Branch: refs/heads/release_18.05
Home: https://github.com/galaxyproject/galaxy
Commit: 5844bdc7aa0a90d992c3b36e041abb8d103e3b95
https://github.com/galaxyproject/galaxy/commit/5844bdc7aa0a90d992c3b36e041a…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-10-10 (Wed, 10 Oct 2018)
Changed paths:
M test/functional/tools/job_environment_default.xml
M test/functional/tools/job_environment_default_legacy.xml
M test/functional/tools/job_environment_explicit_shared_home.xml
A test/integration/test_cli_runners.py
M test/integration/test_job_environments.py
Log Message:
-----------
Add integration test for remote shell CLI runners
This tests both the SecureShell and Paramiko shell plugins and the
Slurm and Torque CLI runner.
Commit: 57a1f19b069597bde97852b3e0d0a3e1c0068bc4
https://github.com/galaxyproject/galaxy/commit/57a1f19b069597bde97852b3e0d0…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-10-10 (Wed, 10 Oct 2018)
Changed paths:
M lib/galaxy/jobs/runners/util/cli/shell/local.py
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
Log Message:
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Fix slurm cli plugin by avoiding `shell=True` in subprocess
Fixes the remaining issue in https://github.com/galaxyproject/galaxy/issues/6831#issuecomment-428097520
Commit: fc28e0bd83a2df59f11b80f0119e67da1326887f
https://github.com/galaxyproject/galaxy/commit/fc28e0bd83a2df59f11b80f0119e…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-10-10 (Wed, 10 Oct 2018)
Changed paths:
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
Log Message:
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Use long-form options
Commit: 5e12e509bf20d7e4f4464a60f04c7479cb4e232d
https://github.com/galaxyproject/galaxy/commit/5e12e509bf20d7e4f4464a60f04c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-10-10 (Wed, 10 Oct 2018)
Changed paths:
M test/integration/test_cli_runners.py
Log Message:
-----------
Fix selection of job plugin and image
Thanks @nsoranzo.
Commit: b08c6219c3fe771e00d0b6d8b9adb1c97e38e9a6
https://github.com/galaxyproject/galaxy/commit/b08c6219c3fe771e00d0b6d8b9ad…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-10-10 (Wed, 10 Oct 2018)
Changed paths:
M test/integration/test_cli_runners.py
Log Message:
-----------
Simplify ssh key handling in integration test
Commit: ac3e1ca1d0d7bb85cc00e2e113f70e3576f0b048
https://github.com/galaxyproject/galaxy/commit/ac3e1ca1d0d7bb85cc00e2e113f7…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-10-10 (Wed, 10 Oct 2018)
Changed paths:
M test/integration/test_cli_runners.py
Log Message:
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Use Crypto to generate SSH keys
Also remove key files in `stop_ssh_docker()`.
Commit: fd0b24ecd2bff2f8baa636304e45eb2dbdcaf3a9
https://github.com/galaxyproject/galaxy/commit/fd0b24ecd2bff2f8baa636304e45…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-10-11 (Thu, 11 Oct 2018)
Changed paths:
M lib/galaxy/jobs/runners/util/cli/shell/local.py
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
M test/functional/tools/job_environment_default.xml
M test/functional/tools/job_environment_default_legacy.xml
M test/functional/tools/job_environment_explicit_shared_home.xml
A test/integration/test_cli_runners.py
M test/integration/test_job_environments.py
Log Message:
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Merge pull request #6845 from mvdbeek/fix_slurm_cli_on_secure_shell
[18.05] Fix slurm cli on secure shell
Compare: https://github.com/galaxyproject/galaxy/compare/fe6c1738c0ea...fd0b24ecd2bf
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/release_18.05
Home: https://github.com/galaxyproject/galaxy
Commit: a1f7634fd7dca45902a2d3f67d2279db3aa2270d
https://github.com/galaxyproject/galaxy/commit/a1f7634fd7dca45902a2d3f67d22…
Author: thobalose <lose.thoba(a)gmail.com>
Date: 2018-10-10 (Wed, 10 Oct 2018)
Changed paths:
M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako
M config/plugins/interactive_environments/neo/templates/neo.mako
Log Message:
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Updated volume kwds.
Commit: fe6c1738c0ea3ee35fa34fec8a2c2e8eb97ec044
https://github.com/galaxyproject/galaxy/commit/fe6c1738c0ea3ee35fa34fec8a2c…
Author: Dannon <dannon.baker(a)gmail.com>
Date: 2018-10-11 (Thu, 11 Oct 2018)
Changed paths:
M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako
M config/plugins/interactive_environments/neo/templates/neo.mako
Log Message:
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Merge pull request #6851 from martenson/backport-gie-kwds
[18.05] Updated volume kwds for GIEs
Compare: https://github.com/galaxyproject/galaxy/compare/4a345b99c3cc...fe6c1738c0ea
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: d60699624139e09c1dd7d979eaaeecfeb77856ad
https://github.com/galaxyproject/galaxy/commit/d60699624139e09c1dd7d979eaae…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-10-08 (Mon, 08 Oct 2018)
Changed paths:
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/exceptions/error_codes.json
M lib/galaxy/managers/context.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/history_imp_exp.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/upload.py
Log Message:
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Don't create jobs for inactive users
Commit: c4374f9a811762db7cc5dd999418ebe922d17a02
https://github.com/galaxyproject/galaxy/commit/c4374f9a811762db7cc5dd999418…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-10-08 (Mon, 08 Oct 2018)
Changed paths:
M lib/galaxy/tools/actions/upload.py
Log Message:
-----------
Fix tabs, wow
Commit: c5700431c48cd0b2a2ebc2484a9e07d860c3aa9a
https://github.com/galaxyproject/galaxy/commit/c5700431c48cd0b2a2ebc2484a9e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-10-09 (Tue, 09 Oct 2018)
Changed paths:
M lib/galaxy/managers/context.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/history_imp_exp.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/actions/upload.py
Log Message:
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check user activation with less duplication/imports
Commit: 2bbabdae02bb08371429ddbda6737faea7ebc6b5
https://github.com/galaxyproject/galaxy/commit/2bbabdae02bb08371429ddbda673…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-10-09 (Tue, 09 Oct 2018)
Changed paths:
M test/unit/tools/test_actions.py
Log Message:
-----------
Fix unit tests for new job_is_active trans property and add a test for
the feature.
Commit: 8edeca024961a7f1856fc5586843137901fb6ff1
https://github.com/galaxyproject/galaxy/commit/8edeca024961a7f1856fc5586843…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-10-09 (Tue, 09 Oct 2018)
Changed paths:
M lib/galaxy/managers/context.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/history_imp_exp.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/actions/upload.py
Log Message:
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Merge pull request #9 from jmchilton/inactive-user-jobs
check user activation with less duplication/imports
Commit: 15944ce6e9d4bdf5818f3125efd63fc85c3161fe
https://github.com/galaxyproject/galaxy/commit/15944ce6e9d4bdf5818f3125efd6…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-10-10 (Wed, 10 Oct 2018)
Changed paths:
M test/unit/tools/test_actions.py
Log Message:
-----------
Fix unit tests broken by the addition of trans.check_user_activation()
Commit: 483a23a5a4bdfe2e74190cb7182fafd05d992461
https://github.com/galaxyproject/galaxy/commit/483a23a5a4bdfe2e74190cb7182f…
Author: Nicola Soranzo <nicola.soranzo(a)gmail.com>
Date: 2018-10-11 (Thu, 11 Oct 2018)
Changed paths:
M lib/galaxy/exceptions/error_codes.json
Log Message:
-----------
Fix sorting of error codes
Commit: 85d4706662969e953dd04a5266dddb7b73d16920
https://github.com/galaxyproject/galaxy/commit/85d4706662969e953dd04a5266dd…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-10-11 (Thu, 11 Oct 2018)
Changed paths:
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/exceptions/error_codes.json
M lib/galaxy/managers/context.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/history_imp_exp.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/actions/upload.py
M test/unit/tools/test_actions.py
Log Message:
-----------
Merge pull request #6837 from natefoo/inactive-user-jobs
Don't create jobs for inactive users
Compare: https://github.com/galaxyproject/galaxy/compare/12929f9acb0b...85d470666296
**NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.