November 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 1325e6: add missing configs to Test also
by GitHub 17 Nov '16

17 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1325e6f41c681247b41d06fc47b00ccd20ae5f3c https://github.com/galaxyproject/usegalaxy-playbook/commit/1325e6f41c681247… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M stage/group_vars/galaxyservers.yml Log Message: ----------- add missing configs to Test also

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[galaxyproject/usegalaxy-playbook] bd61ac: add missing config options
by GitHub 17 Nov '16

17 Nov '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bd61acefe2c0bb525890fce3f66786b7a1a7ba6b https://github.com/galaxyproject/usegalaxy-playbook/commit/bd61acefe2c0bb52… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M production/group_vars/galaxyservers.yml Log Message: ----------- add missing config options spotted by @tnatbaf

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[galaxyproject/galaxy] 9d45f1: Update version to 16.10.rc1
by GitHub 17 Nov '16

17 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9d45f1e48a4321d5df0543bcfcf2994affa35612 https://github.com/galaxyproject/galaxy/commit/9d45f1e48a4321d5df0543bcfcf2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.10.rc1 Commit: e5b56f102ae003707ad97d9fbb75270543397921 https://github.com/galaxyproject/galaxy/commit/e5b56f102ae003707ad97d9fbb75… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 17.01.dev Commit: 3dd28291c339d4ca1f2b165ed6cb2c9d82a7cdd9 https://github.com/galaxyproject/galaxy/commit/3dd28291c339d4ca1f2b165ed6cb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Log Message: ----------- Merge branch 'version-16.10' into version-17.01.dev Commit: 50f5c15f63a388466f8e77437226a93405baa382 https://github.com/galaxyproject/galaxy/commit/50f5c15f63a388466f8e77437226… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #3192 from dannon/version-17.01.dev Version 17.01.dev Compare: https://github.com/galaxyproject/galaxy/compare/d8c75e2dffbf...50f5c15f63a3

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[galaxyproject/galaxy] 9d45f1: Update version to 16.10.rc1
by GitHub 17 Nov '16

17 Nov '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 9d45f1e48a4321d5df0543bcfcf2994affa35612 https://github.com/galaxyproject/galaxy/commit/9d45f1e48a4321d5df0543bcfcf2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Update version to 16.10.rc1 Commit: 6fd58afa6daf708f373513782ac907c154c266da https://github.com/galaxyproject/galaxy/commit/6fd58afa6daf708f373513782ac9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/version.py Log Message: ----------- Merge pull request #3191 from dannon/version-16.10 Update version to 16.10.rc1 Compare: https://github.com/galaxyproject/galaxy/compare/d8c75e2dffbf...6fd58afa6daf

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[galaxyproject/galaxy]
by GitHub 17 Nov '16

17 Nov '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] 953ee3: change parameters to samtools sort command (new sa...
by GitHub 17 Nov '16

17 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 953ee3259999f774887e97d5e72bccb1102540f5 https://github.com/galaxyproject/galaxy/commit/953ee3259999f774887e97d5e72b… Author: Ignacio <ignacio.eguinoa(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- change parameters to samtools sort command (new samtools vers) Commit: 5bb86a3b687732913dee746732060f973b622cff https://github.com/galaxyproject/galaxy/commit/5bb86a3b687732913dee74673206… Author: Ignacio <ignacio.eguinoa(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- correct indentation Commit: efde00d80a916afc20869608a7a1922249581a62 https://github.com/galaxyproject/galaxy/commit/efde00d80a916afc20869608a7a1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- Handle samtools 0.x Commit: 592f15c7b5da3f962dda9f98cb978e5c5c6b4a1d https://github.com/galaxyproject/galaxy/commit/592f15c7b5da3f962dda9f98cb97… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: A test-data/bam_from_sam.bam A test-data/sam_with_header.sam A test/functional/tools/sam_to_bam.xml Log Message: ----------- Add sam-to-bam conversion test tool Commit: 8ace021c0af79e5d325d6a590f525bce881715f8 https://github.com/galaxyproject/galaxy/commit/8ace021c0af79e5d325d6a590f52… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py Log Message: ----------- Single quote variables in sam-to-bam conversion Commit: d8c75e2dffbfa754eda4fae4c6d3365d42278a4c https://github.com/galaxyproject/galaxy/commit/d8c75e2dffbfa754eda4fae4c6d3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-17 (Thu, 17 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py A test-data/bam_from_sam.bam A test-data/sam_with_header.sam A test/functional/tools/sam_to_bam.xml Log Message: ----------- Merge pull request #3187 from mvdbeek/samtools_1_3_fix Make sam to bam converter tool compatible with samtools >= 1.3 Compare: https://github.com/galaxyproject/galaxy/compare/164a0ad20cbb...d8c75e2dffbf

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[galaxyproject/galaxy] 0b395a: Slight clarification of run.sh messaging when usin...
by GitHub 16 Nov '16

16 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0b395a7fb3aaebf5fa3a0448338df73c8774e388 https://github.com/galaxyproject/galaxy/commit/0b395a7fb3aaebf5fa3a0448338d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Slight clarification of run.sh messaging when using conda. Commit: 164a0ad20cbbd55b40583c633c1c52dde9ecb7ba https://github.com/galaxyproject/galaxy/commit/164a0ad20cbbd55b40583c633c1c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #3188 from dannon/startup_output_tweaks Slight clarification of run.sh messaging when using conda. Compare: https://github.com/galaxyproject/galaxy/compare/92105d99fae6...164a0ad20cbb

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[galaxyproject/galaxy] b97281: Cleanup for 16.10 rstudio
by GitHub 16 Nov '16

16 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b97281920b341d141fe0b94ecd5c8ecc5f175454 https://github.com/galaxyproject/galaxy/commit/b97281920b341d141fe0b94ecd5c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-08-18 (Thu, 18 Aug 2016) Changed paths: M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Cleanup for 16.10 rstudio Commit: 0aeb9e816a9807117b26691c248483cbad07e16a https://github.com/galaxyproject/galaxy/commit/0aeb9e816a9807117b26691c2484… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Clean up rstudio conf, now working again Commit: 56a8c01fef6c419d3fb23cec85dbac726831d789 https://github.com/galaxyproject/galaxy/commit/56a8c01fef6c419d3fb23cec85db… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-08-19 (Fri, 19 Aug 2016) Changed paths: M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample Log Message: ----------- Bump image Commit: 65fe971008967bbf477b578852e004e94657e215 https://github.com/galaxyproject/galaxy/commit/65fe971008967bbf477b578852e0… Author: nturaga <nitesh.turaga(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- add correct login url Commit: 198c6d92e608ca78454ca9c06dc2bd8865d8387c https://github.com/galaxyproject/galaxy/commit/198c6d92e608ca78454ca9c06dc2… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-08-23 (Tue, 23 Aug 2016) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Merge pull request #17 from nturaga/rstudio_mako_url add correct login url Commit: 92105d99fae6ec892f2eb6eb60c31d68196b061a https://github.com/galaxyproject/galaxy/commit/92105d99fae6ec892f2eb6eb60c3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Merge pull request #2818 from erasche/rstudio-1610 Return of RStudio Compare: https://github.com/galaxyproject/galaxy/compare/31b73fd5869f...92105d99fae6

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[galaxyproject/galaxy] d48817: Remove redundant .venv activation -- this is handl...
by GitHub 16 Nov '16

16 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d48817adb17b914975c26b90a2dd17887b24744b https://github.com/galaxyproject/galaxy/commit/d48817adb17b914975c26b90a2dd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M run.sh Log Message: ----------- Remove redundant .venv activation -- this is handled in common_startup Commit: 72d360e942da2a614b7d74d3238d2ee0791a8141 https://github.com/galaxyproject/galaxy/commit/72d360e942da2a614b7d74d3238d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Change startup logic for .venv sourcing. If a .venv exists, use it. If not, if conda is there, use it. If no conda, create a .venv. Commit: 7f5d9d2fbd745f2099be15de706112717f9e01f6 https://github.com/galaxyproject/galaxy/commit/7f5d9d2fbd745f2099be15de7061… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- More startup logic tweaks, .venv > conda > new_venv Commit: 985bd0dffd779b55813f6dc1c6bae663e959bd9c https://github.com/galaxyproject/galaxy/commit/985bd0dffd779b55813f6dc1c6ba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M run.sh Log Message: ----------- Because common_startup is executed and not sourced, this block needs to remain in run.sh Commit: 31b73fd5869f1c3ae968fb29773cf1631a3f5843 https://github.com/galaxyproject/galaxy/commit/31b73fd5869f1c3ae968fb29773c… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #3180 from dannon/venv_over_conda Prefer existing .venv over conda, when both are available. Compare: https://github.com/galaxyproject/galaxy/compare/0b8fc7c8cca4...31b73fd5869f

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[galaxyproject/galaxy] 4e6e7d: Validate cycles and step size before building mode...
by GitHub 16 Nov '16

16 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4e6e7d36f87249b93f4a49249e227409e629305e https://github.com/galaxyproject/galaxy/commit/4e6e7d36f87249b93f4a49249e22… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Validate cycles and step size before building model for workflow execution Commit: 0b8fc7c8cca4b7374f12932b26ef3d854e2d8491 https://github.com/galaxyproject/galaxy/commit/0b8fc7c8cca4b7374f12932b26ef… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-11-16 (Wed, 16 Nov 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge remote-tracking branch 'guerler/validate_workflow' into dev Compare: https://github.com/galaxyproject/galaxy/compare/e5b69a711d14...0b8fc7c8cca4

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