Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 63865e11935724a02ae641857d802f8650a7f97d https://github.com/galaxyproject/galaxy/commit/63865e11935724a02ae641857d802... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/tabular.py Log Message: ----------- Add VcfGz datatype This adds support for uploading VcfGz files in the upload box. When a user does this, the file will not be uncompressed. Also adds uncompressed preview. TODO: - Move Vcf class to BaseVcf - Vcf and VcfGz should both inherit from BaseVcf - Add a metadata element for VcfGz indexes (vzf.gz.tbi) - Create index (in set_meta method of VcfGz class) - Write test tools This is a kcikstart to @ffinfo GCC hack project. Commit: 83f1e82e84a79673b2913f9f4a6c63dc6d6526f4 https://github.com/galaxyproject/galaxy/commit/83f1e82e84a79673b2913f9f4a6c6... Author: Peter van 't Hof <p.j.van_t_hof@lumc.nl> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Added index job to vcf.gz files Commit: f4e02700f5c27dfffab0034f2201b208533e42ba https://github.com/galaxyproject/galaxy/commit/f4e02700f5c27dfffab0034f2201b... Author: Peter van 't Hof <p.j.van_t_hof@lumc.nl> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Fixed some spacings Commit: e9daa0d74464534a490129476f027455dbf26a69 https://github.com/galaxyproject/galaxy/commit/e9daa0d74464534a490129476f027... Author: Peter van 't Hof <p.j.van_t_hof@lumc.nl> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Fixed import order Commit: b96b5076cec2624cc1700bfcec43fd7745d0c0e5 https://github.com/galaxyproject/galaxy/commit/b96b5076cec2624cc1700bfcec43f... Author: Peter van 't Hof <p.j.van_t_hof@lumc.nl> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Fixed import order (again ;) ) Commit: 986379fd0d65c0e5d2d6bdcf1428ba5182713ae7 https://github.com/galaxyproject/galaxy/commit/986379fd0d65c0e5d2d6bdcf1428b... Author: Peter van 't Hof <p.j.van_t_hof@lumc.nl> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Fixed import order (again ;) ) Commit: 9d98f10767d7c43e979720ba8a9badee86501c78 https://github.com/galaxyproject/galaxy/commit/9d98f10767d7c43e979720ba8a9ba... Author: Peter van 't Hof <p.j.van_t_hof@lumc.nl> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/vcf_bgzip.xml Log Message: ----------- Adding test tool Commit: 99703469c0a30348683190a894a0fc682f92ff68 https://github.com/galaxyproject/galaxy/commit/99703469c0a30348683190a894a0f... Author: pjvan_thof <pjrvanthof@gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: A test-data/test.vcf.gz Log Message: ----------- Added test file Commit: e29611f52dba5e44924b39009ee28c933f4ba7fd https://github.com/galaxyproject/galaxy/commit/e29611f52dba5e44924b39009ee28... Author: Peter van 't Hof <p.j.van_t_hof@lumc.nl> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M test/functional/tools/vcf_bgzip.xml Log Message: ----------- Fixing formats in test Commit: ed2e71a8383698543d97f339bd2b1175a5c07986 https://github.com/galaxyproject/galaxy/commit/ed2e71a8383698543d97f339bd2b1... Author: Peter van 't Hof <p.j.van_t_hof@lumc.nl> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M test/functional/tools/vcf_bgzip.xml Log Message: ----------- Fixing tool format Commit: 77b948678d69769c3d6c117a4dc718b3b3cb8388 https://github.com/galaxyproject/galaxy/commit/77b948678d69769c3d6c117a4dc71... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Add vcf_bgzip and dependent datatypes to test/functional/tools/sample_datatypes_conf.xml Commit: 5cc71d2e3c009841c96657d2c359dbe5182548b8 https://github.com/galaxyproject/galaxy/commit/5cc71d2e3c009841c96657d2c359d... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/tabular.py M test/functional/tools/vcf_bgzip.xml Log Message: ----------- Simplify vcf_bgzip.xml test wrapper and fix index file access Commit: ed67b117517920affeb71982f08bc355ed0a6cda https://github.com/galaxyproject/galaxy/commit/ed67b117517920affeb71982f08bc... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/datatypes/tabular.py Log Message: ----------- Use with statement in VcfGz class Commit: bcdf2c84f6df020e81c8868b10bcf337e2d72630 https://github.com/galaxyproject/galaxy/commit/bcdf2c84f6df020e81c8868b10bcf... Author: John Chilton <jmchilton@gmail.com> Date: 2017-08-10 (Thu, 10 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/tabular.py A test-data/test.vcf.gz M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/vcf_bgzip.xml Log Message: ----------- Merge pull request #4254 from ffinfo/vcf_gz_datatype Vcf gz datatype Compare: https://github.com/galaxyproject/galaxy/compare/e3de5e250d02...bcdf2c84f6df