- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 07806e: Another fix for Selenium testing on Jenkins.
by GitHub 13 Jan '17

13 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 07806e628adf164e95543393a9f37a187acb9a0e https://github.com/galaxyproject/galaxy/commit/07806e628adf164e95543393a9f3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M .ci/jenkins/selenium/run_galaxy.bash Log Message: ----------- Another fix for Selenium testing on Jenkins. Turns out that random sleep for 30 seconds was every bit as brittle as it seemed. This is a bit better. Commit: e573826e02e822abd63fe452b065efd690e277da https://github.com/galaxyproject/galaxy/commit/e573826e02e822abd63fe452b065… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M .ci/jenkins/selenium/run_galaxy.bash Log Message: ----------- Merge pull request #3422 from jmchilton/selenium_fixes_0 Another fix for Selenium testing on Jenkins. Compare: https://github.com/galaxyproject/galaxy/compare/ec425007b11f...e573826e02e8

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[galaxyproject/galaxy] cc4cd5: Fix RStudio login
by GitHub 13 Jan '17

13 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: cc4cd55c1df0fd3ae78bdbff99ad70c2ed723def https://github.com/galaxyproject/galaxy/commit/cc4cd55c1df0fd3ae78bdbff99ad… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Fix RStudio login Thanks @shiltemann for reporting this Commit: c94ccb3f28cdf3acbfe863b386c5dcb58752fe50 https://github.com/galaxyproject/galaxy/commit/c94ccb3f28cdf3acbfe863b386c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Merge pull request #3414 from erasche/fix-rstudio-login [16.10] Fix RStudio login Compare: https://github.com/galaxyproject/galaxy/compare/2d69909218b2...c94ccb3f28cd

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[galaxyproject/galaxy] f9b9eb: Expose anyway if the user is an admin user
by GitHub 13 Jan '17

13 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f9b9ebdd38cf2ee1634bf7daab171a25a8cec953 https://github.com/galaxyproject/galaxy/commit/f9b9ebdd38cf2ee1634bf7daab17… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M templates/ind_share_base.mako Log Message: ----------- Expose anyway if the user is an admin user Commit: 7c02ed7a9d1ab2c5101fbc4753ae7ee35d770c14 https://github.com/galaxyproject/galaxy/commit/7c02ed7a9d1ab2c5101fbc4753ae… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M templates/webapps/galaxy/history/share.mako Log Message: ----------- Mirror change in #3250 Fixes #3372 Commit: 6fc538837bc541ea9ad46fefc3e54ca676526bc9 https://github.com/galaxyproject/galaxy/commit/6fc538837bc541ea9ad46fefc3e5… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M templates/webapps/galaxy/history/share.mako Log Message: ----------- Remove extraneous tag Commit: ec425007b11fd871b473a488e5321bb4450bccbf https://github.com/galaxyproject/galaxy/commit/ec425007b11fd871b473a488e532… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-13 (Fri, 13 Jan 2017) Changed paths: M templates/ind_share_base.mako M templates/webapps/galaxy/history/share.mako Log Message: ----------- Merge pull request #3417 from erasche/fix-3372 Fix accidental email exposure Compare: https://github.com/galaxyproject/galaxy/compare/4946313fc9dc...ec425007b11f

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[galaxyproject/galaxy] 890107: Reversion of ui-misc messagebox changes.
by GitHub 12 Jan '17

12 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 890107334d25b80ee1fc02d00df011f2e7e9d88a https://github.com/galaxyproject/galaxy/commit/890107334d25b80ee1fc02d00df0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Reversion of ui-misc messagebox changes. Commit: 2d69909218b287f8085a599e0a2a1214480330c9 https://github.com/galaxyproject/galaxy/commit/2d69909218b287f8085a599e0a2a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Merge pull request #3415 from dannon/revert_uimisc [16.10]Reversion of ui-misc messagebox changes. Compare: https://github.com/galaxyproject/galaxy/compare/45a9d586b6e1...2d69909218b2

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[galaxyproject/galaxy] a5c445: Swap the client's ui-misc.Message to escape by def...
by GitHub 12 Jan '17

12 Jan '17

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: a5c445966ef3ea8385493ffd2ca6bf6dce8611aa https://github.com/galaxyproject/galaxy/commit/a5c445966ef3ea8385493ffd2ca6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js A static/maps/libs/showdown.js.map M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/libs/showdown.js M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Swap the client's ui-misc.Message to escape by default. Commit: e1083132b89f854e2ec824f97f187e925ba0abe6 https://github.com/galaxyproject/galaxy/commit/e1083132b89f854e2ec824f97f18… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Add UnescapedMessage, for when we actually need to display a message with html contents. Any users of this must escape contents on their own. Commit: 3060da4ee53e44c0814eebe2c468f2d3dc352233 https://github.com/galaxyproject/galaxy/commit/3060da4ee53e44c0814eebe2c468… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-misc.js Log Message: ----------- Export UnescapedMessage from ui-misc. Commit: 45a9d586b6e1db89bf0813aa93af5b3bbaf72efc https://github.com/galaxyproject/galaxy/commit/45a9d586b6e1db89bf0813aa93af… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/galaxy/scripts/mvc/ui/ui-misc.js M static/maps/mvc/ui/ui-misc.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Formatting cleanup. Compare: https://github.com/galaxyproject/galaxy/compare/b0ac7daecdda...45a9d586b6e1

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[galaxyproject/galaxy]
by GitHub 12 Jan '17

12 Jan '17

Branch: refs/heads/revert-3399-markdown Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] e74ca2: Revert "Markdown datatype support."
by GitHub 12 Jan '17

12 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e74ca27dbfc8c9f6244ba7f786a9460bdf0af753 https://github.com/galaxyproject/galaxy/commit/e74ca27dbfc8c9f6244ba7f786a9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M client/bower.json R client/galaxy/scripts/libs/showdown.js M client/grunt-tasks/install-libs.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/text.py R static/maps/libs/showdown.js.map R static/scripts/libs/showdown.js R templates/webapps/galaxy/dataset/markdown.mako R test/functional/tools/creates_html.xml R test/functional/tools/creates_html_index.html R test/functional/tools/creates_markdown.xml R test/functional/tools/creates_markdown_index.md M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Revert "Markdown datatype support." Commit: 4946313fc9dc27d2bc2e3d0464682d8308b8702c https://github.com/galaxyproject/galaxy/commit/4946313fc9dc27d2bc2e3d046468… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M client/bower.json R client/galaxy/scripts/libs/showdown.js M client/grunt-tasks/install-libs.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/text.py R static/maps/libs/showdown.js.map R static/scripts/libs/showdown.js R templates/webapps/galaxy/dataset/markdown.mako R test/functional/tools/creates_html.xml R test/functional/tools/creates_html_index.html R test/functional/tools/creates_markdown.xml R test/functional/tools/creates_markdown_index.md M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3408 from galaxyproject/revert-3399-markdown Revert "Markdown datatype support." Compare: https://github.com/galaxyproject/galaxy/compare/7bb8376490a2...4946313fc9dc

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[galaxyproject/galaxy] a60b7d: fix typo
by GitHub 12 Jan '17

12 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a60b7da85e2b9ef83aa86a0593dd5b810802ddf3 https://github.com/galaxyproject/galaxy/commit/a60b7da85e2b9ef83aa86a0593dd… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- fix typo Commit: 7bb8376490a251573252177ab4112caba64b4684 https://github.com/galaxyproject/galaxy/commit/7bb8376490a251573252177ab411… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-01-12 (Thu, 12 Jan 2017) Changed paths: M doc/source/admin/webhooks.rst Log Message: ----------- Merge pull request #3409 from manabuishii/patch-4 fix typo Compare: https://github.com/galaxyproject/galaxy/compare/a87feb11ff61...7bb8376490a2

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[galaxyproject/galaxy] e74ca2: Revert "Markdown datatype support."
by GitHub 12 Jan '17

12 Jan '17

Branch: refs/heads/revert-3399-markdown Home: https://github.com/galaxyproject/galaxy Commit: e74ca27dbfc8c9f6244ba7f786a9460bdf0af753 https://github.com/galaxyproject/galaxy/commit/e74ca27dbfc8c9f6244ba7f786a9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-01-11 (Wed, 11 Jan 2017) Changed paths: M client/bower.json R client/galaxy/scripts/libs/showdown.js M client/grunt-tasks/install-libs.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/text.py R static/maps/libs/showdown.js.map R static/scripts/libs/showdown.js R templates/webapps/galaxy/dataset/markdown.mako R test/functional/tools/creates_html.xml R test/functional/tools/creates_html_index.html R test/functional/tools/creates_markdown.xml R test/functional/tools/creates_markdown_index.md M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Revert "Markdown datatype support."

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[galaxyproject/galaxy] 5ab4ae: Changes for Fastq Compression.
by GitHub 12 Jan '17

12 Jan '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5ab4ae4f2f630ea12c8b4e82e90cd8dca2758a6f https://github.com/galaxyproject/galaxy/commit/5ab4ae4f2f630ea12c8b4e82e90c… Author: ashok <ashok(a)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/7597da61e5de1796f0cf4ce2f6ea… Author: ashok <ashok(a)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/aabfa4283d396ba01ea42b47ab0b… Author: ashok <ashvark(a)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/7d4840ce6b46a2b51f0d5332d72e… Author: mvdbeek <m.vandenbeek(a)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/10f1bb5459c4d27ca9142c0f4da1… Author: mvdbeek <m.vandenbeek(a)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/b44a977e649e3c6ac7cfc0bc519c… Author: mvdbeek <m.vandenbeek(a)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/bcf08f630d40b45b852db56e4a59… Author: mvdbeek <m.vandenbeek(a)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/304c05f3a3a99a9d450c06145bf3… Author: mvdbeek <m.vandenbeek(a)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/99a037d5b92828cbef097ae8434e… Author: Anthony Bretaudeau <anthony.bretaudeau(a)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/833f2c3dbef2469fe7437e8939e3… Author: Marius van den Beek <m.vandenbeek(a)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/500ed949e66cb0ddec757022cae8… Author: Anthony Bretaudeau <abretaud(a)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/b327523c3011c81e164f12833ff0… Author: Anthony Bretaudeau <abretaud(a)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/7d8bbd599a2528a3e0e9264d64d0… Author: Anthony Bretaudeau <anthony.bretaudeau(a)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/43abc55284fd4a1d7ea62535797d… Author: Anthony Bretaudeau <anthony.bretaudeau(a)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/296889d0dfa767c3649c6331a911… Author: Anthony Bretaudeau <anthony.bretaudeau(a)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/a87feb11ff61dc0a8ea2657c8afe… Author: John Chilton <jmchilton(a)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

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