,116 Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,116 Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,117 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,117 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,117 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,117 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,118 Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,118 Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,118 Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,118 Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,119 Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,119 Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,119 Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,120 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,120 Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,120 Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,121 Retrieved datatype module galaxy.datatypes.images:Image from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,121 Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,121 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,122 Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,122 Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,122 Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,123 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,123 Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,123 Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,124 Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,124 Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,124 Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,125 Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,125 Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,125 Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,126 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,126 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,126 Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,127 Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,127 Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,128 Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,131 Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,146 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,147 Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,148 Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,148 Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,151 Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,152 Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,152 Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,152 Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,153 Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,153 Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,154 Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,154 Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,154 Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,155 Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,155 Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,157 Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,157 Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,157 Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,158 Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,165 Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,166 Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,166 Retrieved datatype module galaxy.datatypes.graph:Rdf from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,166 Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,166 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,167 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,167 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,168 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,168 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,169 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,169 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,170 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,170 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,171 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,173 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,173 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,174 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,174 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,176 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,176 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,180 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,180 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,181 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,182 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,182 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,182 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,183 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,183 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,186 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,188 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,190 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,191 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,191 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,192 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,192 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,193 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,195 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,197 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,197 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,197 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,198 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,199 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,200 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,204 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,204 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,204 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,205 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,205 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,206 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,206 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,207 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,207 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,209 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,210 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,210 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,211 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,213 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,213 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,220 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,220 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,221 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,221 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,222 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,222 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,222 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,223 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,223 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,224 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,224 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,224 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,225 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,225 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,226 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,226 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,227 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,227 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,227 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,231 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,232 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,232 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,233 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,233 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,234 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,234 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,234 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,238 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,246 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,247 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,247 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,248 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,248 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,249 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,249 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,250 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,250 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,251 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,251 Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,253 Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,253 Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,254 Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,259 Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,260 Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,261 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,261 Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,261 Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,262 Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,262 Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,262 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,262 Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,262 Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,267 Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,269 Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,270 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,270 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,271 Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,271 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,271 Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,271 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,272 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,272 Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,272 Loaded sniffer for datatype 'galaxy.datatypes.images:Html'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,272 Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,272 Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,273 Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,273 Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,277 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,278 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,278 Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,278 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,278 Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,279 Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,279 Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,279 Loaded sniffer for datatype 'galaxy.datatypes.data:Newick'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,279 Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,280 Loaded sniffer for datatype 'galaxy.datatypes.text:Obo'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,280 Loaded sniffer for datatype 'galaxy.datatypes.text:Arff'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,280 Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,280 Loaded sniffer for datatype 'galaxy.datatypes.text:Json'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,280 Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,281 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,281 Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,281 Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,281 Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,282 Loaded sniffer for datatype 'galaxy.datatypes.binary:RData'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,282 Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,282 Loaded sniffer for datatype 'galaxy.datatypes.images:Png'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,282 Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,282 Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,283 Loaded sniffer for datatype 'galaxy.datatypes.images:Gif'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,283 Loaded sniffer for datatype 'galaxy.datatypes.images:Im'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,283 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,283 Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,283 Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,284 Loaded sniffer for datatype 'galaxy.datatypes.images:Psd'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,284 Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,284 Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,284 Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,285 Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,285 Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,285 Loaded sniffer for datatype 'galaxy.datatypes.images:Eps'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,285 Loaded sniffer for datatype 'galaxy.datatypes.images:Rast'\n",
      "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\n",
      "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\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,290 Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt\n",
      "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\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,290 Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:40,290 Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt\n",
      "galaxy.tools.data DEBUG 2015-11-03 11:17:40,334 Loaded tool data table 'ccat_configurations'\n",
      "galaxy.tools.data DEBUG 2015-11-03 11:17:40,335 Loaded tool data table 'all_fasta'\n",
      "galaxy.tools.data DEBUG 2015-11-03 11:17:40,336 Loaded tool data table 'blastdb'\n",
      "galaxy.tools.data DEBUG 2015-11-03 11:17:40,336 Loaded tool data table 'blastdb_p'\n",
      "galaxy.tools.data DEBUG 2015-11-03 11:17:40,337 Loaded tool data table 'blastdb_d'\n",
      "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\n",
      "galaxy.jobs DEBUG 2015-11-03 11:17:40,588 Loading job configuration from /tmp/tmpV60k0e/galaxy.ini\n",
      "galaxy.jobs DEBUG 2015-11-03 11:17:40,588 Done loading job configuration\n",
      "beaker.container DEBUG 2015-11-03 11:17:40,608 data file /tmp/tmpV60k0e/citations/data/container_file/4/48/48e563f148dc04d8b31c94878c138019862e580d.cache\n",
      "galaxy.tools.toolbox.watcher INFO 2015-11-03 11:17:40,609 Failed to load ToolWatcher (watchdog is likely unavailable) - proceeding without tool monitoring.\n",
      "galaxy.tools.toolbox.base INFO 2015-11-03 11:17:40,609 Parsing the tool configuration /tmp/tmpV60k0e/tool_conf.xml\n",
      "galaxy.tools.toolbox.base DEBUG 2015-11-03 11:17:40,623 Loaded tool id: upload1, version: 1.1.4 into tool panel..\n",
      "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.\n",
      "galaxy.tools.parser.cwl WARNING 2015-11-03 11:17:42,797 TOOL ID is cat3-tool\n",
      "galaxy.tools.toolbox.base DEBUG 2015-11-03 11:17:42,798 Loaded tool id: cat3-tool, version: 0.0.1 into tool panel..\n",
      "galaxy.tools.toolbox.base INFO 2015-11-03 11:17:42,798 Parsing the tool configuration /tmp/tmpV60k0e/shed_tool_conf.xml\n",
      "galaxy.tools.toolbox.base INFO 2015-11-03 11:17:42,798 Parsing the tool configuration /tmp/tmpV60k0e/empty_tool_conf.xml\n",
      "galaxy.tools.deps WARNING 2015-11-03 11:17:42,799 Path '/tmp/tmpV60k0e/deps' does not exist, ignoring\n",
      "galaxy.tools.deps WARNING 2015-11-03 11:17:42,799 Path '/tmp/tmpV60k0e/deps' is not directory, ignoring\n",
      "galaxy.tools.deps DEBUG 2015-11-03 11:17:42,800 Unable to find config file './dependency_resolvers_conf.xml'\n",
      "galaxy.tools.search DEBUG 2015-11-03 11:17:42,892 Starting to build toolbox index.\n",
      "galaxy.tools.search DEBUG 2015-11-03 11:17:43,127 Toolbox index finished.\n",
      "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.\n",
      "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\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,158 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,160 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False.\n",
      "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\".\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,163 Loaded display application 'igv_bam' for datatype 'bam', inherit=False.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,164 Loaded display application 'igb_bam' for datatype 'bam', inherit=False.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,165 Loaded display application 'igb_bed' for datatype 'bed', inherit=False.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,166 Loaded display application 'igb_bedgraph' for datatype 'bedgraph', inherit=False.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,170 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,171 Loaded display application 'igb_bb' for datatype 'bigbed', inherit=False.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,175 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,176 Loaded display application 'igb_bigwig' for datatype 'bigwig', inherit=False.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,186 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True.\n",
      "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\".\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,189 Loaded display application 'igv_gff' for datatype 'gff', inherit=True.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,190 Loaded display application 'igb_gtf' for datatype 'gtf', inherit=False.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,200 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,215 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,217 Loaded display application 'rviewer_interval' for datatype 'interval', inherit=True.\n",
      "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\".\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,220 Loaded display application 'igv_interval_as_bed' for datatype 'interval', inherit=True.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,223 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,228 Loaded display application 'ucsc_vcf' for datatype 'vcf', inherit=False.\n",
      "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\".\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,231 Loaded display application 'igv_vcf' for datatype 'vcf', inherit=False.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,233 Loaded display application 'rviewer_vcf' for datatype 'vcf', inherit=True.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,234 Loaded display application 'igb_wig' for datatype 'wig', inherit=False.\n",
      "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\".\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,237 Loaded display application 'igv_vcf' for datatype 'vcf_bgzip', inherit=False.\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,238 Adding inherited display application 'ensembl_gff' to datatype 'gtf'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,238 Adding inherited display application 'igv_gff' to datatype 'gtf'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,238 Adding inherited display application 'ensembl_interval' to datatype 'bedstrict'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,238 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedstrict'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,238 Adding inherited display application 'rviewer_interval' to datatype 'bedstrict'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,239 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedstrict'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,240 Adding inherited display application 'ensembl_interval' to datatype 'bedgraph'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,240 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bedgraph'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,240 Adding inherited display application 'rviewer_interval' to datatype 'bedgraph'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,240 Adding inherited display application 'igv_interval_as_bed' to datatype 'bedgraph'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,240 Adding inherited display application 'ensembl_interval' to datatype 'bed12'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,240 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed12'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,241 Adding inherited display application 'rviewer_interval' to datatype 'bed12'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,241 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed12'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,242 Adding inherited display application 'ensembl_interval' to datatype 'chrint'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,242 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'chrint'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,242 Adding inherited display application 'rviewer_interval' to datatype 'chrint'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,242 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,244 Adding inherited display application 'ensembl_interval' to datatype 'bed'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,244 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,244 Adding inherited display application 'rviewer_interval' to datatype 'bed'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,244 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,245 Adding inherited display application 'ensembl_gff' to datatype 'gff3'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,245 Adding inherited display application 'igv_gff' to datatype 'gff3'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,246 Adding inherited display application 'ensembl_interval' to datatype 'bed6'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,246 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'bed6'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,247 Adding inherited display application 'rviewer_interval' to datatype 'bed6'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,247 Adding inherited display application 'igv_interval_as_bed' to datatype 'bed6'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,247 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,247 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,247 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,247 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak'\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,250 Loaded converter: CONVERTER_Bam_Bai_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,252 Loaded converter: CONVERTER_bam_to_bigwig_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,254 Loaded converter: CONVERTER_bed_to_gff_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,256 Loaded converter: CONVERTER_bed_to_bgzip_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,259 Loaded converter: CONVERTER_bed_to_tabix_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,261 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,264 Loaded converter: CONVERTER_bed_to_fli_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,266 Loaded converter: CONVERTER_bedgraph_to_bigwig\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,269 Loaded converter: CONVERTER_len_to_linecount\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,271 Loaded converter: CONVERTER_interval_to_bgzip_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,273 Loaded converter: CONVERTER_interval_to_tabix_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,275 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,277 Loaded converter: CONVERTER_fasta_to_tabular\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,280 Loaded converter: CONVERTER_fasta_to_bowtie_base_index\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,282 Loaded converter: CONVERTER_fasta_to_bowtie_color_index\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,285 Loaded converter: CONVERTER_fasta_to_2bit\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,287 Loaded converter: CONVERTER_fasta_to_len\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,289 Loaded converter: CONVERTER_fastq_to_fqtoc0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,291 Loaded converter: CONVERTER_fastq_to_fqtoc0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,293 Loaded converter: CONVERTER_fastq_to_fqtoc0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,295 Loaded converter: CONVERTER_fastq_to_fqtoc0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,298 Loaded converter: CONVERTER_fastq_to_fqtoc0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,300 Loaded converter: CONVERTER_gff_to_bed_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,301 Loaded converter: CONVERTER_gff_to_interval_index_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,304 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,306 Loaded converter: CONVERTER_gff_to_fli_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,307 Loaded converter: CONVERTER_gff_to_interval_index_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,310 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,312 Loaded converter: CONVERTER_interval_to_bed_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,315 Loaded converter: CONVERTER_interval_to_bedstrict_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,317 Loaded converter: CONVERTER_interval_to_bed6_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,319 Loaded converter: CONVERTER_interval_to_bed12_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,321 Loaded converter: CONVERTER_interval_to_bgzip_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,324 Loaded converter: CONVERTER_interval_to_tabix_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,326 Loaded converter: CONVERTER_interval_to_bigwig_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,328 Loaded converter: CONVERTER_picard_interval_list_to_bed6\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,331 Loaded converter: CONVERTER_maf_to_fasta_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,333 Loaded converter: CONVERTER_maf_to_interval_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,335 Loaded converter: CONVERTER_encodepeak_to_tabix_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,337 Loaded converter: CONVERTER_encodepeak_to_bgzip_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,339 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,340 Loaded converter: CONVERTER_interval_to_bgzip_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,342 Loaded converter: CONVERTER_interval_to_tabix_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,346 Loaded converter: CONVERTER_sam_to_bam\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,349 Loaded converter: CONVERTER_sam_to_bigwig_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,351 Loaded converter: tabular_to_dbnsfp\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,352 Loaded converter: CONVERTER_vcf_to_bgzip_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,354 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,356 Loaded converter: CONVERTER_vcf_to_tabix_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,358 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,360 Loaded converter: CONVERTER_wig_to_bigwig\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,362 Loaded converter: CONVERTER_wiggle_to_interval_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,364 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,366 Loaded converter: lped2fpedconvert\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,369 Loaded converter: lped2pbedconvert\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,370 Loaded converter: pbed2lpedconvert\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,372 Loaded converter: pbed2ldindepconvert\n",
      "galaxy.datatypes.registry DEBUG 2015-11-03 11:17:43,375 Loaded external metadata tool: __SET_METADATA__\n",
      "galaxy.tools.imp_exp DEBUG 2015-11-03 11:17:43,377 Loaded history export tool: __EXPORT_HISTORY__\n",
      "galaxy.tools.imp_exp DEBUG 2015-11-03 11:17:43,379 Loaded history import tool: __IMPORT_HISTORY__\n",
      "galaxy.web.base.pluginframework INFO 2015-11-03 11:17:43,382 VisualizationsRegistry, loaded plugin: charts\n",
      "galaxy.visualization.plugins.config_parser INFO 2015-11-03 11:17:43,383 Visualizations plugin disabled: Circster. Skipping...\n",
      "galaxy.web.base.pluginframework INFO 2015-11-03 11:17:43,385 VisualizationsRegistry, loaded plugin: graphview\n",
      "galaxy.visualization.plugins.config_parser INFO 2015-11-03 11:17:43,386 template syntax is deprecated: use entry_point instead\n",
      "galaxy.web.base.pluginframework INFO 2015-11-03 11:17:43,386 VisualizationsRegistry, loaded plugin: graphviz\n",
      "galaxy.web.base.pluginframework INFO 2015-11-03 11:17:43,388 VisualizationsRegistry, loaded plugin: phyloviz\n",
      "galaxy.web.base.pluginframework INFO 2015-11-03 11:17:43,390 VisualizationsRegistry, loaded plugin: scatterplot\n",
      "galaxy.visualization.plugins.config_parser INFO 2015-11-03 11:17:43,391 Visualizations plugin disabled: Sweepster. Skipping...\n",
      "galaxy.web.base.pluginframework INFO 2015-11-03 11:17:43,393 VisualizationsRegistry, loaded plugin: trackster\n",
      "galaxy.jobs.manager DEBUG 2015-11-03 11:17:43,398 Starting job handler\n",
      "galaxy.jobs INFO 2015-11-03 11:17:43,398 Handler 'main' will load all configured runner plugins\n",
      "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\n",
      "galaxy.jobs.runners DEBUG 2015-11-03 11:17:43,400 Starting 5 LocalRunner workers\n",
      "galaxy.jobs DEBUG 2015-11-03 11:17:43,401 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local'\n",
      "galaxy.jobs DEBUG 2015-11-03 11:17:43,402 Legacy destination with id 'local:///', url 'local:///' converted, got params:\n",
      "galaxy.jobs.handler DEBUG 2015-11-03 11:17:43,402 Loaded job runners plugins: local\n",
      "galaxy.jobs.handler INFO 2015-11-03 11:17:43,402 job handler stop queue started\n",
      "galaxy.jobs.handler INFO 2015-11-03 11:17:43,436 job handler queue started\n",
      "galaxy.sample_tracking.external_service_types DEBUG 2015-11-03 11:17:43,439 Loaded external_service_type: Simple unknown sequencer 1.0.0\n",
      "galaxy.sample_tracking.external_service_types DEBUG 2015-11-03 11:17:43,442 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0\n",
      "galaxy.workflow.scheduling_manager DEBUG 2015-11-03 11:17:43,453 Starting workflow schedulers\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,466 Enabling 'external_service' controller, class: ExternalService\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,466 Enabling 'requests_common' controller, class: RequestsCommon\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,487 Enabling 'library_common' controller, class: LibraryCommon\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,490 Enabling 'visualization' controller, class: VisualizationController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,492 Enabling 'page' controller, class: PageController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,493 Enabling 'async' controller, class: ASync\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,500 Enabling 'forms' controller, class: Forms\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,508 Enabling 'history' controller, class: HistoryController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,510 Enabling 'user' controller, class: User\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,516 Enabling 'library_admin' controller, class: LibraryAdmin\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,520 Enabling 'requests' controller, class: Requests\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,520 Enabling 'mobile' controller, class: Mobile\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,521 Enabling 'biostar' controller, class: BiostarController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,526 Enabling 'workflow' controller, class: WorkflowController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,582 Enabling 'admin_toolshed' controller, class: AdminGalaxy\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,583 Enabling 'admin_toolshed' controller, class: AdminToolshed\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,583 Enabling 'search' controller, class: SearchController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,583 Enabling 'library' controller, class: Library\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,585 Enabling 'requests_admin' controller, class: RequestsAdmin\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,586 Enabling 'data_manager' controller, class: DataManager\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,586 Enabling 'userskeys' controller, class: User\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,587 Enabling 'tag' controller, class: TagsController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,591 Enabling 'dataset' controller, class: DatasetInterface\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,592 Enabling 'root' controller, class: RootController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,593 Enabling 'tool_runner' controller, class: ToolRunner\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,594 Enabling 'request_type' controller, class: RequestType\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,594 Enabling 'error' controller, class: Error\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,594 Enabling 'external_services' controller, class: ExternalServiceController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,594 Enabling 'admin' controller, class: AdminGalaxy\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,597 Enabling 'history_content_provenance' API controller, class: HDAProvenanceController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,597 Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,598 Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,598 Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,599 Enabling 'visualizations' API controller, class: VisualizationsController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,599 Enabling 'jobs' API controller, class: JobController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,600 Enabling 'request_types' API controller, class: RequestTypeAPIController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,601 Enabling 'forms' API controller, class: FormDefinitionAPIController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,601 Enabling 'group_roles' API controller, class: GroupRolesAPIController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,602 Enabling 'authenticate' API controller, class: AuthenticationController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,602 Enabling 'group_users' API controller, class: GroupUsersAPIController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,603 Enabling 'roles' API controller, class: RoleAPIController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,603 Enabling 'pages' API controller, class: PagesController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,605 Enabling 'configuration' API controller, class: ConfigurationController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,606 Enabling 'workflows' API controller, class: WorkflowsAPIController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,607 Enabling 'samples' API controller, class: SamplesAPIController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,607 Enabling 'users' API controller, class: UserAPIController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,608 Enabling 'requests' API controller, class: RequestsAPIController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,609 Enabling 'history_annotations' API controller, class: HistoryAnnotationsController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,609 Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,609 Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,610 Enabling 'genomes' API controller, class: GenomesController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,612 Enabling 'lda_datasets' API controller, class: LibraryDatasetsController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,612 Enabling 'folders' API controller, class: FoldersController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,613 Enabling 'job_files' API controller, class: JobFilesAPIController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,614 Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,628 Enabling 'search' API controller, class: SearchController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,629 Enabling 'history_contents' API controller, class: HistoryContentsController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,630 Enabling 'page_revisions' API controller, class: PageRevisionsController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,631 Enabling 'library_contents' API controller, class: LibraryContentsController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,631 Enabling 'quotas' API controller, class: QuotaAPIController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,632 Enabling 'datatypes' API controller, class: DatatypesController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,632 Enabling 'datasets' API controller, class: DatasetsController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,633 Enabling 'groups' API controller, class: GroupAPIController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,633 Enabling 'folder_contents' API controller, class: FolderContentsController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,634 Enabling 'dataset_collections' API controller, class: DatasetCollectionsController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,635 Enabling 'tools' API controller, class: ToolsController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,635 Enabling 'tool_data' API controller, class: ToolData\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,636 Enabling 'histories' API controller, class: HistoriesController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,637 Enabling 'libraries' API controller, class: LibrariesController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,638 Enabling 'metrics' API controller, class: MetricsController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,639 Enabling 'remote_files' API controller, class: RemoteFilesAPIController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,640 Enabling 'history_content_tags' API controller, class: HistoryContentTagsController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,640 Enabling 'history_tags' API controller, class: HistoryTagsController\n",
      "galaxy.web.framework.base DEBUG 2015-11-03 11:17:43,640 Enabling 'workflow_tags' API controller, class: WorkflowTagsController\n",
      "galaxy.webapps.galaxy.buildapp DEBUG 2015-11-03 11:17:44,276 Enabling 'httpexceptions' middleware\n",
      "galaxy.webapps.galaxy.buildapp DEBUG 2015-11-03 11:17:44,277 Enabling 'recursive' middleware\n",
      "galaxy.webapps.galaxy.buildapp DEBUG 2015-11-03 11:17:44,281 Enabling 'error' middleware\n",
      "galaxy.webapps.galaxy.buildapp DEBUG 2015-11-03 11:17:44,282 Enabling 'trans logger' middleware\n",
      "galaxy.webapps.galaxy.buildapp DEBUG 2015-11-03 11:17:44,283 Enabling 'x-forwarded-host' middleware\n",
      "galaxy.webapps.galaxy.buildapp DEBUG 2015-11-03 11:17:44,283 Enabling 'Request ID' middleware\n",
      "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\n",
      "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\n",
      "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\n",
      "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\n",
      "galaxy.queue_worker INFO 2015-11-03 11:17:44,291 Binding and starting galaxy control worker for main\n",
      "Starting server in PID 7761.\n",
      "serving on http://127.0.0.1:9991\n",
      "/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.\n",
      "  'storage.' % (dialect.name, dialect.driver))\n",
      "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\"\n",
      "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\"\n",
      "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\"\n",
      "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\"\n",
      "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\"\n",
      "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\"\n",
      "galaxy.tools.actions.upload_common INFO 2015-11-03 11:18:20,908 tool upload1 created job id 1\n",
      "galaxy.tools.execute DEBUG 2015-11-03 11:18:21,060 Tool [upload1] created job [1] (670.783 ms)\n",
      "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\"\n",
      "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\"\n",
      "galaxy.jobs DEBUG 2015-11-03 11:18:21,736 (1) Working directory for job is: /tmp/tmpV60k0e/job_working_directory/000/1\n",
      "galaxy.jobs.handler DEBUG 2015-11-03 11:18:21,743 (1) Dispatching to local runner\n",
      "galaxy.jobs DEBUG 2015-11-03 11:18:21,951 (1) Persisting job destination (destination id: local:///)\n",
      "galaxy.jobs.runners DEBUG 2015-11-03 11:18:22,024 Job [1] queued (280.634 ms)\n",
      "galaxy.jobs.handler INFO 2015-11-03 11:18:22,037 (1) Job dispatched\n",
      "galaxy.tools.deps DEBUG 2015-11-03 11:18:22,382 Building dependency shell command for dependency 'samtools'\n",
      "galaxy.tools.deps WARNING 2015-11-03 11:18:22,386 Failed to resolve dependency on 'samtools', ignoring\n",
      "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\"\n",
      "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\n",
      "galaxy.jobs DEBUG 2015-11-03 11:18:22,757 (1) Persisting job destination (destination id: local:///)\n",
      "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\"\n",
      "galaxy.jobs.runners.local DEBUG 2015-11-03 11:18:25,626 execution finished: /tmp/tmpV60k0e/job_working_directory/000/1/galaxy_1.sh\n",
      "galaxy.datatypes.metadata DEBUG 2015-11-03 11:18:25,983 loading metadata from file for: HistoryDatasetAssociation 1\n",
      "galaxy.jobs DEBUG 2015-11-03 11:18:26,411 job 1 ended (finish() executed in (785.504 ms))\n",
      "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\"\n",
      "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\"\n",
      "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\"\n",
      "galaxy.tools.actions INFO 2015-11-03 11:18:41,590 Handled output (285.044 ms)\n",
      "galaxy.tools.actions INFO 2015-11-03 11:18:41,859 Verified access to datasets (13.535 ms)\n",
      "galaxy.tools.execute DEBUG 2015-11-03 11:18:41,942 Tool [cat3-tool] created job [2] (649.957 ms)\n",
      "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\"\n",
      "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\"\n",
      "galaxy.jobs DEBUG 2015-11-03 11:18:42,686 (2) Working directory for job is: /tmp/tmpV60k0e/job_working_directory/000/2\n",
      "galaxy.jobs.handler DEBUG 2015-11-03 11:18:42,693 (2) Dispatching to local runner\n",
      "galaxy.jobs DEBUG 2015-11-03 11:18:42,916 (2) Persisting job destination (destination id: local:///)\n",
      "galaxy.jobs.runners DEBUG 2015-11-03 11:18:42,971 Job [2] queued (277.979 ms)\n",
      "galaxy.jobs.handler INFO 2015-11-03 11:18:43,011 (2) Job dispatched\n",
      "galaxy.tools INFO 2015-11-03 11:18:43,368 exec_before_job for CWL tool\n",
      "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\"\n",
      "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\"\n",
      "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\n",
      "galaxy.jobs DEBUG 2015-11-03 11:18:43,733 (2) Persisting job destination (destination id: local:///)\n",
      "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\"\n",
      "galaxy.jobs.runners.local DEBUG 2015-11-03 11:18:49,008 execution finished: /tmp/tmpV60k0e/job_working_directory/000/2/galaxy_2.sh\n",
      "galaxy.datatypes.metadata DEBUG 2015-11-03 11:18:49,203 loading metadata from file for: HistoryDatasetAssociation 2\n",
      "galaxy.jobs DEBUG 2015-11-03 11:18:49,530 job 2 ended (finish() executed in (522.083 ms))\n",
      "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\"\n",
      "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\"\n",
      "^C^C caught in monitor process\n",
      "\n",
      "Aborted!\n",
      "\n"
     ]
    }
   ],
   "source": [
    "!planemo serve --cwl cat3-tool.cwl"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[32m\u001b[1mStarting galaxy with command [/home/john/workspace/galaxy/run.sh --daemon --wait]\u001b[0m\n",
      "Activating virtualenv at /home/john/workspace/galaxy/.venv\n",
      "Ignoring indexes: https://pypi.python.org/simple\n",
      "/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.\n",
      "  InsecurePlatformWarning\n",
      "Requirement already up-to-date: pip in ./.venv/lib/python2.7/site-packages\n",
      "Requirement already satisfied (use --upgrade to upgrade): Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2))\n",
      "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))\n",
      "Requirement already satisfied (use --upgrade to upgrade): MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4))\n",
      "Requirement already satisfied (use --upgrade to upgrade): PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5))\n",
      "Requirement already satisfied (use --upgrade to upgrade): SQLAlchemy==1.0.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 6))\n",
      "Requirement already satisfied (use --upgrade to upgrade): mercurial==3.5 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7))\n",
      "Requirement already satisfied (use --upgrade to upgrade): numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8))\n",
      "Requirement already satisfied (use --upgrade to upgrade): pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9))\n",
      "Requirement already satisfied (use --upgrade to upgrade): python-lzo==1.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 10))\n",
      "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))\n",
      "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))\n",
      "Requirement already satisfied (use --upgrade to upgrade): PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17))\n",
      "Requirement already satisfied (use --upgrade to upgrade): docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18))\n",
      "Requirement already satisfied (use --upgrade to upgrade): wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19))\n",
      "Requirement already satisfied (use --upgrade to upgrade): repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20))\n",
      "Requirement already satisfied (use --upgrade to upgrade): Routes==2.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21))\n",
      "Requirement already satisfied (use --upgrade to upgrade): WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22))\n",
      "Requirement already satisfied (use --upgrade to upgrade): WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23))\n",
      "Requirement already satisfied (use --upgrade to upgrade): Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24))\n",
      "Requirement already satisfied (use --upgrade to upgrade): pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25))\n",
      "Requirement already satisfied (use --upgrade to upgrade): Babel==2.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26))\n",
      "Requirement already satisfied (use --upgrade to upgrade): Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27))\n",
      "Requirement already satisfied (use --upgrade to upgrade): bioblend==0.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30))\n",
      "Requirement already satisfied (use --upgrade to upgrade): boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31))\n",
      "Requirement already satisfied (use --upgrade to upgrade): requests==2.8.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 32))\n",
      "Requirement already satisfied (use --upgrade to upgrade): WebError==0.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35))\n",
      "Requirement already satisfied (use --upgrade to upgrade): Pygments==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36))\n",
      "Requirement already satisfied (use --upgrade to upgrade): kombu==3.0.26 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 39))\n",
      "Requirement already satisfied (use --upgrade to upgrade): amqp==1.4.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40))\n",
      "Requirement already satisfied (use --upgrade to upgrade): anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41))\n",
      "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))\n",
      "Requirement already satisfied (use --upgrade to upgrade): decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45))\n",
      "Requirement already satisfied (use --upgrade to upgrade): Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 46))\n",
      "Requirement already satisfied (use --upgrade to upgrade): sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 47))\n",
      "Requirement already satisfied (use --upgrade to upgrade): pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48))\n",
      "Requirement already satisfied (use --upgrade to upgrade): six==1.9.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49))\n",
      "Requirement already satisfied (use --upgrade to upgrade): Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 50))\n",
      "Requirement already satisfied (use --upgrade to upgrade): nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51))\n",
      "Requirement already satisfied (use --upgrade to upgrade): SVGFig==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 52))\n",
      "Requirement already satisfied (use --upgrade to upgrade): Fabric==1.10.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 55))\n",
      "Requirement already satisfied (use --upgrade to upgrade): paramiko==1.15.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 56))\n",
      "Requirement already satisfied (use --upgrade to upgrade): ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 57))\n",
      "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))\n",
      "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))\n",
      "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))\n",
      "Activating virtualenv at /home/john/workspace/galaxy/.venv\n",
      "Entering daemon mode\n",
      ".........\n",
      "{u'stdin': None, u'command_line': [u'cat', u'/tmp/tmptEYGQR/files/000/dataset_1.dat'], u'stdout': u'output.txt'}\n"
     ]
    }
   ],
   "source": [
    "!planemo cwl_run cat3-tool.cwl cat-job.json"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 2",
   "language": "python",
   "name": "python2"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 2
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython2",
   "version": "2.7.6"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 0
}