Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 80c9763757a626355a70e360fd9aedffd8f8dac3 https://github.com/galaxyproject/galaxy/commit/80c9763757a626355a70e360fd9ae... Author: shiltemann <zazkia@gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py Log Message: ----------- add biom2 datatype Commit: 86902068268903292d1caf003a2274e0a5438f7d https://github.com/galaxyproject/galaxy/commit/86902068268903292d1caf003a227... Author: shiltemann <zazkia@gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom Log Message: ----------- add test biom2 file Commit: b9fb935be594db1224c524bfd03c22b8b90f4bea https://github.com/galaxyproject/galaxy/commit/b9fb935be594db1224c524bfd03c2... Author: shiltemann <zazkia@gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/datatypes/text.py Log Message: ----------- add edam format to biom1 datatype Commit: 8314867ecb57b58caceb4843c021f300dc39472e https://github.com/galaxyproject/galaxy/commit/8314867ecb57b58caceb4843c021f... Author: shiltemann <zazkia@gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- fix sniffer order Commit: 6feb3e22d19c2cb162adc0b5d80655540305a805 https://github.com/galaxyproject/galaxy/commit/6feb3e22d19c2cb162adc0b5d8065... Author: shiltemann <zazkia@gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- order matters Commit: 07ef9b4f4b2a38259ae55f382ebee36e43743a9d https://github.com/galaxyproject/galaxy/commit/07ef9b4f4b2a38259ae55f382ebee... Author: shiltemann <zazkia@gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- use h5py to parse hdf5 header Commit: ca1ebf97c02e7261fc36352206834de5ab74a0fd https://github.com/galaxyproject/galaxy/commit/ca1ebf97c02e7261fc36352206834... Author: Saskia Hiltemann <zazkia@gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- set metadata Commit: ac61072452cd345d45e87d3548e6564858589029 https://github.com/galaxyproject/galaxy/commit/ac61072452cd345d45e87d3548e65... Author: Saskia Hiltemann <zazkia@gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- add h5py requirement for extracting metadata from biom2/hdf5 datatypes Commit: 92e25158410238bfbc80a931fedb80a55b570e2d https://github.com/galaxyproject/galaxy/commit/92e25158410238bfbc80a931fedb8... Author: Saskia Hiltemann <zazkia@gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- fix import order Commit: 4119caf9b7fbd1fc9c374403e7f7836b8d9397c1 https://github.com/galaxyproject/galaxy/commit/4119caf9b7fbd1fc9c374403e7f78... Author: Saskia Hiltemann <zazkia@gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- remove unused variable Commit: 062c88a3cce66df350dc0da7aed14542fe6ad65b https://github.com/galaxyproject/galaxy/commit/062c88a3cce66df350dc0da7aed14... Author: shiltemann <zazkia@gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/biom1_to_biom2.xml A lib/galaxy/datatypes/converters/biom2_to_biom1.xml Log Message: ----------- add converters Commit: a3b316031c5aa1565d7255eab5aa92ff4a749f4d https://github.com/galaxyproject/galaxy/commit/a3b316031c5aa1565d7255eab5aa9... Author: shiltemann <zazkia@gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- simplify Commit: 995f2cee4a2914c157420467829ff647a2e8c7d6 https://github.com/galaxyproject/galaxy/commit/995f2cee4a2914c157420467829ff... Author: shiltemann <zazkia@gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- add guess_ext test Commit: 95aacc010e730ce24e2e10557bac8395c538d2af https://github.com/galaxyproject/galaxy/commit/95aacc010e730ce24e2e10557bac8... Author: shiltemann <zazkia@gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- add metadata to peek Commit: 907e931fa8f62856fa846d2b9a9bc6392f26952a https://github.com/galaxyproject/galaxy/commit/907e931fa8f62856fa846d2b9a9bc... Author: shiltemann <zazkia@gmail.com> Date: 2017-08-30 (Wed, 30 Aug 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- don't cast to string Commit: 8f3c65c59efe623c325f54e2407c383688ffeedb https://github.com/galaxyproject/galaxy/commit/8f3c65c59efe623c325f54e2407c3... Author: Saskia Hiltemann <shiltemann@users.noreply.github.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- use version 2.7.1 of h5py Commit: d4cf4bff4f249c5e100fde8a31315c92acbe4fc8 https://github.com/galaxyproject/galaxy/commit/d4cf4bff4f249c5e100fde8a31315... Author: shiltemann <zazkia@gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- PEP8 fix Commit: 2615094597ff6bdb0b03e496ea075c2a16f561b9 https://github.com/galaxyproject/galaxy/commit/2615094597ff6bdb0b03e496ea075... Author: shiltemann <zazkia@gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M lib/galaxy/datatypes/data.py Log Message: ----------- Revert "remove unused variable" This reverts commit 4119caf9b7fbd1fc9c374403e7f7836b8d9397c1. Commit: a8df8729b8670e23c4f77616cd775aed98463ca7 https://github.com/galaxyproject/galaxy/commit/a8df8729b8670e23c4f77616cd775... Author: Dannon Baker <dannon.baker@gmail.com> Date: 2017-09-07 (Thu, 07 Sep 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/converters/biom1_to_biom2.xml A lib/galaxy/datatypes/converters/biom2_to_biom1.xml M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Merge pull request #4519 from shiltemann/biom2_datatype add biom2 datatype Compare: https://github.com/galaxyproject/galaxy/compare/b3f0f36c89a0...a8df8729b867