September 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 150c17: Do not explicitly require pexpect. If anyone wants...
by GitHub 17 Sep '15

17 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 150c17b9e8adc03fe8684962ca76f19bf0c93705 https://github.com/galaxyproject/galaxy/commit/150c17b9e8adc03fe8684962ca76… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/web/framework/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M scripts/transfer.py Log Message: ----------- Do not explicitly require pexpect. If anyone wants to use the old and mostly unused features that depend on it (namely remote sequencer transfers via scp) they can pip install pexpect. Commit: 63e35965401a2eac2ef3308913fb48be89961c10 https://github.com/galaxyproject/galaxy/commit/63e35965401a2eac2ef3308913fb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/web/framework/__init__.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M scripts/transfer.py Log Message: ----------- Merge pull request #741 from natefoo/drop-pexpect Do not explicitly require pexpect Compare: https://github.com/galaxyproject/galaxy/compare/d717ec833de5...63e35965401a

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[galaxyproject/galaxy] ce3e79: Use setup.py for all installations instead of the ...
by GitHub 17 Sep '15

17 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ce3e7931f6cb19a4a0c1e7cd2bdcbe301c9060f3 https://github.com/galaxyproject/galaxy/commit/ce3e7931f6cb19a4a0c1e7cd2bdc… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-09-05 (Sat, 05 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Use setup.py for all installations instead of the depreceated easy_install method. Commit: 4e063e793f6ddea0ae4c36183b8b4ad96d193f08 https://github.com/galaxyproject/galaxy/commit/4e063e793f6ddea0ae4c36183b8b… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- add mkdir as safeguard and remove old warning Commit: d717ec833de5615fdb949fdfd0a3c69ab90a7a7f https://github.com/galaxyproject/galaxy/commit/d717ec833de5615fdb949fdfd0a3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #698 from bgruening/pip_install Use setup.py for Python all installations Compare: https://github.com/galaxyproject/galaxy/compare/c74cda3c60b0...d717ec833de5

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[galaxyproject/galaxy] bd5565: Add testing environment variable GALAXY_TEST_LOGGI...
by GitHub 17 Sep '15

17 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bd55650f0624e4218cbf898a73579979e7bc6072 https://github.com/galaxyproject/galaxy/commit/bd55650f0624e4218cbf898a7357… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M scripts/functional_tests.py A test/base/test_logging.py Log Message: ----------- Add testing environment variable GALAXY_TEST_LOGGING_CONFIG. Unifies logging through the testing process. Requires adding a Galaxy option to disable its own attempts to configure a different root logger. Commit: c74cda3c60b0b0e8c8698946c373999fac300b4c https://github.com/galaxyproject/galaxy/commit/c74cda3c60b0b0e8c8698946c373… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M scripts/functional_tests.py A test/base/test_logging.py Log Message: ----------- Merge pull request #738 from jmchilton/logging Add testing environment variable GALAXY_TEST_LOGGING_CONFIG. Compare: https://github.com/galaxyproject/galaxy/compare/7c78e01b7da0...c74cda3c60b0

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[galaxyproject/galaxy] 1a5ef1: First pass of updating rerun to use the new modal....
by GitHub 17 Sep '15

17 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1a5ef156d9d58966bee8dba95ac2cf2803fe16a7 https://github.com/galaxyproject/galaxy/commit/1a5ef156d9d58966bee8dba95ac2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M lib/galaxy/managers/hdas.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/tools.py M static/maps/galaxy-app-base.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/galaxy-app-base.js M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- First pass of updating rerun to use the new modal. Pretty hacky, needs cleanup. Commit: c51bfaa51aefff1e6be5c54b72fc51c4fc666264 https://github.com/galaxyproject/galaxy/commit/c51bfaa51aefff1e6be5c54b72fc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/tools/tools-form-base.js M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Flip API endpoint to the jobs API instead of hacking it into the existing tools api. Commit: 5953fb592202cd12cf4cfb78900a4f1b89e85c79 https://github.com/galaxyproject/galaxy/commit/5953fb592202cd12cf4cfb78900a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Use tool.to_json optional kwd to parse old job inputs instead of doing it manually. Commit: 3348715971bc85901553fe8b87f9d3962962b40c https://github.com/galaxyproject/galaxy/commit/3348715971bc85901553fe8b87f9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Add documentation to new API endpoint. Commit: a7ca9586bb8bffaf61d751e6b21da46a187bbad1 https://github.com/galaxyproject/galaxy/commit/a7ca9586bb8bffaf61d751e6b21d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M lib/galaxy/managers/hdas.py M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Allow serialization of hdas without 'creating job', though we should probably look into how/why this can ever happen. Seems like there's a bug hidden here somewhere, but this allows the existing functionality to work and pass tests. Commit: 7c78e01b7da020d11cad29c906536e1ff95b484d https://github.com/galaxyproject/galaxy/commit/7c78e01b7da020d11cad29c90653… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M lib/galaxy/managers/hdas.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/galaxy-app-base.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/scripts/galaxy-app-base.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/tools/tools-form-base.js Log Message: ----------- Merge pull request #739 from dannon/rerun_newform Swap rerun to use iframe-less Galaxy.display. Compare: https://github.com/galaxyproject/galaxy/compare/4d4e19b37904...7c78e01b7da0

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[galaxyproject/infrastructure-playbook] 1120d1: Add new BX mail servers to SpamAssassin config
by GitHub 17 Sep '15

17 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1120d1b74114b7631b36692127a2afe0249a15db https://github.com/galaxyproject/infrastructure-playbook/commit/1120d1b7411… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M roles/postfix/templates/local.cf.j2 Log Message: ----------- Add new BX mail servers to SpamAssassin config

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[galaxyproject/infrastructure-playbook] 8ae8b2: add unzip to n2
by GitHub 17 Sep '15

17 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 8ae8b2acfcf244356af751e58945ac7059035784 https://github.com/galaxyproject/infrastructure-playbook/commit/8ae8b2acfcf… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml Log Message: ----------- add unzip to n2

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[galaxyproject/galaxy] d3e14e: Check to make sure a job is actually part of a wor...
by GitHub 17 Sep '15

17 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d3e14ec6731d6f0524ff8f2575a100555de2fe25 https://github.com/galaxyproject/galaxy/commit/d3e14ec6731d6f0524ff8f2575a1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Check to make sure a job is actually part of a workflow invocation prior to attempting to clean other workflow steps. This prevents an error when a 'clean intermediates' type job is remapped. TODO: Perhaps the job should actually be replaced in the workflow invocation as well, but this is a decent defensive check anyway. Commit: 4d4e19b37904907201217bff7a6d295411b93968 https://github.com/galaxyproject/galaxy/commit/4d4e19b37904907201217bff7a6d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-17 (Thu, 17 Sep 2015) Changed paths: M lib/galaxy/jobs/actions/post.py Log Message: ----------- Merge pull request #736 from dannon/pja_wf_rerun_fix Check to make sure a job is actually part of a workflow invocation pr… Compare: https://github.com/galaxyproject/galaxy/compare/43c13ee16267...4d4e19b37904

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[galaxyproject/usegalaxy-playbook] 83fc23: show 'Test' in the masthead on Test; update dispos...
by GitHub 16 Sep '15

16 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 83fc23c1d5be14f351a8718f1b7fa2c4c1b5bedc https://github.com/galaxyproject/usegalaxy-playbook/commit/83fc23c1d5be14f3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M stage/group_vars/galaxyservers.yml M stage/secret_vars/galaxyservers.yml Log Message: ----------- show 'Test' in the masthead on Test; update disposable domain list

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[galaxyproject/infrastructure-playbook] 6547ae: add python-virtualenv package to n2, remove whites...
by GitHub 16 Sep '15

16 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6547ae51e15e02470019d0700d2995fcdd8fa1d2 https://github.com/galaxyproject/infrastructure-playbook/commit/6547ae51e15… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml Log Message: ----------- add python-virtualenv package to n2, remove whitespace Commit: 10afb69d72a5f1f1fcaf82ab00195b0319b86628 https://github.com/galaxyproject/infrastructure-playbook/commit/10afb69d72a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M common_roles Log Message: ----------- Rev common_roles. Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/dc91d3c8e8…

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[galaxyproject/usegalaxy-playbook] bf2a23: Update Main Galaxy and Pulsar, enable AMQP acknowl...
by GitHub 16 Sep '15

16 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bf2a23c417dd527d3f0a7f799fb6e95ff7c3604e https://github.com/galaxyproject/usegalaxy-playbook/commit/bf2a23c417dd527d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M production/group_vars/all.yml M production/group_vars/pulsarservers.yml M production/host_vars/login5.stampede.tacc.utexas.edu.yml M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Update Main Galaxy and Pulsar, enable AMQP acknowledgements

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