Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f5af9539b9d50e0c0e99ade18eea8af6f7beb0e4 https://github.com/galaxyproject/galaxy/commit/f5af9539b9d50e0c0e99ade18eea8... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- add BamNative datatype Commit: 017dad025db9a06c9c6d2430203f52fdec959f68 https://github.com/galaxyproject/galaxy/commit/017dad025db9a06c9c6d2430203f5... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: A test-data/bam_native_from_sam.bam Log Message: ----------- add new test file Commit: eea55a9258342e8de32162c9e62563de0f6438b8 https://github.com/galaxyproject/galaxy/commit/eea55a9258342e8de32162c9e6256... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: A test/functional/tools/sam_to_bam_native.xml Log Message: ----------- add new test tool Commit: 2a093f25f6fdb6ebf4a8bba84050130c4929e6c3 https://github.com/galaxyproject/galaxy/commit/2a093f25f6fdb6ebf4a8bba840501... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- add new bam_native datatype to the registry Commit: 4d7bc9a778afa171bd7498004733943543af5730 https://github.com/galaxyproject/galaxy/commit/4d7bc9a778afa171bd74980047339... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml Log Message: ----------- bam to bigwig converter, converts also bam_native Commit: 2569851498f76d2fc416bd96ab4007c579bb0ffd https://github.com/galaxyproject/galaxy/commit/2569851498f76d2fc416bd96ab400... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: M test-data/sam_with_header.sam Log Message: ----------- use unsorted sam file for tests Commit: 8b55e0a33a52fe45fc5fdaa171607c7f253021c9 https://github.com/galaxyproject/galaxy/commit/8b55e0a33a52fe45fc5fdaa171607... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2017-12-10 (Sun, 10 Dec 2017) Changed paths: A lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml A lib/galaxy/datatypes/converters/sam_to_bam_native.xml Log Message: ----------- add two converters Commit: 640cfb1e7d8be8ceaba96920cfb1be72c48f4974 https://github.com/galaxyproject/galaxy/commit/640cfb1e7d8be8ceaba96920cfb1b... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2018-01-04 (Thu, 04 Jan 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Bam to BAM Commit: e519f4e7efcbb055a66a861588ceabd09e0b9b58 https://github.com/galaxyproject/galaxy/commit/e519f4e7efcbb055a66a861588cea... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2018-01-04 (Thu, 04 Jan 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- rearrange sniffer Commit: 295e5712ee2c020292754ddcb75d6d5744c4ed10 https://github.com/galaxyproject/galaxy/commit/295e5712ee2c020292754ddcb75d6... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2018-01-04 (Thu, 04 Jan 2018) Changed paths: M test/functional/tools/sam_to_bam_native.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- adjust tests Commit: 2b5b6cf74fb29eb4608318477c062982d8ad955c https://github.com/galaxyproject/galaxy/commit/2b5b6cf74fb29eb4608318477c062... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-04 (Thu, 04 Jan 2018) Changed paths: M test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Fix test and add datatypes to test/functional/tools/sample_datatypes_conf.xml This test is still failing because `CONVERTER_sam_to_bam` will be invoked instead of CONVERTER_sam_to_bam_native. Possibly becasue Bam inherits from BamNative, so this isn't strictly speaking wrong, though not what one would expect. Commit: a8b3d23f1438f31436b86d24b48868fd3e133dad https://github.com/galaxyproject/galaxy/commit/a8b3d23f1438f31436b86d24b4886... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-04 (Thu, 04 Jan 2018) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Adjust sniffer test for unsorted bam Commit: 43dd7910f4865c9c4205ad8eaa5e8f1a71b6b6c6 https://github.com/galaxyproject/galaxy/commit/43dd7910f4865c9c4205ad8eaa5e8... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2018-01-04 (Thu, 04 Jan 2018) Changed paths: M lib/galaxy/datatypes/sniff.py M test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge pull request #37 from mvdbeek/bam_native_tests Fix test and add datatypes to test/functional/tools/sample_datatypes_… Commit: 446643159540f8db67dfd0752560b387b63fc4b8 https://github.com/galaxyproject/galaxy/commit/446643159540f8db67dfd0752560b... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2018-01-04 (Thu, 04 Jan 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- resort the converters so that the accepted_formats are infront Commit: 8928b34506c1ba1f4856fad82dc42aef0f7c68f6 https://github.com/galaxyproject/galaxy/commit/8928b34506c1ba1f4856fad82dc42... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2018-01-07 (Sun, 07 Jan 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- implement priority converters Commit: b139726ed380192ecf03f10e91220a0488b573f3 https://github.com/galaxyproject/galaxy/commit/b139726ed380192ecf03f10e91220... Author: Bjoern Gruening <bjoern.gruening@gmail.com> Date: 2018-01-07 (Sun, 07 Jan 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- fix spelling Commit: ea34bdc34d560962f3f149d9f019d0ac3a3c4f0a https://github.com/galaxyproject/galaxy/commit/ea34bdc34d560962f3f149d9f019d... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2018-01-07 (Sun, 07 Jan 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Merge pull request #38 from bgruening/converter_resorting resort the converters so that the accepted_formats are infront Commit: 49dd02f4090b525beba735fc9ff16e32388b3fcd https://github.com/galaxyproject/galaxy/commit/49dd02f4090b525beba735fc9ff16... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam_native.xml M test/functional/tools/sam_to_bam_native.xml Log Message: ----------- Keep header when converting sam to bam Otherwise the converted datasets are not valid BAM files. Commit: c32680733c8985d0db48a10d0b50fab7514dc4ff https://github.com/galaxyproject/galaxy/commit/c32680733c8985d0db48a10d0b50f... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Revert "fix spelling" This reverts commit b139726ed380192ecf03f10e91220a0488b573f3. Commit: 38c5f711983033bb01072a769e6a618528724955 https://github.com/galaxyproject/galaxy/commit/38c5f711983033bb01072a769e6a6... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-11 (Thu, 11 Jan 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Revert "implement priority converters" This reverts commit 8928b34506c1ba1f4856fad82dc42aef0f7c68f6. Commit: 6b444f609d3a48d17a783e581dc077b0731673ca https://github.com/galaxyproject/galaxy/commit/6b444f609d3a48d17a783e581dc07... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-13 (Sat, 13 Jan 2018) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Revert "resort the converters so that the accepted_formats are infront" This reverts commit 446643159540f8db67dfd0752560b387b63fc4b8. Commit: c2328e32eb18bd7a4a5c791306203b933fc73603 https://github.com/galaxyproject/galaxy/commit/c2328e32eb18bd7a4a5c791306203... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-13 (Sat, 13 Jan 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Move up sam_to_bam_native converter That should allow implicit conversion from sam to bam_native for tools that support bam_native. Commit: a36ebe35521e3e45c5c3301eef9535ebdf630f9d https://github.com/galaxyproject/galaxy/commit/a36ebe35521e3e45c5c3301eef953... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-13 (Sat, 13 Jan 2018) Changed paths: M test/functional/tools/sam_to_bam_native.xml Log Message: ----------- Enhance tests for sam_to_bam conversion This demonstrates that the `sam_to_bam` converter will be used for an input with `format="bam"`, and not `sam_to_bam_native`. Commit: d544adf5ee45557f2e40c2f1050f4f2a427d56e1 https://github.com/galaxyproject/galaxy/commit/d544adf5ee45557f2e40c2f1050f4... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/converters/sam_to_bam_native.xml M lib/galaxy/datatypes/registry.py M test/functional/tools/sam_to_bam_native.xml Log Message: ----------- Merge pull request #39 from mvdbeek/bam_unsorted Fix tests and revert additional sorting of converters Commit: ae0c3524b87d1f14374ee04d452320ff0c091cf8 https://github.com/galaxyproject/galaxy/commit/ae0c3524b87d1f14374ee04d45232... Author: Björn Grüning <bjoern@gruenings.eu> Date: 2018-01-15 (Mon, 15 Jan 2018) Changed paths: A .ci/check_py3_compatibility.sh M .ci/first_startup.sh R .ci/py3_sources.txt M .gitignore M .travis.yml M Makefile M client/GruntFile.js M client/README.md M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/extended.js M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/scripts/components/Citations.vue M client/galaxy/scripts/components/HistoryImport.vue A client/galaxy/scripts/components/Message.vue R client/galaxy/scripts/components/UserAPIKeys.vue A client/galaxy/scripts/components/admin/BaseGrid.vue A client/galaxy/scripts/components/admin/DataManagerGrid.vue A client/galaxy/scripts/components/admin/DataTables.vue A client/galaxy/scripts/components/admin/DataTablesGrid.vue A client/galaxy/scripts/components/admin/UserAPIKeys.vue M client/galaxy/scripts/galaxy.interactive_environments.js M 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test-data/neostore.zip A test-data/new_element_sort_order.txt M test/api/test_configuration.py M test/api/test_history_contents.py M test/api/test_jobs.py M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_tools_upload.py M test/api/test_workflows.py M test/base/api.py M test/base/data/test_workflow_1.ga M test/base/driver_util.py M test/base/interactor.py M test/base/populators.py A test/functional/tools/compressed_neostorezip_neostore_conversion.xml A test/functional/tools/compressed_neostorezip_neostore_no_conversion.xml A test/functional/tools/exit_code_oom.xml A test/functional/tools/fail_identifier.xml M test/functional/tools/job_properties.xml M test/functional/tools/samples_tool_conf.xml M test/functional/webhooks/phdcomics/helper/__init__.py M test/galaxy_selenium/navigates_galaxy.py M test/galaxy_selenium/navigation.yml A test/integration/resubmission_small_memory_job_conf.xml A test/integration/resubmission_small_memory_resubmission_to_large_job_conf.xml M test/integration/test_job_resubmission.py M test/integration/test_upload_configuration_options.py M test/selenium_tests/test_library_contents.py A test/selenium_tests/test_library_to_collections.py M test/selenium_tests/test_tool_form.py M test/shed_functional/base/twilltestcase.py M test/unit/jobs/test_job_output_checker.py M test/unit/jobs/test_runner_local.py M test/unit/tools/test_parsing.py M tools/data_source/upload.py M tools/genomespace/genomespace_importer.py M tools/stats/aggregate_scores_in_intervals.py M tox.ini Log Message: ----------- Merge branch 'dev' into bam_unsorted Commit: aaaf7b50a7a227e5344712f6441fce337a20d1ba https://github.com/galaxyproject/galaxy/commit/aaaf7b50a7a227e5344712f6441fc... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M scripts/functional_tests.py M test/base/driver_util.py Log Message: ----------- Enable conda_auto_init and conda_auto_install for framework tests Commit: 680bf685c2dfdc874277321e2c7d0673516bf62a https://github.com/galaxyproject/galaxy/commit/680bf685c2dfdc874277321e2c7d0... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Fix datatype order Commit: 8ecc86cb677bc3971baa75bf0e8c1481d8e3aef4 https://github.com/galaxyproject/galaxy/commit/8ecc86cb677bc3971baa75bf0e8c1... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-01-17 (Wed, 17 Jan 2018) Changed paths: M test/base/driver_util.py Log Message: ----------- Simplify conda framework setup Thanks @nsoranzo! Commit: 8f65cd46b0ec7c1a92a305219f43c837cd2a471a https://github.com/galaxyproject/galaxy/commit/8f65cd46b0ec7c1a92a305219f43c... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2018-01-19 (Fri, 19 Jan 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml A lib/galaxy/datatypes/converters/sam_to_bam_native.xml M lib/galaxy/datatypes/sniff.py M scripts/functional_tests.py A test-data/bam_native_from_sam.bam M test-data/sam_with_header.sam M test/base/driver_util.py A test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #5180 from bgruening/bam_unsorted Add BamNative datatype Compare: https://github.com/galaxyproject/galaxy/compare/33bd54079be7...8f65cd46b0ec