Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: bb19c7e44844bd724ba2ad3920abd078aae083a0 https://github.com/galaxyproject/galaxy/commit/bb19c7e44844bd724ba2ad3920abd... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml A lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml A test-data/qname_sorted.bam M test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Add queryname sorted and input sorted datatypes The queryname sorted datatype (BamQuerynameSorted) ensures that the file is queryname ordered. The BamInputSorted datatype can be used to describe the output of aligners, which usually keep mate pairs adjacent. The BamInputSorted datatype allows using tools that require mates to be adjacent, without requiring an explicit sorting step. This can reduce the time and space required for duplicate marking tools, HiC tools and structural variant detection tools that require mates to be grouped together in an alignment file. The BamQuerynameSorted has a converter that works for all datatypes that can be consumed by samtools. There is no converter for BamInputSorted, since BamQuerynameSorted is valid input for tools requiring BamInputSorted input. I'm targeting 18.01 since I think it would be very unfortunate if we start annotating aligners with the very loose BamNative datatype, since this datatype does not make any promises about sort order at all. This closes https://github.com/galaxyproject/galaxy/issues/5497, goes a long way towards the problems mentioned in https://github.com/galaxyproject/galaxy/issues/5496 and would make https://github.com/galaxyproject/tools-iuc/pull/1732 and https://github.com/galaxyproject/tools-iuc/pull/1591 better Commit: 3dec3bdd21176d0fb66d7606a1e513ef244e4e86 https://github.com/galaxyproject/galaxy/commit/3dec3bdd21176d0fb66d7606a1e51... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Move `Extract genomic DNA 1` to list of version galaxy lib tools Commit: 2d132a45d9af112a9d96e6a1d58646aff1a72910 https://github.com/galaxyproject/galaxy/commit/2d132a45d9af112a9d96e6a1d5864... Author: Nicola Soranzo <nsoranzo@tiscali.it> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #5626 from mvdbeek/limit_extract_dna_legacy_versions [17.09] Move `Extract genomic DNA 1` to list of versioned galaxy tools requiring galaxy to be importable Commit: 87c70d844747b6d99880e495be0102fe386ccdb0 https://github.com/galaxyproject/galaxy/commit/87c70d844747b6d99880e495be010... Author: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge branch 'release_17.09' into release_18.01 Conflicts: lib/galaxy/tools/__init__.py Commit: d648e22080ac97b3940799d35e3be304d1a0aed7 https://github.com/galaxyproject/galaxy/commit/d648e22080ac97b3940799d35e3be... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py Log Message: ----------- fix for cases where panel elements have to_dict with different signature we want to only cache Tools anyways, so this fixes other possible bug where section/label etc would have same id as a Tool change the detection of Tool object to avoid circular import errors Also use cache for dictifying sections, we should gain more speed from that. Commit: 5406a7153bd6a51174145d04eda26b6796211154 https://github.com/galaxyproject/galaxy/commit/5406a7153bd6a51174145d04eda26... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py Log Message: ----------- pass the toolbox obj to make sure cache is available Commit: b96fd2c74010009a7dc85c09e77f87a9d4eff271 https://github.com/galaxyproject/galaxy/commit/b96fd2c74010009a7dc85c09e77f8... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py Log Message: ----------- enable cache for tools that inherit from Tool Commit: 77d085a40f5d5d2e131dc2fc8073e0c030599988 https://github.com/galaxyproject/galaxy/commit/77d085a40f5d5d2e131dc2fc8073e... Author: John Chilton <jmchilton@gmail.com> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml A lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml A test-data/qname_sorted.bam M test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge pull request #5589 from mvdbeek/samtools_queryname_and_input_order_datatypes [18.01] Add queryname sorted and input sorted datatypes Commit: 41910f824ea311e8ce7d93e4dc03a44c75c8132b https://github.com/galaxyproject/galaxy/commit/41910f824ea311e8ce7d93e4dc03a... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py Log Message: ----------- Merge pull request #5615 from martenson/distinct-elts [18.01] fix for cases where panel elements have to_dict with different signature Commit: 56b8ecd3d50340c366aa22d5327fd635a3485ff0 https://github.com/galaxyproject/galaxy/commit/56b8ecd3d50340c366aa22d5327fd... Author: Martin Cech <marten@bx.psu.edu> Date: 2018-03-01 (Thu, 01 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py R lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml M lib/galaxy/datatypes/converters/sam_to_bam_native.xml A lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml A lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/panel.py A test-data/qname_sorted.bam M test/functional/tools/sam_to_bam_native.xml M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge branch 'release_18.01' into usegalaxy Compare: https://github.com/galaxyproject/galaxy/compare/ab928fe55ed1...56b8ecd3d503