Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: d791a2c80f3290d66c2252f29981a16a4459661b
https://github.com/galaxyproject/galaxy/commit/d791a2c80f3290d66c2252f29981…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-10-11 (Thu, 11 Oct 2018)
Changed paths:
M lib/galaxy/model/metadata.py
Log Message:
-----------
Revert selective metadata flushing - seems to break upload changes.
Commit: f3da0864b45a3aa307c7fe9eeb8c5d26dd9c8527
https://github.com/galaxyproject/galaxy/commit/f3da0864b45a3aa307c7fe9eeb8c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-10-12 (Fri, 12 Oct 2018)
Changed paths:
M test/api/test_tools.py
A test/functional/tools/for_workflows/mapper_two.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
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Test case for regression #6856.
Commit: 01f1f1b95fba671a2d92d7111676229a7ed5d58a
https://github.com/galaxyproject/galaxy/commit/01f1f1b95fba671a2d92d7111676…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-10-12 (Fri, 12 Oct 2018)
Changed paths:
M lib/galaxy/model/metadata.py
M test/api/test_tools.py
A test/functional/tools/for_workflows/mapper_two.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
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Merge pull request #6858 from jmchilton/fix_metadata_revert
[18.09] Revert selective metadata flushing - breaks multiple uploads/outputs.
Commit: ca95d7a26e70ca02159febd971fa8b63c2667ab5
https://github.com/galaxyproject/galaxy/commit/ca95d7a26e70ca02159febd971fa…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-10-12 (Fri, 12 Oct 2018)
Changed paths:
M lib/galaxy/model/metadata.py
M test/api/test_tools.py
A test/functional/tools/for_workflows/mapper_two.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_18.09' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/ff32e5434145...ca95d7a26e70
**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_18.09
Home: https://github.com/galaxyproject/galaxy
Commit: 02410b270d025e5fb8cb4e2036fb627051c7850a
https://github.com/galaxyproject/galaxy/commit/02410b270d025e5fb8cb4e2036fb…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-10-08 (Mon, 08 Oct 2018)
Changed paths:
M lib/galaxy/util/monitors.py
Log Message:
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Register job monitor as postfork function
This should fix https://github.com/galaxyproject/galaxy/issues/6831,
and might fix https://github.com/galaxyproject/galaxy/issues/6261.
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:
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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: 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
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
Commit: baa992d217032b809d321cb800cd2f41af401c63
https://github.com/galaxyproject/galaxy/commit/baa992d217032b809d321cb800cd…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-10-11 (Thu, 11 Oct 2018)
Changed paths:
M lib/galaxy/util/monitors.py
Log Message:
-----------
Merge pull request #6836 from mvdbeek/fix_job_monitor_thread
[18.01] Register job monitor thread as postfork function
Commit: a8fa5a1d4a6c801fc230c037129671978955916c
https://github.com/galaxyproject/galaxy/commit/a8fa5a1d4a6c801fc230c0371296…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-10-12 (Fri, 12 Oct 2018)
Changed paths:
M lib/galaxy/util/monitors.py
Log Message:
-----------
Merge branch 'release_18.01' into release_18.05
Commit: d22f652f918f7a49d80ede8652d335d41c478546
https://github.com/galaxyproject/galaxy/commit/d22f652f918f7a49d80ede8652d3…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-10-12 (Fri, 12 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
M lib/galaxy/jobs/runners/util/cli/shell/local.py
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
M lib/galaxy/util/monitors.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:
-----------
Merge branch 'release_18.05' into release_18.09
Compare: https://github.com/galaxyproject/galaxy/compare/2c14c2afc4d3...d22f652f918f
**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.