Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5ab4ae4f2f630ea12c8b4e82e90cd8dca2758a6f https://github.com/galaxyproject/galaxy/commit/5ab4ae4f2f630ea12c8b4e82e90cd... Author: ashok <ashok@localhost.localdomain> Date: 2016-11-09 (Wed, 09 Nov 2016) Changed paths: A lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml A lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Changes for Fastq Compression. Commit: 7597da61e5de1796f0cf4ce2f6ea577cb390f311 https://github.com/galaxyproject/galaxy/commit/7597da61e5de1796f0cf4ce2f6ea5... Author: ashok <ashok@localhost.localdomain> Date: 2016-11-09 (Wed, 09 Nov 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py Log Message: ----------- Updated sequence.py and datatypes_conf.xml Commit: aabfa4283d396ba01ea42b47ab0b8601122096bd https://github.com/galaxyproject/galaxy/commit/aabfa4283d396ba01ea42b47ab0b8... Author: ashok <ashvark@gmail.com> Date: 2016-11-09 (Wed, 09 Nov 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py M tools/data_source/upload.py Log Message: ----------- Changes to keep the compressed fastq file as it is with out decompressing. Commit: 7d4840ce6b46a2b51f0d5332d72e7b4d956ac808 https://github.com/galaxyproject/galaxy/commit/7d4840ce6b46a2b51f0d5332d72e7... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-10 (Thu, 10 Nov 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py M tools/data_source/upload.py Log Message: ----------- For fastq.gz support inherit from Fastq and Binary and enhance FastQ format to be gzip aware. Commit: 10f1bb5459c4d27ca9142c0f4da1c8502ac9f1b2 https://github.com/galaxyproject/galaxy/commit/10f1bb5459c4d27ca9142c0f4da1c... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-11 (Fri, 11 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py A test-data/1.fastqsanger.gz A test/functional/tools/compressed_fastq_conversion.xml A test/functional/tools/compressed_fastq_no_conversion.xml Log Message: ----------- Create a BaseFastq class and add test tools Having a BaseFastq class allows Fastq and FastqGz classes to inherit from BaseFastq. FastqGz is therfor not a Fastq datatype and goes through the converter. Also add 2 tools to demonstrate that compressed fastq will be converted to uncompressed fastq if the tool specifies `format="fastq"`, while `format="fastq.gz"` leaves files compressed. The tool test can be run with: ``` planemo test --galaxy_root . test/functional/tools/compressed_fastq_no_conversion.xml planemo test --galaxy_root . test/functional/tools/compressed_fastq_conversion.xml ``` Note that fastq conversion appears to required a galaxy user session, and planemo testing fails. Interactive testing with `planemo serve` is not affected and works fine. Commit: b44a977e649e3c6ac7cfc0bc519c242139296789 https://github.com/galaxyproject/galaxy/commit/b44a977e649e3c6ac7cfc0bc519c2... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-12 (Sat, 12 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml M lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml M lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml M lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml M lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml Log Message: ----------- Quote paths in converters Commit: bcf08f630d40b45b852db56e4a59c362c3cfc2bf https://github.com/galaxyproject/galaxy/commit/bcf08f630d40b45b852db56e4a59c... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-12 (Sat, 12 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Ensure closing of open files Commit: 304c05f3a3a99a9d450c06145bf3985f72f8b7db https://github.com/galaxyproject/galaxy/commit/304c05f3a3a99a9d450c06145bf39... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2016-11-12 (Sat, 12 Nov 2016) Changed paths: M lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml M lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml M lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml M lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml Log Message: ----------- Remove deprecated page attribute Commit: 99a037d5b92828cbef097ae8434e1d172df3c888 https://github.com/galaxyproject/galaxy/commit/99a037d5b92828cbef097ae8434e1... Author: Anthony Bretaudeau <anthony.bretaudeau@inria.fr> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml A lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml M lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml M lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml M lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py A test-data/1.fastqsanger.bz2 A test/functional/tools/compressed_bz2_fastq_conversion.xml A test/functional/tools/compressed_bz2_fastq_no_conversion.xml R test/functional/tools/compressed_fastq_conversion.xml R test/functional/tools/compressed_fastq_no_conversion.xml A test/functional/tools/compressed_gz_fastq_conversion.xml A test/functional/tools/compressed_gz_fastq_no_conversion.xml Log Message: ----------- add fastq(*).bz2 datatypes and converters Commit: 833f2c3dbef2469fe7437e8939e329ddff8d2793 https://github.com/galaxyproject/galaxy/commit/833f2c3dbef2469fe7437e8939e32... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml A lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml M lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml M lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml M lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py A test-data/1.fastqsanger.bz2 A test/functional/tools/compressed_bz2_fastq_conversion.xml A test/functional/tools/compressed_bz2_fastq_no_conversion.xml R test/functional/tools/compressed_fastq_conversion.xml R test/functional/tools/compressed_fastq_no_conversion.xml A test/functional/tools/compressed_gz_fastq_conversion.xml A test/functional/tools/compressed_gz_fastq_no_conversion.xml Log Message: ----------- Merge pull request #1 from abretaud/bz2 Add fastq(*).bz2 datatypes and converters Commit: 500ed949e66cb0ddec757022cae8be230722d755 https://github.com/galaxyproject/galaxy/commit/500ed949e66cb0ddec757022cae8b... Author: Anthony Bretaudeau <abretaud@irisa.fr> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Fix indentation and import (#2) * fix indentation and import * import fix * refix indentation * better looking imports Commit: b327523c3011c81e164f12833ff010eb411d963e https://github.com/galaxyproject/galaxy/commit/b327523c3011c81e164f12833ff01... Author: Anthony Bretaudeau <abretaud@irisa.fr> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- wrong import name (#3) Commit: 7d8bbd599a2528a3e0e9264d64d0da3e494b5016 https://github.com/galaxyproject/galaxy/commit/7d8bbd599a2528a3e0e9264d64d0d... Author: Anthony Bretaudeau <anthony.bretaudeau@inria.fr> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- python lint Commit: 43abc55284fd4a1d7ea62535797d29f9977ef0af https://github.com/galaxyproject/galaxy/commit/43abc55284fd4a1d7ea62535797d2... Author: Anthony Bretaudeau <anthony.bretaudeau@inria.fr> Date: 2016-11-24 (Thu, 24 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- python lint Commit: 296889d0dfa767c3649c6331a911ba0fd904f9fd https://github.com/galaxyproject/galaxy/commit/296889d0dfa767c3649c6331a911b... Author: Anthony Bretaudeau <anthony.bretaudeau@inria.fr> Date: 2016-11-25 (Fri, 25 Nov 2016) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- lint fix Commit: a87feb11ff61dc0a8ea2657c8afe99cd115d1eda https://github.com/galaxyproject/galaxy/commit/a87feb11ff61dc0a8ea2657c8afe9... Author: John Chilton <jmchilton@gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml A lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml A lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml A lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml A lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml A lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml A lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py A test-data/1.fastqsanger.bz2 A test-data/1.fastqsanger.gz A test/functional/tools/compressed_bz2_fastq_conversion.xml A test/functional/tools/compressed_bz2_fastq_no_conversion.xml A test/functional/tools/compressed_gz_fastq_conversion.xml A test/functional/tools/compressed_gz_fastq_no_conversion.xml Log Message: ----------- Merge pull request #3145 from mvdbeek/fastqgz Support for gzipped fastq formats Compare: https://github.com/galaxyproject/galaxy/compare/34458725b826...a87feb11ff61