wc-env-manager container build fails with the default config

[artgoldberg]

wc-env-manager container build fails with the default config/core.default.cfg:

$ docker image ls -a; docker container ls -a
REPOSITORY                               TAG                 IMAGE ID            CREATED             SIZE
circleci/postgres                        11.2-alpine-ram     9bba4a631f6d        3 months ago        70.8MB
karrlab/wc_env                           0.0.51              3d35a1beb777        4 months ago        5.81GB
karrlab/wc_env                           latest              3d35a1beb777        4 months ago        5.81GB
karrlab/wc_env_dependencies              latest              953edb5668b3        4 months ago        5.72GB
karrlab/wc_env_dependencies_unsquashed   latest              d4322c96ccd6        4 months ago        6.52GB
CONTAINER ID        IMAGE               COMMAND             CREATED             STATUS              PORTS               NAMES

$ wc-env-manager container build
/anaconda3/lib/python3.6/site-packages/wc_env_manager/core.py:443: UserWarning: Third party configuration files will not be copied to the image because no index of third party configuration files was found at "/Users/arthur_at_sinai/.wc/third_party/paths.yml".  This path should be a YAML-encoded dictionary which maps the names of files within "{}" to locations in the image where each file should be copied. See "https://github.com/KarrLab/karr_lab_build_config/tree/master/third_party" for an example.
  UserWarning)

Creating directory /root/.config/bioservices 
/usr/local/lib/python3.6/site-packages/psycopg2/__init__.py:144: UserWarning: The psycopg2 wheel package will be renamed from release 2.8; in order to keep installing from binary please use "pip install psycopg2-binary" instead. For details see: <http://initd.org/psycopg/docs/install.html#binary-install-from-pypi>.
  """)
Creating directory /root/migrations ... done
Creating directory /root/migrations/versions ... done
Generating /root/migrations/script.py.mako ... done
Generating /root/migrations/README ... done
Generating /root/migrations/alembic.ini ... done
Generating /root/migrations/env.py ... done
Please edit configuration/connection/logging settings in '/root/migrations/alembic.ini' before proceeding.
/usr/local/lib/python3.6/site-packages/psycopg2/__init__.py:144: UserWarning: The psycopg2 wheel package will be renamed from release 2.8; in order to keep installing from binary please use "pip install psycopg2-binary" instead. For details see: <http://initd.org/psycopg/docs/install.html#binary-install-from-pypi>.
  """)
INFO  [alembic.runtime.migration] Context impl PostgresqlImpl.
INFO  [alembic.runtime.migration] Will assume transactional DDL.
INFO  [alembic.ddl.postgresql] Detected sequence named 'synonym_id_seq' as owned by integer column 'synonym(id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'dna_binding_data_position_id_seq' as owned by integer column 'dna_binding_data(position_id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'cell_compartment_id_seq' as owned by integer column 'cell_compartment(id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'reaction_reaction_id_seq' as owned by integer column 'reaction(reaction_id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'conditions_id_seq' as owned by integer column 'conditions(id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'parameter_parameter_id_seq' as owned by integer column 'parameter(parameter_id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'abundance_data_abundance_id_seq' as owned by integer column 'abundance_data(abundance_id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'data_format__id_seq' as owned by integer column 'data_format(_id)', assuming SERIAL and omitting
INFO  [alembic.env] No changes in schema detected.
INFO  [alembic.runtime.migration] Context impl PostgresqlImpl.
INFO  [alembic.runtime.migration] Will assume transactional DDL.
/usr/local/lib/python3.6/site-packages/psycopg2/__init__.py:144: UserWarning: The psycopg2 wheel package will be renamed from release 2.8; in order to keep installing from binary please use "pip install psycopg2-binary" instead. For details see: <http://initd.org/psycopg/docs/install.html#binary-install-from-pypi>.
  """)
Traceback (most recent call last):
  File "/usr/local/bin/datanator", line 10, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.6/site-packages/datanator/__main__.py", line 840, in main
    app.run()
  File "/usr/local/lib/python3.6/site-packages/cement/core/foundation.py", line 916, in run
    return_val = self.controller._dispatch()
  File "/usr/local/lib/python3.6/site-packages/cement/ext/ext_argparse.py", line 808, in _dispatch
    return func()
  File "/usr/local/lib/python3.6/site-packages/datanator/__main__.py", line 773, in _default
    verbose=True)
  File "/usr/local/lib/python3.6/site-packages/datanator/core/common_schema.py", line 64, in __init__
    verbose=verbose)
  File "/usr/local/lib/python3.6/site-packages/datanator/core/data_source.py", line 110, in __init__
    exit_on_error=restore_backup_exit_on_error)
  File "/usr/local/lib/python3.6/site-packages/datanator/core/data_source.py", line 187, in restore_backup
    manager.download(system_path=path, sym_links=True)
  File "/usr/local/lib/python3.6/site-packages/wc_utils/quilt.py", line 104, in download
    quilt.login_with_token(self.token)
  File "/usr/local/lib/python3.6/site-packages/quilt/tools/command.py", line 423, in login_with_token
    auth = _update_auth(team, refresh_token)
  File "/usr/local/lib/python3.6/site-packages/quilt/tools/command.py", line 199, in _update_auth
    raise CommandException("Authentication error: %s" % response.status_code)
quilt.tools.command.CommandException: Authentication error: 401
Traceback (most recent call last):
  File "/anaconda3/bin/wc-env-manager", line 10, in <module>
    sys.exit(main())
  File "/anaconda3/lib/python3.6/site-packages/wc_env_manager/__main__.py", line 274, in main
    app.run()
  File "/anaconda3/lib/python3.6/site-packages/cement/core/foundation.py", line 916, in run
    return_val = self.controller._dispatch()
  File "/anaconda3/lib/python3.6/site-packages/cement/ext/ext_argparse.py", line 806, in _dispatch
    return func()
  File "/anaconda3/lib/python3.6/site-packages/wc_env_manager/__main__.py", line 175, in build
    mgr.setup_container()
  File "/anaconda3/lib/python3.6/site-packages/wc_env_manager/core.py", line 668, in setup_container
    self.run_process_in_container(['bash', '-c', cmd], container_user=WcEnvUser.root)
  File "/anaconda3/lib/python3.6/site-packages/wc_env_manager/core.py", line 810, in run_process_in_container
    result.output.decode('utf-8')))
wc_env_manager.core.WcEnvManagerError: Command not successfully executed in Docker container:
  command: ['bash', '-c', '\n            if [ -x "$(command -v datanator)" ]; then\n                datanator db create\n                datanator db migrate\n                datanator db restore --restore-schema --do-not-exit-on-error\n            fi\n            ']
  working directory: /root
  environment:

  exit code: 1
  output: Creating directory /root/.config/bioservices 
/usr/local/lib/python3.6/site-packages/psycopg2/__init__.py:144: UserWarning: The psycopg2 wheel package will be renamed from release 2.8; in order to keep installing from binary please use "pip install psycopg2-binary" instead. For details see: <http://initd.org/psycopg/docs/install.html#binary-install-from-pypi>.
  """)
Creating directory /root/migrations ... done
Creating directory /root/migrations/versions ... done
Generating /root/migrations/script.py.mako ... done
Generating /root/migrations/README ... done
Generating /root/migrations/alembic.ini ... done
Generating /root/migrations/env.py ... done
Please edit configuration/connection/logging settings in '/root/migrations/alembic.ini' before proceeding.
/usr/local/lib/python3.6/site-packages/psycopg2/__init__.py:144: UserWarning: The psycopg2 wheel package will be renamed from release 2.8; in order to keep installing from binary please use "pip install psycopg2-binary" instead. For details see: <http://initd.org/psycopg/docs/install.html#binary-install-from-pypi>.
  """)
INFO  [alembic.runtime.migration] Context impl PostgresqlImpl.
INFO  [alembic.runtime.migration] Will assume transactional DDL.
INFO  [alembic.ddl.postgresql] Detected sequence named 'synonym_id_seq' as owned by integer column 'synonym(id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'dna_binding_data_position_id_seq' as owned by integer column 'dna_binding_data(position_id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'cell_compartment_id_seq' as owned by integer column 'cell_compartment(id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'reaction_reaction_id_seq' as owned by integer column 'reaction(reaction_id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'conditions_id_seq' as owned by integer column 'conditions(id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'parameter_parameter_id_seq' as owned by integer column 'parameter(parameter_id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'abundance_data_abundance_id_seq' as owned by integer column 'abundance_data(abundance_id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'data_format__id_seq' as owned by integer column 'data_format(_id)', assuming SERIAL and omitting
INFO  [alembic.env] No changes in schema detected.
INFO  [alembic.runtime.migration] Context impl PostgresqlImpl.
INFO  [alembic.runtime.migration] Will assume transactional DDL.
/usr/local/lib/python3.6/site-packages/psycopg2/__init__.py:144: UserWarning: The psycopg2 wheel package will be renamed from release 2.8; in order to keep installing from binary please use "pip install psycopg2-binary" instead. For details see: <http://initd.org/psycopg/docs/install.html#binary-install-from-pypi>.
  """)
Traceback (most recent call last):
  File "/usr/local/bin/datanator", line 10, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.6/site-packages/datanator/__main__.py", line 840, in main
    app.run()
  File "/usr/local/lib/python3.6/site-packages/cement/core/foundation.py", line 916, in run
    return_val = self.controller._dispatch()
  File "/usr/local/lib/python3.6/site-packages/cement/ext/ext_argparse.py", line 808, in _dispatch
    return func()
  File "/usr/local/lib/python3.6/site-packages/datanator/__main__.py", line 773, in _default
    verbose=True)
  File "/usr/local/lib/python3.6/site-packages/datanator/core/common_schema.py", line 64, in __init__
    verbose=verbose)
  File "/usr/local/lib/python3.6/site-packages/datanator/core/data_source.py", line 110, in __init__
    exit_on_error=restore_backup_exit_on_error)
  File "/usr/local/lib/python3.6/site-packages/datanator/core/data_source.py", line 187, in restore_backup
    manager.download(system_path=path, sym_links=True)
  File "/usr/local/lib/python3.6/site-packages/wc_utils/quilt.py", line 104, in download
    quilt.login_with_token(self.token)
  File "/usr/local/lib/python3.6/site-packages/quilt/tools/command.py", line 423, in login_with_token
    auth = _update_auth(team, refresh_token)
  File "/usr/local/lib/python3.6/site-packages/quilt/tools/command.py", line 199, in _update_auth
    raise CommandException("Authentication error: %s" % response.status_code)
quilt.tools.command.CommandException: Authentication error: 401

[jonrkarr]

It looks like you're missing the wc_utils configuration with the Quilt password.

I do not recommend trying to build the full image.

Building the full image takes a bit of work because some tasks cannot be automated. You would need to obtain new licenses (Gurobi licenses can only be used once), as well as copies of the proprietary software that is loaded into the image (CPLEX cannot be downloaded programmatically).

However, its comparatively easy to use the configuration to build images which only contain a subset of the dependencies (i.e., none of the packages which require licenses, passwords, or manual downloads -- no datatantor, Gurobi, CPLEX, Mosek, Xpress, etc.).

Note, because the building the full image cannot be completely automated, I am only testing wc-env-manager periodically. In addition, its difficult to automate the tests of wc-env-manager because many of the tests cannot be run in CircleCI. These tests can't easily be run in CircleCI because docker cannot be run within docker with the options that CircleCI sets on the top-level container, and CircleCI doesn't provide a way to change these options. (I think this can be done in CircleCI, but it would need to be implemented with a different type of executor which would require significant effort to setup. See #3 .)

[artgoldberg]

I'm not interested in building the full image.

I would like to build a partial image without datanator (in which case I wouldn't need the Quilt password), alembic, postgres, and other things I don't need. I just submitted another issue that used a custom config to do that but that didn't work. Don't worry about it, however, as I've hacked a working Docker container which I'll use for a while. Just think of it as a reminder about wc-env-manager complexitis that someone might address in the future.

wc-env-manager takes a lot of time to use, so I do that rarely.

[jonrkarr]

I've been working on wc_env_manager periodically as major changes to the image are needed. I can take care of these issues then.

Likely the next major change will be upgrading to Python 3.7. I've been waiting for CPLEX to release a version compatible with 3.7. When I do this, I'll upgrade all of our dependencies.

[artgoldberg]

I provided the karr_lab_build_config/wc_utils.cfg file and tried again:

$ wc-env-manager container build
/anaconda3/lib/python3.6/site-packages/wc_env_manager/core.py:443: UserWarning: Third party configuration files will not be copied to the image because no index of third party configuration files was found at "/Users/arthur_at_sinai/.wc/third_party/paths.yml".  This path should be a YAML-encoded dictionary which maps the names of files within "{}" to locations in the image where each file should be copied. See "https://github.com/KarrLab/karr_lab_build_config/tree/master/third_party" for an example.
  UserWarning)

Creating directory /root/.config/bioservices 
/usr/local/lib/python3.6/site-packages/psycopg2/__init__.py:144: UserWarning: The psycopg2 wheel package will be renamed from release 2.8; in order to keep installing from binary please use "pip install psycopg2-binary" instead. For details see: <http://initd.org/psycopg/docs/install.html#binary-install-from-pypi>.
  """)
Creating directory /root/migrations ... done
Creating directory /root/migrations/versions ... done
Generating /root/migrations/script.py.mako ... done
Generating /root/migrations/README ... done
Generating /root/migrations/alembic.ini ... done
Generating /root/migrations/env.py ... done
Please edit configuration/connection/logging settings in '/root/migrations/alembic.ini' before proceeding.
/usr/local/lib/python3.6/site-packages/psycopg2/__init__.py:144: UserWarning: The psycopg2 wheel package will be renamed from release 2.8; in order to keep installing from binary please use "pip install psycopg2-binary" instead. For details see: <http://initd.org/psycopg/docs/install.html#binary-install-from-pypi>.
  """)
INFO  [alembic.runtime.migration] Context impl PostgresqlImpl.
INFO  [alembic.runtime.migration] Will assume transactional DDL.
INFO  [alembic.ddl.postgresql] Detected sequence named 'reaction_reaction_id_seq' as owned by integer column 'reaction(reaction_id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'cell_line_id_seq' as owned by integer column 'cell_line(id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'experiment_type_id_seq' as owned by integer column 'experiment_type(id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'method_id_seq' as owned by integer column 'method(id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'parameter_parameter_id_seq' as owned by integer column 'parameter(parameter_id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'abundance_data_abundance_id_seq' as owned by integer column 'abundance_data(abundance_id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'experiment_id_seq' as owned by integer column 'experiment(id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'data_format__id_seq' as owned by integer column 'data_format(_id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'conditions_id_seq' as owned by integer column 'conditions(id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'synonym_id_seq' as owned by integer column 'synonym(id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'taxon_ncbi_id_seq' as owned by integer column 'taxon(ncbi_id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'variable_id_seq' as owned by integer column 'variable(id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'dna_binding_data_position_id_seq' as owned by integer column 'dna_binding_data(position_id)', assuming SERIAL and omitting
INFO  [alembic.env] No changes in schema detected.
INFO  [alembic.runtime.migration] Context impl PostgresqlImpl.
INFO  [alembic.runtime.migration] Will assume transactional DDL.
/usr/local/lib/python3.6/site-packages/psycopg2/__init__.py:144: UserWarning: The psycopg2 wheel package will be renamed from release 2.8; in order to keep installing from binary please use "pip install psycopg2-binary" instead. For details see: <http://initd.org/psycopg/docs/install.html#binary-install-from-pypi>.
  """)
Traceback (most recent call last):
  File "/usr/local/bin/datanator", line 10, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.6/site-packages/datanator/__main__.py", line 840, in main
    app.run()
  File "/usr/local/lib/python3.6/site-packages/cement/core/foundation.py", line 916, in run
    return_val = self.controller._dispatch()
  File "/usr/local/lib/python3.6/site-packages/cement/ext/ext_argparse.py", line 808, in _dispatch
    return func()
  File "/usr/local/lib/python3.6/site-packages/datanator/__main__.py", line 773, in _default
    verbose=True)
  File "/usr/local/lib/python3.6/site-packages/datanator/core/common_schema.py", line 64, in __init__
    verbose=verbose)
  File "/usr/local/lib/python3.6/site-packages/datanator/core/data_source.py", line 110, in __init__
    exit_on_error=restore_backup_exit_on_error)
  File "/usr/local/lib/python3.6/site-packages/datanator/core/data_source.py", line 185, in restore_backup
    manager = wc_utils.quilt.QuiltManager(tmp_dirname, self.quilt_package, owner=self.quilt_owner)
  File "/usr/local/lib/python3.6/site-packages/wc_utils/quilt.py", line 52, in __init__
    config = wc_utils.config.get_config()['wc_utils']['quilt']
  File "/usr/local/lib/python3.6/site-packages/wc_utils/config/core.py", line 348, in get_config
    return ConfigManager(paths).get_config(extra=extra)
  File "/usr/local/lib/python3.6/site-packages/wc_utils/config/core.py", line 132, in get_config
    raise ExtraValuesError(value_sources, config)
wc_utils.config.core.ExtraValuesError: The following configuration sources
  /usr/local/lib/python3.6/site-packages/wc_utils/config/core.default.cfg
  /root/.wc/wc_utils.cfg

contain the following configuration errors
  Extra entry in section 'wc_utils'. Entry 'github' is a section.
Traceback (most recent call last):
  File "/anaconda3/bin/wc-env-manager", line 10, in <module>
    sys.exit(main())
  File "/anaconda3/lib/python3.6/site-packages/wc_env_manager/__main__.py", line 274, in main
    app.run()
  File "/anaconda3/lib/python3.6/site-packages/cement/core/foundation.py", line 916, in run
    return_val = self.controller._dispatch()
  File "/anaconda3/lib/python3.6/site-packages/cement/ext/ext_argparse.py", line 806, in _dispatch
    return func()
  File "/anaconda3/lib/python3.6/site-packages/wc_env_manager/__main__.py", line 175, in build
    mgr.setup_container()
  File "/anaconda3/lib/python3.6/site-packages/wc_env_manager/core.py", line 668, in setup_container
    self.run_process_in_container(['bash', '-c', cmd], container_user=WcEnvUser.root)
  File "/anaconda3/lib/python3.6/site-packages/wc_env_manager/core.py", line 810, in run_process_in_container
    result.output.decode('utf-8')))
wc_env_manager.core.WcEnvManagerError: Command not successfully executed in Docker container:
  command: ['bash', '-c', '\n            if [ -x "$(command -v datanator)" ]; then\n                datanator db create\n                datanator db migrate\n                datanator db restore --restore-schema --do-not-exit-on-error\n            fi\n            ']
  working directory: /root
  environment:

  exit code: 1
  output: Creating directory /root/.config/bioservices 
/usr/local/lib/python3.6/site-packages/psycopg2/__init__.py:144: UserWarning: The psycopg2 wheel package will be renamed from release 2.8; in order to keep installing from binary please use "pip install psycopg2-binary" instead. For details see: <http://initd.org/psycopg/docs/install.html#binary-install-from-pypi>.
  """)
Creating directory /root/migrations ... done
Creating directory /root/migrations/versions ... done
Generating /root/migrations/script.py.mako ... done
Generating /root/migrations/README ... done
Generating /root/migrations/alembic.ini ... done
Generating /root/migrations/env.py ... done
Please edit configuration/connection/logging settings in '/root/migrations/alembic.ini' before proceeding.
/usr/local/lib/python3.6/site-packages/psycopg2/__init__.py:144: UserWarning: The psycopg2 wheel package will be renamed from release 2.8; in order to keep installing from binary please use "pip install psycopg2-binary" instead. For details see: <http://initd.org/psycopg/docs/install.html#binary-install-from-pypi>.
  """)
INFO  [alembic.runtime.migration] Context impl PostgresqlImpl.
INFO  [alembic.runtime.migration] Will assume transactional DDL.
INFO  [alembic.ddl.postgresql] Detected sequence named 'reaction_reaction_id_seq' as owned by integer column 'reaction(reaction_id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'cell_line_id_seq' as owned by integer column 'cell_line(id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'experiment_type_id_seq' as owned by integer column 'experiment_type(id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'method_id_seq' as owned by integer column 'method(id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'parameter_parameter_id_seq' as owned by integer column 'parameter(parameter_id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'abundance_data_abundance_id_seq' as owned by integer column 'abundance_data(abundance_id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'experiment_id_seq' as owned by integer column 'experiment(id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'data_format__id_seq' as owned by integer column 'data_format(_id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'conditions_id_seq' as owned by integer column 'conditions(id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'synonym_id_seq' as owned by integer column 'synonym(id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'taxon_ncbi_id_seq' as owned by integer column 'taxon(ncbi_id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'variable_id_seq' as owned by integer column 'variable(id)', assuming SERIAL and omitting
INFO  [alembic.ddl.postgresql] Detected sequence named 'dna_binding_data_position_id_seq' as owned by integer column 'dna_binding_data(position_id)', assuming SERIAL and omitting
INFO  [alembic.env] No changes in schema detected.
INFO  [alembic.runtime.migration] Context impl PostgresqlImpl.
INFO  [alembic.runtime.migration] Will assume transactional DDL.
/usr/local/lib/python3.6/site-packages/psycopg2/__init__.py:144: UserWarning: The psycopg2 wheel package will be renamed from release 2.8; in order to keep installing from binary please use "pip install psycopg2-binary" instead. For details see: <http://initd.org/psycopg/docs/install.html#binary-install-from-pypi>.
  """)
Traceback (most recent call last):
  File "/usr/local/bin/datanator", line 10, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.6/site-packages/datanator/__main__.py", line 840, in main
    app.run()
  File "/usr/local/lib/python3.6/site-packages/cement/core/foundation.py", line 916, in run
    return_val = self.controller._dispatch()
  File "/usr/local/lib/python3.6/site-packages/cement/ext/ext_argparse.py", line 808, in _dispatch
    return func()
  File "/usr/local/lib/python3.6/site-packages/datanator/__main__.py", line 773, in _default
    verbose=True)
  File "/usr/local/lib/python3.6/site-packages/datanator/core/common_schema.py", line 64, in __init__
    verbose=verbose)
  File "/usr/local/lib/python3.6/site-packages/datanator/core/data_source.py", line 110, in __init__
    exit_on_error=restore_backup_exit_on_error)
  File "/usr/local/lib/python3.6/site-packages/datanator/core/data_source.py", line 185, in restore_backup
    manager = wc_utils.quilt.QuiltManager(tmp_dirname, self.quilt_package, owner=self.quilt_owner)
  File "/usr/local/lib/python3.6/site-packages/wc_utils/quilt.py", line 52, in __init__
    config = wc_utils.config.get_config()['wc_utils']['quilt']
  File "/usr/local/lib/python3.6/site-packages/wc_utils/config/core.py", line 348, in get_config
    return ConfigManager(paths).get_config(extra=extra)
  File "/usr/local/lib/python3.6/site-packages/wc_utils/config/core.py", line 132, in get_config
    raise ExtraValuesError(value_sources, config)
wc_utils.config.core.ExtraValuesError: The following configuration sources
  /usr/local/lib/python3.6/site-packages/wc_utils/config/core.default.cfg
  /root/.wc/wc_utils.cfg

contain the following configuration errors
  Extra entry in section 'wc_utils'. Entry 'github' is a section.

I temporarily fixed the incompatibility between wc_utils and karr_lab_build_config/wc_utils.cfg by removing the github section in my local copy of karr_lab_build_config/wc_utils.cfg. wc-env-manager container build then built a container.

I filed a bug issue for wc_utils and updated the documentation for wc-env-manager.

[jonrkarr]

This appears to be due to incompatible versions of the config schema in wc_utils and karr_lab_build_config on your machine.

I believe this issue can be closed.