- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] b1fe6f: Refactor collection mapping workflows toward indep...
by GitHub 05 Nov '18

05 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b1fe6fee9373f025341e25b248ffa003a10213b3 https://github.com/galaxyproject/galaxy/commit/b1fe6fee9373f025341e25b248ff… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-24 (Wed, 24 Oct 2018) Changed paths: M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Refactor collection mapping workflows toward independence from tools. Refactor get_data_inputs into get_all_inputs and use the resulting dictionaries to reason about if collection mapping should occur during invocation of tools. Using these dictionaries instead of explicit tool input objects should allow reuse within other module types since they may produce the same interface. Commit: c1e4b0111a70e3bae63791f60a44e6b14b259a5c https://github.com/galaxyproject/galaxy/commit/c1e4b0111a70e3bae63791f60a44… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Merge pull request #6911 from jmchilton/workflow_mapping_refactor Refactor collection mapping workflows toward independence from tools. Compare: https://github.com/galaxyproject/galaxy/compare/a3f213e3c531...c1e4b0111a70 **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] 0beac8: rma: add RMA6 data type (MEGAN6 read-match archive...
by GitHub 05 Nov '18

05 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0beac8fdf4835271ccafefd6a50f928afa055c2c https://github.com/galaxyproject/galaxy/commit/0beac8fdf4835271ccafefd6a50f… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/diamond.rma Log Message: ----------- rma: add RMA6 data type (MEGAN6 read-match archive) Commit: dcae06624a7561d082a7630917d095925795d30e https://github.com/galaxyproject/galaxy/commit/dcae06624a7561d082a7630917d0… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- rma: RMA->RMA6 Commit: 09de6fe4961adcfe09f8701989ac37b8f8df1930 https://github.com/galaxyproject/galaxy/commit/09de6fe4961adcfe09f8701989ac… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- rma: fix test Commit: ee0038a01f8ddd9f8b99d0612497fc6681a14acc https://github.com/galaxyproject/galaxy/commit/ee0038a01f8ddd9f8b99d0612497… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- rma: extension rma6 for consistency Commit: 562b10b7efc93c5ab15bd3a3d5918f32491d934d https://github.com/galaxyproject/galaxy/commit/562b10b7efc93c5ab15bd3a3d591… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/test/diamond.rma A lib/galaxy/datatypes/test/diamond.rma6 Log Message: ----------- rma: renamed test data to rma6 Commit: a3f213e3c5319bd8125e4856e0094fd3cd7ef737 https://github.com/galaxyproject/galaxy/commit/a3f213e3c5319bd8125e4856e009… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/diamond.rma6 Log Message: ----------- Merge pull request #6962 from bernt-matthias/topic/rma add RMA6 data type (MEGAN6 read-match archive) Compare: https://github.com/galaxyproject/galaxy/compare/0ede377925c4...a3f213e3c531 **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/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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