- galaxy-commits - lists.galaxyproject.org

[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

1 0

[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

1 0

[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

1 0

[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

1 0

[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

1 0

[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

1 0

[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…

1 0

[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

1 0

[galaxyproject/usegalaxy-playbook] 659dbc: Update Test
by GitHub 16 Sep '15

16 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 659dbced678c878d79b396982d9b046fb03dc4f5 https://github.com/galaxyproject/usegalaxy-playbook/commit/659dbced678c878d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test

1 0

[galaxyproject/galaxy] d41c13: Fix for logging in using OpenID when the OpenID is...
by GitHub 16 Sep '15

16 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d41c137e2d6b4d9871bb25c5162745dda36e2f31 https://github.com/galaxyproject/galaxy/commit/d41c137e2d6b4d9871bb25c51627… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M templates/user/login.mako Log Message: ----------- Fix for logging in using OpenID when the OpenID isn't associated with a user yet. (cherry picked from commit 451196e4d39800995d7b1ea1f69b177294c3c632) Commit: 358dc4071462347dacecd1f6ec125d650b261db0 https://github.com/galaxyproject/galaxy/commit/358dc4071462347dacecd1f6ec12… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M templates/user/login.mako Log Message: ----------- Merge pull request #718 from blankenberg/openid_15.07 [15.07] Fix for logging in using OpenID when the OpenID isn't associated with a user yet. Commit: 88abd3451d1b8cb7161fde7559684d5378dc76fc https://github.com/galaxyproject/galaxy/commit/88abd3451d1b8cb7161fde755968… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/pulsar/client/amqp_exchange.py Log Message: ----------- Merge pull request #719 from natefoo/amqp_ack [15.07] Pulsar client: Fix deepcopy() error with copying the errback method from PulsarExchange. Commit: d3bd0fa57765bd2d03f255099c2b4f0501ac6466 https://github.com/galaxyproject/galaxy/commit/d3bd0fa57765bd2d03f255099c2b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py Log Message: ----------- Do not change the state of jobs if a state update is received after they are set to a terminal state. Commit: 85552f73f712a9491af8d141a27369b21b615075 https://github.com/galaxyproject/galaxy/commit/85552f73f712a9491af8d141a273… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #737 from natefoo/job-terminal-update [15.07] Don't update the state of terminal jobs Commit: 43c13ee1626779a4127f67b564ee88bb6b9af3ca https://github.com/galaxyproject/galaxy/commit/43c13ee1626779a4127f67b564ee… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge branch 'release_15.07' into dev Conflicts: lib/galaxy/model/__init__.py Compare: https://github.com/galaxyproject/galaxy/compare/1e2adc6b5703...43c13ee16267

1 0

[galaxyproject/galaxy] d3bd0f: Do not change the state of jobs if a state update ...
by GitHub 16 Sep '15

16 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: d3bd0fa57765bd2d03f255099c2b4f0501ac6466 https://github.com/galaxyproject/galaxy/commit/d3bd0fa57765bd2d03f255099c2b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py Log Message: ----------- Do not change the state of jobs if a state update is received after they are set to a terminal state. Commit: 85552f73f712a9491af8d141a27369b21b615075 https://github.com/galaxyproject/galaxy/commit/85552f73f712a9491af8d141a273… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #737 from natefoo/job-terminal-update [15.07] Don't update the state of terminal jobs Compare: https://github.com/galaxyproject/galaxy/compare/88abd3451d1b...85552f73f712

1 0

[galaxyproject/infrastructure-playbook] dc91d3: add jenkins to the docker group
by GitHub 16 Sep '15

16 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: dc91d3c8e8dc57e05bd9efa0022c0d237edfbcd9 https://github.com/galaxyproject/infrastructure-playbook/commit/dc91d3c8e8d… 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 jenkins to the docker group jenkins user was created by apt

1 0

[galaxyproject/infrastructure-playbook] 6a54a5: Install packages before managing local users
by GitHub 16 Sep '15

16 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6a54a5f3801a01a016124167b9dae56a9e227fdd https://github.com/galaxyproject/infrastructure-playbook/commit/6a54a5f3801… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-16 (Wed, 16 Sep 2015) Changed paths: M playbook.yml Log Message: ----------- Install packages before managing local users Allows managing properties of apt managed users.

1 0

[galaxyproject/infrastructure-playbook] c90d0f: add more packages to n2; add backports
by GitHub 16 Sep '15

16 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c90d0f928a4c618ad756eea52b4added68cb5830 https://github.com/galaxyproject/infrastructure-playbook/commit/c90d0f928a4… 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 more packages to n2; add backports

1 0

[galaxyproject/infrastructure-playbook] 5a2674: fix packages to host_packages so it actually gets ...
by GitHub 16 Sep '15

16 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 5a2674a9c9a06ad8345077298486d19fc4df86e7 https://github.com/galaxyproject/infrastructure-playbook/commit/5a2674a9c9a… 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: ----------- fix packages to host_packages so it actually gets recognized

1 0

[galaxyproject/infrastructure-playbook] 49e5db: add TS dependencies in order to get func tests wor...
by GitHub 16 Sep '15

16 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 49e5dba92773f83924e4c145fac09670726fa31b https://github.com/galaxyproject/infrastructure-playbook/commit/49e5dba9277… 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 TS dependencies in order to get func tests working

1 0

[galaxyproject/galaxy] 89cc67: Trigger iframe event for history
by GitHub 15 Sep '15

15 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 89cc67baf67e295b3eaa2449e6fd6727317df942 https://github.com/galaxyproject/galaxy/commit/89cc67baf67e295b3eaa2449e6fd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Trigger iframe event for history Commit: 1e2adc6b57034fb27b3a12f0a13d6f0ace1b096a https://github.com/galaxyproject/galaxy/commit/1e2adc6b57034fb27b3a12f0a13d… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Merge pull request #732 from guerler/fix_history_001 Trigger iframe event for history Compare: https://github.com/galaxyproject/galaxy/compare/71a1def3219d...1e2adc6b5703

1 0

[galaxyproject/galaxy] 555b6d: Fix for 13ea86753ad778aaaf6e6470a9370190fc2e91a0.
by GitHub 15 Sep '15

15 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 555b6d745d245d5fa6d6868e92cc3797d6855343 https://github.com/galaxyproject/galaxy/commit/555b6d745d245d5fa6d6868e92cc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Fix for 13ea86753ad778aaaf6e6470a9370190fc2e91a0. Fixes tests and functionality broken with 13ea86753ad778aaaf6e6470a9370190fc2e91a0 as spotted by eagle eye @nsoranzo here https://github.com/galaxyproject/galaxy/commit/13ea86753ad778aaaf6e6470a937…. Commit: 71a1def3219db8763e76b87a4bb1aefdfdc082d3 https://github.com/galaxyproject/galaxy/commit/71a1def3219db8763e76b87a4bb1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Merge pull request #735 from jmchilton/collection_fix Fix for 13ea86753ad778aaaf6e6470a9370190fc2e91a0. Compare: https://github.com/galaxyproject/galaxy/compare/89b42bf06034...71a1def3219d

1 0

[galaxyproject/infrastructure-playbook] 80bb94: Update README.md
by GitHub 15 Sep '15

15 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 80bb94e97d6cb83b07e1f40b2575a933734c2a72 https://github.com/galaxyproject/infrastructure-playbook/commit/80bb94e97d6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M README.md Log Message: ----------- Update README.md

1 0

[galaxyproject/galaxy] 3fafbb: Fix more MissingToolException when running "./run_...
by GitHub 15 Sep '15

15 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3fafbb5e34ed3f6f547bf1f184782b0f6967cf2f https://github.com/galaxyproject/galaxy/commit/3fafbb5e34ed3f6f547bf1f18478… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M test/api/test_workflow_extraction.py Log Message: ----------- Fix more MissingToolException when running "./run_tests.sh -api" without "-with_framework_test_tools". Commit: 63d1715679fb714f4c8f5ae426106edf6988e7ab https://github.com/galaxyproject/galaxy/commit/63d1715679fb714f4c8f5ae42610… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix API tests using collection_creates_pair tool. Commit: 89b42bf0603433b2b66a264c9a3a3d3fe4e12280 https://github.com/galaxyproject/galaxy/commit/89b42bf0603433b2b66a264c9a3a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M lib/galaxy/tools/__init__.py M test/api/test_workflow_extraction.py Log Message: ----------- Merge pull request #731 from nsoranzo/dev Fix more API tests. Compare: https://github.com/galaxyproject/galaxy/compare/4671ae8d4509...89b42bf06034

1 0

[galaxyproject/infrastructure-playbook] fb8175: add virtualenv to n2
by GitHub 15 Sep '15

15 Sep '15

Branch: refs/heads/martenson-patch-2 Home: https://github.com/galaxyproject/infrastructure-playbook Commit: fb81757b634892f1b717b68a7ee3275a5e1ec2e1 https://github.com/galaxyproject/infrastructure-playbook/commit/fb81757b634… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml Log Message: ----------- add virtualenv to n2

1 0

[galaxyproject/infrastructure-playbook] 41f8d6: install postgresql-9.4 on n2
by GitHub 15 Sep '15

15 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 41f8d6cc7e261b9f200ccc8e0efb57e41d8e846f https://github.com/galaxyproject/infrastructure-playbook/commit/41f8d6cc7e2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml Log Message: ----------- install postgresql-9.4 on n2 Commit: eafac90f95fb5e7674655ccc98419d9d4f3341fc https://github.com/galaxyproject/infrastructure-playbook/commit/eafac90f95f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml Log Message: ----------- Merge pull request #1 from galaxyproject/martenson-patch-1 install postgresql-9.4 on n2 Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/113caf158f…

1 0

[galaxyproject/galaxy] 23051d: When rerunning a job w/ remap, reassociate PostJob...
by GitHub 15 Sep '15

15 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 23051da68c88f1173be8094c2597cc60cb054f27 https://github.com/galaxyproject/galaxy/commit/23051da68c88f1173be8094c2597… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- When rerunning a job w/ remap, reassociate PostJobActions when possible to the new job. Commit: 4671ae8d45092824db2f7b19b7d6896e6524c672 https://github.com/galaxyproject/galaxy/commit/4671ae8d45092824db2f7b19b7d6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Merge pull request #730 from dannon/pja_wf_rerun_fix When rerunning a job w/ remap, reassociate PostJobActions when possib… Compare: https://github.com/galaxyproject/galaxy/compare/1ea1da02291d...4671ae8d4509

1 0

[galaxyproject/galaxy] 8dadfd: remove no-op __init__ methods
by GitHub 15 Sep '15

15 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8dadfdcaa0492bce485fb786aed0d29243356258 https://github.com/galaxyproject/galaxy/commit/8dadfdcaa0492bce485fb786aed0… Author: Michael R. Crusoe <crusoe(a)ucdavis.edu> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- remove no-op __init__ methods Commit: 1ea1da02291d3d9abbec32a09d63a16ddcef1084 https://github.com/galaxyproject/galaxy/commit/1ea1da02291d3d9abbec32a09d63… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-15 (Tue, 15 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #729 from mr-c/drop-noop-init remove no-op __init__ methods from lib/galaxy/datatypes/binary.py Compare: https://github.com/galaxyproject/galaxy/compare/34165913ba1e...1ea1da02291d

1 0

[galaxyproject/galaxy] 471664: Merge "Issues" and "Galaxy Development" from READM...
by GitHub 14 Sep '15

14 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 471664c2692315b6699c586efccb6c7522fd6b56 https://github.com/galaxyproject/galaxy/commit/471664c2692315b6699c586efccb… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-07 (Mon, 07 Sep 2015) Changed paths: M CONTRIBUTING.md M README.rst Log Message: ----------- Merge "Issues" and "Galaxy Development" from README.rst in CONTRIBUTING.md . Commit: 3f40b7ca8f41403cc00e9fbbc88d8b48b6be6259 https://github.com/galaxyproject/galaxy/commit/3f40b7ca8f41403cc00e9fbbc88d… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-07 (Mon, 07 Sep 2015) Changed paths: M CONTRIBUTING.md M doc/source/project/organization.rst Log Message: ----------- Move "Handling Pull Requests" from CONTRIBUTING.md to organization.rst . Commit: 34165913ba1e70ee72db363aeea74cc1824301ec https://github.com/galaxyproject/galaxy/commit/34165913ba1e70ee72db363aeea7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M CONTRIBUTING.md M README.rst M doc/source/project/organization.rst Log Message: ----------- Merge pull request #702 from nsoranzo/readme_contributing [PROCEDURES] Reorganize content Compare: https://github.com/galaxyproject/galaxy/compare/08668104e5aa...34165913ba1e

1 0