November 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/ansible-galaxy] 89a26c: Update print statement syntax to support Python 3.
by GitHub 05 Nov '18

05 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 89a26cb0833845986893c08fadf7db4c57e4e14c https://github.com/galaxyproject/ansible-galaxy/commit/89a26cb0833845986893… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2018-11-04 (Sun, 04 Nov 2018) Changed paths: M files/makepyc.py M tasks/dependencies.yml Log Message: ----------- Update print statement syntax to support Python 3. Commit: 1eed620a4a1fe95c94169f5580722e088b58e2c1 https://github.com/galaxyproject/ansible-galaxy/commit/1eed620a4a1fe95c9416… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M files/makepyc.py M tasks/dependencies.yml Log Message: ----------- Merge pull request #39 from ic4f/master Update print statement syntax to support Python 3. Compare: https://github.com/galaxyproject/ansible-galaxy/compare/9ee412e2d63d...1eed… **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.

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[galaxyproject/galaxy] cc8e1c: fix empty loc file bug
by GitHub 04 Nov '18

04 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cc8e1c211ee5c7f6af3d358619b44b3a14ce4deb https://github.com/galaxyproject/galaxy/commit/cc8e1c211ee5c7f6af3d358619b4… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- fix empty loc file bug Commit: 13a4238510de2330bcf460519eac2198f66e0c33 https://github.com/galaxyproject/galaxy/commit/13a4238510de2330bcf460519eac… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- removed debug output Commit: 0ede377925c415cf5b7805de03d57d8d0bd2bca4 https://github.com/galaxyproject/galaxy/commit/0ede377925c415cf5b7805de03d5… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-11-04 (Sun, 04 Nov 2018) Changed paths: M lib/galaxy/tools/data/__init__.py Log Message: ----------- Merge pull request #6957 from bernt-matthias/topic/empty-data-table Topic/empty data table Compare: https://github.com/galaxyproject/galaxy/compare/d6af6b7bd1ef...0ede377925c4 **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.

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[galaxyproject/galaxy] 03eac8: Fix for workflow parameter collection in workflows...
by GitHub 04 Nov '18

04 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 03eac8315d64e05df74f1f6fb286cff29e75f6b2 https://github.com/galaxyproject/galaxy/commit/03eac8315d64e05df74f1f6fb286… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix for workflow parameter collection in workflows view. Commit: 18644f91cf59265c1473d806845baffbf7a8132f https://github.com/galaxyproject/galaxy/commit/18644f91cf59265c1473d806845b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Avoid using var; let. Commit: 3d91738a697ff57047bc3cd505d5afc75de38f45 https://github.com/galaxyproject/galaxy/commit/3d91738a697ff57047bc3cd505d5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-04 (Sun, 04 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #6955 from dannon/wf_param_fix [18.09] Fix for workflow parameter collection in workflows view. Compare: https://github.com/galaxyproject/galaxy/compare/357e2f39c770...3d91738a697f **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.

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[galaxyproject/usegalaxy-playbook] deafd8: Update Test mutable configs
by GitHub 02 Nov '18

02 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: deafd85205f935de94d2acfb767f9522f660c2d6 https://github.com/galaxyproject/usegalaxy-playbook/commit/deafd85205f935de… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Update Test mutable configs **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.

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[galaxyproject/galaxy] 30aaa2: Fix sniffing of readname sorted BAM files
by GitHub 02 Nov '18

02 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 30aaa296dd50471001323cc9895560219a33ce71 https://github.com/galaxyproject/galaxy/commit/30aaa296dd50471001323cc98955… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/1.qname_sorted.bam Log Message: ----------- Fix sniffing of readname sorted BAM files This fixes https://github.com/galaxyproject/galaxy/issues/6949. The problem is that `super` would fall back to the BamInputSorted sniffer, which prevents sniffing. Includes a test file for the new datatype upload testing framework. Commit: 6b5f0a2ad1f21bbda92b06ff2700c961c34e84ea https://github.com/galaxyproject/galaxy/commit/6b5f0a2ad1f21bbda92b06ff2700… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Allow upload for ``rdata.sce`` format Commit: 6da5157181a085d183c099645216893fe512a1f9 https://github.com/galaxyproject/galaxy/commit/6da5157181a085d183c099645216… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #6963 from nsoranzo/release_18.05_allow_rdata.sce_upload [18.05] Allow upload for ``rdata.sce`` format Commit: 357e2f39c77026c81c56ed30ffae9f1905d2d82a https://github.com/galaxyproject/galaxy/commit/357e2f39c77026c81c56ed30ffae… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: d6af6b7bd1ef9c9429d1362ac9473168be7ba471 https://github.com/galaxyproject/galaxy/commit/d6af6b7bd1ef9c9429d1362ac947… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/f035d642ceb2...d6af6b7bd1ef **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.

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[galaxyproject/galaxy] 6b5f0a: Allow upload for ``rdata.sce`` format
by GitHub 02 Nov '18

02 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 6b5f0a2ad1f21bbda92b06ff2700c961c34e84ea https://github.com/galaxyproject/galaxy/commit/6b5f0a2ad1f21bbda92b06ff2700… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Allow upload for ``rdata.sce`` format Commit: 6da5157181a085d183c099645216893fe512a1f9 https://github.com/galaxyproject/galaxy/commit/6da5157181a085d183c099645216… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #6963 from nsoranzo/release_18.05_allow_rdata.sce_upload [18.05] Allow upload for ``rdata.sce`` format Commit: 357e2f39c77026c81c56ed30ffae9f1905d2d82a https://github.com/galaxyproject/galaxy/commit/357e2f39c77026c81c56ed30ffae… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Compare: https://github.com/galaxyproject/galaxy/compare/30aaa296dd50...357e2f39c770 **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.

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[galaxyproject/galaxy] 6b5f0a: Allow upload for ``rdata.sce`` format
by GitHub 02 Nov '18

02 Nov '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 6b5f0a2ad1f21bbda92b06ff2700c961c34e84ea https://github.com/galaxyproject/galaxy/commit/6b5f0a2ad1f21bbda92b06ff2700… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Allow upload for ``rdata.sce`` format Commit: 6da5157181a085d183c099645216893fe512a1f9 https://github.com/galaxyproject/galaxy/commit/6da5157181a085d183c099645216… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #6963 from nsoranzo/release_18.05_allow_rdata.sce_upload [18.05] Allow upload for ``rdata.sce`` format Compare: https://github.com/galaxyproject/galaxy/compare/3411852fedf3...6da5157181a0 **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.

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[galaxyproject/usegalaxy-playbook] d6d332: update fastqc, multiqc, trimgalore
by GitHub 01 Nov '18

01 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d6d3322f5eb0681a6425b6f2f00b545f38da5826 https://github.com/galaxyproject/usegalaxy-playbook/commit/d6d3322f5eb0681a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_data_manager_conf.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- update fastqc, multiqc, trimgalore also add forgotten data_manager mutable confs **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.

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[galaxyproject/infrastructure-playbook] fd3deb: Clean /tmp files older than 2 days on jenkins work...
by GitHub 01 Nov '18

01 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: fd3deb354b80f4a855d3f29ebf35b6764168641e https://github.com/galaxyproject/infrastructure-playbook/commit/fd3deb354b8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: A env/galaxy/files/jenkins/tmpfiles.d-clean-tmp.conf M env/galaxy/group_vars/jenkinsslaves/vars.yml Log Message: ----------- Clean /tmp files older than 2 days on jenkins workers **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.

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[galaxyproject/galaxy] 30aaa2: Fix sniffing of readname sorted BAM files
by GitHub 01 Nov '18

01 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 30aaa296dd50471001323cc9895560219a33ce71 https://github.com/galaxyproject/galaxy/commit/30aaa296dd50471001323cc98955… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/1.qname_sorted.bam Log Message: ----------- Fix sniffing of readname sorted BAM files This fixes https://github.com/galaxyproject/galaxy/issues/6949. The problem is that `super` would fall back to the BamInputSorted sniffer, which prevents sniffing. Includes a test file for the new datatype upload testing framework. **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.

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