December 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 854b24: Fix linting of gff_filter_by_attribute.
by GitHub 19 Dec '16

19 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: 854b24bb009c46c8e48eb799aef3bf142610bcad https://github.com/galaxyproject/galaxy/commit/854b24bb009c46c8e48eb799aef3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py Log Message: ----------- Fix linting of gff_filter_by_attribute. Broken during security patching - Travis tests are failing now against dev. Commit: 5eafa8bae312182a58f27e55bb93a9a471d95dd2 https://github.com/galaxyproject/galaxy/commit/5eafa8bae312182a58f27e55bb93… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py Log Message: ----------- Merge pull request #3335 from nsoranzo/release_16.10_backport_3324 [16.10] Backport #3324 Compare: https://github.com/galaxyproject/galaxy/compare/553ec588ed11...5eafa8bae312

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[galaxyproject/galaxy] c36fbe: genbank datatype
by GitHub 19 Dec '16

19 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c36fbebb443ae5b5263ba6cad6ad36113bb52f44 https://github.com/galaxyproject/galaxy/commit/c36fbebb443ae5b5263ba6cad6ad… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py Log Message: ----------- genbank datatype Commit: 5e2249c1b4698db4880fb74e422a903585bc3054 https://github.com/galaxyproject/galaxy/commit/5e2249c1b4698db4880fb74e422a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Address review concerns Commit: 43075015dd7bd81bef0394259f0a60721f4163df https://github.com/galaxyproject/galaxy/commit/43075015dd7bd81bef0394259f0a… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py Log Message: ----------- Merge pull request #3339 from erasche/genbank Genbank datatype Compare: https://github.com/galaxyproject/galaxy/compare/415ddbb3bf8d...43075015dd7b

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[galaxyproject/infrastructure-playbook] c436aa: Run CVMFS client on cvmfs1-psu0 and serve datacach...
by GitHub 19 Dec '16

19 Dec '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c436aa3d213fb7b4caa3ca0a891c03be6e3ef24f https://github.com/galaxyproject/infrastructure-playbook/commit/c436aa3d213… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M common_roles M galaxyenv/host_vars/cvmfs1-psu0.galaxyproject.org.yml M galaxyenv/inventory M galaxyenv/playbook.yml Log Message: ----------- Run CVMFS client on cvmfs1-psu0 and serve datacache rsync from there

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[galaxyproject/galaxy] b6e9ba: Allow multiple workflow parameters in a single lin...
by GitHub 19 Dec '16

19 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b6e9ba402df42a5843455dbc129928086628c35e https://github.com/galaxyproject/galaxy/commit/b6e9ba402df42a5843455dbc1299… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Allow multiple workflow parameters in a single line Commit: 733a53adcfbd90bf3a02e2e1fadbc81ba3c512ea https://github.com/galaxyproject/galaxy/commit/733a53adcfbd90bf3a02e2e1fadb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Replace workflow parameter values in template value string Commit: 3f07c7b52e1128ad3902ded6723eb575198de7e1 https://github.com/galaxyproject/galaxy/commit/3f07c7b52e1128ad3902ded6723e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Preserve template value if no workflow parameter value has been specified Commit: 5c3a0e1df06a1690a132498398298b742745e98f https://github.com/galaxyproject/galaxy/commit/5c3a0e1df06a1690a13249839829… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Identify workflow parameters through regex from original value Commit: 553ec588ed11effb3be665c92a3a7878914d3c1b https://github.com/galaxyproject/galaxy/commit/553ec588ed11effb3be665c92a3a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #3329 from guerler/fix_workflow_parameters [16.10] Fix workflow parameter handling Commit: 415ddbb3bf8d44acdcabc29478544420a45fc7e4 https://github.com/galaxyproject/galaxy/commit/415ddbb3bf8d44acdcabc2947854… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge branch 'release_16.10' into dev Compare: https://github.com/galaxyproject/galaxy/compare/f83a1bacf653...415ddbb3bf8d

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[galaxyproject/galaxy] b6e9ba: Allow multiple workflow parameters in a single lin...
by GitHub 19 Dec '16

19 Dec '16

Branch: refs/heads/release_16.10 Home: https://github.com/galaxyproject/galaxy Commit: b6e9ba402df42a5843455dbc129928086628c35e https://github.com/galaxyproject/galaxy/commit/b6e9ba402df42a5843455dbc1299… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Allow multiple workflow parameters in a single line Commit: 733a53adcfbd90bf3a02e2e1fadbc81ba3c512ea https://github.com/galaxyproject/galaxy/commit/733a53adcfbd90bf3a02e2e1fadb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Replace workflow parameter values in template value string Commit: 3f07c7b52e1128ad3902ded6723eb575198de7e1 https://github.com/galaxyproject/galaxy/commit/3f07c7b52e1128ad3902ded6723e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Preserve template value if no workflow parameter value has been specified Commit: 5c3a0e1df06a1690a132498398298b742745e98f https://github.com/galaxyproject/galaxy/commit/5c3a0e1df06a1690a13249839829… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Identify workflow parameters through regex from original value Commit: 553ec588ed11effb3be665c92a3a7878914d3c1b https://github.com/galaxyproject/galaxy/commit/553ec588ed11effb3be665c92a3a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-12-19 (Mon, 19 Dec 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #3329 from guerler/fix_workflow_parameters [16.10] Fix workflow parameter handling Compare: https://github.com/galaxyproject/galaxy/compare/c1397908cd1f...553ec588ed11

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[galaxyproject/galaxy] 48bc9b: add an option to specify the port, which is used t...
by GitHub 17 Dec '16

17 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 48bc9ba31d43af09823b66726af86c7cfb0b8bba https://github.com/galaxyproject/galaxy/commit/48bc9ba31d43af09823b66726af8… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- add an option to specify the port, which is used to connect the UIs Commit: f83a1bacf6531a3efe404e93faca924d5a01bd3f https://github.com/galaxyproject/galaxy/commit/f83a1bacf6531a3efe404e93faca… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-12-17 (Sat, 17 Dec 2016) Changed paths: M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #3328 from bgruening/ie_port_overwrite IE enhancement Compare: https://github.com/galaxyproject/galaxy/compare/02501b938724...f83a1bacf653

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[galaxyproject/galaxy] a473c0: Provide a fallback to old IPython named config opt...
by GitHub 16 Dec '16

16 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a473c0787a42618d26269e79732f6e997016c9d2 https://github.com/galaxyproject/galaxy/commit/a473c0787a42618d26269e79732f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Provide a fallback to old IPython named config option... ... as suggested by @bgruening in https://github.com/galaxyproject/galaxy/pull/3294#pullrequestreview-12532937. Commit: 02501b938724ce7a788c6e6d91b7b506e0e5f25b https://github.com/galaxyproject/galaxy/commit/02501b938724ce7a788c6e6d91b7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #3325 from jmchilton/juypter_fixes Provide a fallback to old IPython named config option... Compare: https://github.com/galaxyproject/galaxy/compare/a504e8ea7be4...02501b938724

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[galaxyproject/galaxy] 27673f: Addition of Genome fasta file loading in local IGV...
by GitHub 16 Dec '16

16 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 27673f5e08b67d432a0bd369aea6eac248ba8f93 https://github.com/galaxyproject/galaxy/commit/27673f5e08b67d432a0bd369aea6… Author: Delphine-L <lariviere.delphine(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M config/datatypes_conf.xml.sample A display_applications/igv/genome_fasta.xml A lib/galaxy/datatypes/converters/fasta_to_fai.xml Log Message: ----------- Addition of Genome fasta file loading in local IGV instance, and addition of fai format and fasta to fai converter Commit: 8cc2efb74f6679aee72cfdbc35a592d7abd2f4dc https://github.com/galaxyproject/galaxy/commit/8cc2efb74f6679aee72cfdbc35a5… Author: Delphine-L <lariviere.delphine(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M lib/galaxy/datatypes/converters/fasta_to_fai.xml Log Message: ----------- removal of old commented line Commit: 1d0f15d1750e88dc1bf6ba835be2561771f99ce6 https://github.com/galaxyproject/galaxy/commit/1d0f15d1750e88dc1bf6ba835be2… Author: Delphine-L <lariviere.delphine(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M display_applications/igv/genome_fasta.xml Log Message: ----------- Edit of Authors Commit: f4070ba9815ffacd28523f6e87398dea42271e8f https://github.com/galaxyproject/galaxy/commit/f4070ba9815ffacd28523f6e8739… Author: Delphine-L <lariviere.delphine(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Syntax cleaning Commit: a504e8ea7be42940800dcb67d2c00d478868fb2c https://github.com/galaxyproject/galaxy/commit/a504e8ea7be42940800dcb67d2c0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M config/datatypes_conf.xml.sample A display_applications/igv/genome_fasta.xml A lib/galaxy/datatypes/converters/fasta_to_fai.xml Log Message: ----------- Merge pull request #3327 from Delphine-L/IGV_display_fasta Addition of IGV display for genome fasta file Compare: https://github.com/galaxyproject/galaxy/compare/2845bfaf9609...a504e8ea7be4

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[galaxyproject/galaxy] 58a3a5: Fix linting of gff_filter_by_attribute.
by GitHub 16 Dec '16

16 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 58a3a5b71b00c974b19eae514b09abfc04b74170 https://github.com/galaxyproject/galaxy/commit/58a3a5b71b00c974b19eae514b09… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py Log Message: ----------- Fix linting of gff_filter_by_attribute. Broken during security patching - Travis tests are failing now against dev. Commit: 2845bfaf9609e55e785a71606ec535a225e7529d https://github.com/galaxyproject/galaxy/commit/2845bfaf9609e55e785a71606ec5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py Log Message: ----------- Merge pull request #3324 from jmchilton/fix_lint_security Fix linting of gff_filter_by_attribute. Compare: https://github.com/galaxyproject/galaxy/compare/f4282c8672df...2845bfaf9609

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[galaxyproject/galaxy] 6fd77d: Preliminary fix for mapping tools with paired
by GitHub 16 Dec '16

16 Dec '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6fd77db920d088ba6ebc64a4ac8ab7524d5ce654 https://github.com/galaxyproject/galaxy/commit/6fd77db920d088ba6ebc64a4ac8a… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/tools/actions/__init__.py A test/functional/tools/paired_collection_map_over_structured_like.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Preliminary fix for mapping tools with paired collection input over list:paired collections. Commit: 1aba7549debca136048d2850dae28b1185e30469 https://github.com/galaxyproject/galaxy/commit/1aba7549debca136048d2850dae2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M test/functional/tools/paired_collection_map_over_structured_like.xml Log Message: ----------- Add inherit_format tag to paired_collection_map_over_structured_like tool Commit: 55eac47d0fe9083c84afc613f451bfa68649b4d8 https://github.com/galaxyproject/galaxy/commit/55eac47d0fe9083c84afc613f451… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M test/functional/tools/paired_collection_map_over_structured_like.xml Log Message: ----------- Fix test tool -- functional test framework appears to not support mapping over test-data Commit: a39941a3c57f0cf1d0db848debfed4d54c321627 https://github.com/galaxyproject/galaxy/commit/a39941a3c57f0cf1d0db848debfe… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-22 (Tue, 22 Nov 2016) Changed paths: M test/api/test_tools.py Log Message: ----------- Add failing test for structured_like paired input Commit: cbd9f68f760178b113b624078372f955b486d32e https://github.com/galaxyproject/galaxy/commit/cbd9f68f760178b113b624078372… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M test/api/test_tools.py Log Message: ----------- Fixup test case for #3209. Commit: f4282c8672df5fb1f4d1f401c0209e1c6f253ca5 https://github.com/galaxyproject/galaxy/commit/f4282c8672df5fb1f4d1f401c020… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-12-16 (Fri, 16 Dec 2016) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/tools/actions/__init__.py M test/api/test_tools.py A test/functional/tools/paired_collection_map_over_structured_like.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3209 from mvdbeek/fix_paired_list Fix for mapping tools with paired collection input and a structured_like tag over list:paired collections Compare: https://github.com/galaxyproject/galaxy/compare/147de088177c...f4282c8672df

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