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

[galaxyproject/galaxy] e06581: Extended the linter rules to accept a help attribu...
by GitHub 07 Nov '16

07 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e06581c587cdfe24822fba2f79ddaf60619858d2 https://github.com/galaxyproject/galaxy/commit/e06581c587cdfe24822fba2f79dd… Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de> Date: 2016-11-02 (Wed, 02 Nov 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Extended the linter rules to accept a help attribute for sections Commit: b169299b5efbd144d5ab43f28e079a3fa5cf45a8 https://github.com/galaxyproject/galaxy/commit/b169299b5efbd144d5ab43f28e07… Author: Joachim Wolff <wolffj(a)informatik.uni-freiburg.de> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Extended linter rule for help attribute in section Commit: 78dfb95f0264e349ee03b5c1a7c1cde9c6e38ba4 https://github.com/galaxyproject/galaxy/commit/78dfb95f0264e349ee03b5c1a7c1… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #3131 from joachimwolff/dev Extended the linter rules to accept a help attribute for sections Compare: https://github.com/galaxyproject/galaxy/compare/04935ce94b86...78dfb95f0264

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[galaxyproject/galaxy] 05fbef: Add doc for conda_copy_dependencies option
by GitHub 07 Nov '16

07 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 05fbef510c7497911a2abea83c5bdc26bf338460 https://github.com/galaxyproject/galaxy/commit/05fbef510c7497911a2abea83c5b… Author: Anthony Bretaudeau <abretaud(a)irisa.fr> Date: 2016-10-28 (Fri, 28 Oct 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Add doc for conda_copy_dependencies option Discussed on IUC gitter, related to https://github.com/galaxyproject/galaxy/issues/3008 Commit: 16866b5e8075d648bd17ac3786f76356e23c43a2 https://github.com/galaxyproject/galaxy/commit/16866b5e8075d648bd17ac3786f7… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-10-28 (Fri, 28 Oct 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- add extra time problem Commit: 69cda7ee10d78a61830f90f957500ba41821640b https://github.com/galaxyproject/galaxy/commit/69cda7ee10d78a61830f90f95750… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-10-28 (Fri, 28 Oct 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- clarify links Commit: 8a972cc325fd39b71d89f28d9eec62630d9859ac https://github.com/galaxyproject/galaxy/commit/8a972cc325fd39b71d89f28d9eec… Author: Anthony Bretaudeau <anthony.bretaudeau(a)inria.fr> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- be stronger Commit: 04935ce94b864a7898dc62895a11023dec805580 https://github.com/galaxyproject/galaxy/commit/04935ce94b864a7898dc62895a11… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #3105 from abretaud/patch-2 Add doc for conda_copy_dependencies option Compare: https://github.com/galaxyproject/galaxy/compare/3200fa343b12...04935ce94b86

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[galaxyproject/galaxy] c94b22: Escape section id and name when writing integrated...
by GitHub 07 Nov '16

07 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c94b2205b27d1d527f159bcf13ba62ce937457f6 https://github.com/galaxyproject/galaxy/commit/c94b2205b27d1d527f159bcf13ba… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Escape section id and name when writing integrated_tool_panel.xml This should fix #3084. Commit: f6ca913809330922a3bc96bcf0f77d3f60e9bbe9 https://github.com/galaxyproject/galaxy/commit/f6ca913809330922a3bc96bcf0f7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Log invalid xml filename Commit: c5245219567562f67556548cbc0b8a9624ea0308 https://github.com/galaxyproject/galaxy/commit/c5245219567562f67556548cbc0b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Make catching XML parsing errors python2.6 compatible Commit: a274e635a6f7f2b169506ebf4a5a2363578bbfb1 https://github.com/galaxyproject/galaxy/commit/a274e635a6f7f2b169506ebf4a5a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-11-05 (Sat, 05 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #3128 from mvdbeek/backport_3122_3124 [16.01] Backport #3122 #3124 - fix unescaped & in integrated_tool_panel.xml Commit: 788dc1ebef5110fded19d23e4a2c48e06e3c5e63 https://github.com/galaxyproject/galaxy/commit/788dc1ebef5110fded19d23e4a2c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: lib/galaxy/util/__init__.py Commit: 53a66c9d46780a4910a8a03de565eb3fb53f5bdc https://github.com/galaxyproject/galaxy/commit/53a66c9d46780a4910a8a03de565… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: 3200fa343b12b2c40ad6b3e29b77c6628d66b7a0 https://github.com/galaxyproject/galaxy/commit/3200fa343b12b2c40ad6b3e29b77… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-07 (Mon, 07 Nov 2016) Log Message: ----------- Merge branch 'release_16.07' into dev Conflicts: lib/galaxy/util/__init__.py Compare: https://github.com/galaxyproject/galaxy/compare/202f96c73114...3200fa343b12

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[galaxyproject/galaxy] c94b22: Escape section id and name when writing integrated...
by GitHub 07 Nov '16

07 Nov '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: c94b2205b27d1d527f159bcf13ba62ce937457f6 https://github.com/galaxyproject/galaxy/commit/c94b2205b27d1d527f159bcf13ba… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Escape section id and name when writing integrated_tool_panel.xml This should fix #3084. Commit: f6ca913809330922a3bc96bcf0f77d3f60e9bbe9 https://github.com/galaxyproject/galaxy/commit/f6ca913809330922a3bc96bcf0f7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Log invalid xml filename Commit: c5245219567562f67556548cbc0b8a9624ea0308 https://github.com/galaxyproject/galaxy/commit/c5245219567562f67556548cbc0b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Make catching XML parsing errors python2.6 compatible Commit: a274e635a6f7f2b169506ebf4a5a2363578bbfb1 https://github.com/galaxyproject/galaxy/commit/a274e635a6f7f2b169506ebf4a5a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-11-05 (Sat, 05 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #3128 from mvdbeek/backport_3122_3124 [16.01] Backport #3122 #3124 - fix unescaped & in integrated_tool_panel.xml Commit: 788dc1ebef5110fded19d23e4a2c48e06e3c5e63 https://github.com/galaxyproject/galaxy/commit/788dc1ebef5110fded19d23e4a2c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: lib/galaxy/util/__init__.py Commit: 53a66c9d46780a4910a8a03de565eb3fb53f5bdc https://github.com/galaxyproject/galaxy/commit/53a66c9d46780a4910a8a03de565… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Compare: https://github.com/galaxyproject/galaxy/compare/d72cc77bebd4...53a66c9d4678

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[galaxyproject/galaxy] c94b22: Escape section id and name when writing integrated...
by GitHub 07 Nov '16

07 Nov '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: c94b2205b27d1d527f159bcf13ba62ce937457f6 https://github.com/galaxyproject/galaxy/commit/c94b2205b27d1d527f159bcf13ba… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Escape section id and name when writing integrated_tool_panel.xml This should fix #3084. Commit: f6ca913809330922a3bc96bcf0f77d3f60e9bbe9 https://github.com/galaxyproject/galaxy/commit/f6ca913809330922a3bc96bcf0f7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Log invalid xml filename Commit: c5245219567562f67556548cbc0b8a9624ea0308 https://github.com/galaxyproject/galaxy/commit/c5245219567562f67556548cbc0b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Make catching XML parsing errors python2.6 compatible Commit: a274e635a6f7f2b169506ebf4a5a2363578bbfb1 https://github.com/galaxyproject/galaxy/commit/a274e635a6f7f2b169506ebf4a5a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-11-05 (Sat, 05 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #3128 from mvdbeek/backport_3122_3124 [16.01] Backport #3122 #3124 - fix unescaped & in integrated_tool_panel.xml Commit: 788dc1ebef5110fded19d23e4a2c48e06e3c5e63 https://github.com/galaxyproject/galaxy/commit/788dc1ebef5110fded19d23e4a2c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-11-07 (Mon, 07 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Conflicts: lib/galaxy/util/__init__.py Compare: https://github.com/galaxyproject/galaxy/compare/65338b3adb92...788dc1ebef51

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[galaxyproject/galaxy] 51c586: Fix tools placed outside of panel section
by GitHub 06 Nov '16

06 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 51c586c264f2acd912060297804d61c2539f2483 https://github.com/galaxyproject/galaxy/commit/51c586c264f2acd912060297804d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix tools placed outside of panel section Occasionally tools were being installed outside of the selected too panel section. In the log one would find contradicting messages such as ``` tool_shed.util.repository_util DEBUG 2016-11-04 11:06:17,854 Adding new row for repository 'sra_tools' in the tool_shed_repository table, status set to 'New'. galaxy.tools.toolbox.base DEBUG 2016-11-04 11:06:17,886 Appending to tool panel section: NCBI SRA Tools 172.17.0.1 - - [04/Nov/2016:11:06:15 +0000] "POST /admin_toolshed/prepare_for_install HTTP/1.1" 200 - "http://localhost/admin_toolshed/prepare_for_install?changeset_revisions=62e…" " Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/54.0.2840.71 Safari/537.36 nvalid tool_panel_section_key "ncbi_sra_tools" specified. Tools will be loaded outside of sections in the tool panel. ``` The intermittent POST is picked up by a different thread, that didn't have its toolbox updated with the new section. To circumvent this, we send the `create_panel_section` task to all threads. Commit: 4365b907293e366d4ad48396bb5c9dc00f134611 https://github.com/galaxyproject/galaxy/commit/4365b907293e366d4ad48396bb5c… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M test/unit/tools/test_toolbox.py Log Message: ----------- Fix toolbox unittests Commit: 202f96c73114fe9f05ed295505243ba17716b0e2 https://github.com/galaxyproject/galaxy/commit/202f96c73114fe9f05ed29550524… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-11-06 (Sun, 06 Nov 2016) Changed paths: M lib/galaxy/queue_worker.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #3125 from mvdbeek/fix_invalid_section_key Fix tools placed outside of panel section Compare: https://github.com/galaxyproject/galaxy/compare/58b7b6cf15c5...202f96c73114

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[galaxyproject/ansible-galaxy] ac29aa: Drop support for "Galaxy pip"
by GitHub 05 Nov '16

05 Nov '16

Branch: refs/tags/0.6.4 Home: https://github.com/galaxyproject/ansible-galaxy Commit: ac29aad5e27b546c51a4ce584b78056cb0a4631f https://github.com/galaxyproject/ansible-galaxy/commit/ac29aad5e27b546c51a4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-11-05 (Sat, 05 Nov 2016) Changed paths: M defaults/main.yml M tasks/dependencies.yml Log Message: ----------- Drop support for "Galaxy pip"

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[galaxyproject/galaxy] c94b22: Escape section id and name when writing integrated...
by GitHub 05 Nov '16

05 Nov '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: c94b2205b27d1d527f159bcf13ba62ce937457f6 https://github.com/galaxyproject/galaxy/commit/c94b2205b27d1d527f159bcf13ba… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py Log Message: ----------- Escape section id and name when writing integrated_tool_panel.xml This should fix #3084. Commit: f6ca913809330922a3bc96bcf0f77d3f60e9bbe9 https://github.com/galaxyproject/galaxy/commit/f6ca913809330922a3bc96bcf0f7… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Log invalid xml filename Commit: c5245219567562f67556548cbc0b8a9624ea0308 https://github.com/galaxyproject/galaxy/commit/c5245219567562f67556548cbc0b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py Log Message: ----------- Make catching XML parsing errors python2.6 compatible Commit: a274e635a6f7f2b169506ebf4a5a2363578bbfb1 https://github.com/galaxyproject/galaxy/commit/a274e635a6f7f2b169506ebf4a5a… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-11-05 (Sat, 05 Nov 2016) Changed paths: M lib/galaxy/tools/toolbox/integrated_panel.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #3128 from mvdbeek/backport_3122_3124 [16.01] Backport #3122 #3124 - fix unescaped & in integrated_tool_panel.xml Compare: https://github.com/galaxyproject/galaxy/compare/f7c3e25e5db1...a274e635a6f7

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[galaxyproject/galaxy] 2956f9: BLAST database *.loc.sample files
by GitHub 05 Nov '16

05 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2956f94aa06f62fc0adde93d5aacc69e693a62d8 https://github.com/galaxyproject/galaxy/commit/2956f94aa06f62fc0adde93d5aac… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: A tool-data/blastdb.loc.sample A tool-data/blastdb_d.loc.sample A tool-data/blastdb_p.loc.sample Log Message: ----------- BLAST database *.loc.sample files Commit: 2e36fdb0bd0fff246eeff6322542c31150804eb2 https://github.com/galaxyproject/galaxy/commit/2e36fdb0bd0fff246eeff6322542… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M config/tool_data_table_conf.xml.sample Log Message: ----------- Include all three BLAST .loc files in data table conf Commit: f060795335e564f79ed3f28b5390db4ac8e7d735 https://github.com/galaxyproject/galaxy/commit/f060795335e564f79ed3f28b5390… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: A lib/galaxy/datatypes/blast.py Log Message: ----------- BLAST datatypes as of standalone blast_datatypes v0.0.21 Copied from separate BLAST+ Galaxy repository, https://github.com/peterjc/galaxy_blast/blob/master/datatypes/blast_datatyp… Currently available from the Galaxy Tool Shed, http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes Primary contributors to the BLAST datatypes for Galaxy: * Peter Cock (The James Hutton Institute, UK) * Edward Kirton * Nicola Soranzo * Bjoern Gruening This work and the associated BLAST+ wrappers can be cited as: NCBI BLAST+ integrated into Galaxy. P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo *GigaScience* 2015, 4:39 DOI: http://dx.doi.org/10.1186/s13742-015-0080-7 Commit: a53e9fa9dbd635ee6359fb6b68371a3d0e5159c6 https://github.com/galaxyproject/galaxy/commit/a53e9fa9dbd635ee6359fb6b6837… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/datatypes/blast.py Log Message: ----------- Remove unused imports Commit: bdd046a2e86c935e1c932421a25e7ed480aacdf8 https://github.com/galaxyproject/galaxy/commit/bdd046a2e86c935e1c932421a25e… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/datatypes/blast.py Log Message: ----------- Missing import required for use as doctest Commit: 193651c88d325a5c1710def37386524e956ac147 https://github.com/galaxyproject/galaxy/commit/193651c88d325a5c1710def37386… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml Log Message: ----------- Sample blastxml file for sniff doctest Commit: ea717dd0013c9ef69d5ea0cd8edb72f44546e5d8 https://github.com/galaxyproject/galaxy/commit/ea717dd0013c9ef69d5ea0cd8edb… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add BLAST datatypes to datatypes_conf.xml.sample Commit: 8b73de6f50572ea2fb815fa75460f5850b877f12 https://github.com/galaxyproject/galaxy/commit/8b73de6f50572ea2fb815fa75460… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/datatypes/blast.py Log Message: ----------- Adjust import order as per Galaxy tox flake8 checks Commit: f9eff95613cdf27f5300ea393418f017da8e8012 https://github.com/galaxyproject/galaxy/commit/f9eff95613cdf27f5300ea393418… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/datatypes/blast.py Log Message: ----------- More accurate module docstring Commit: 0152254a6f455bae538c96f3ce85baee1ae1c9f8 https://github.com/galaxyproject/galaxy/commit/0152254a6f455bae538c96f3ce85… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- megablast_xml_parser_test1.blastxml should now sniff as blastxml Commit: 48664fa2fe7f43ee667e9fa4ece51852632570e7 https://github.com/galaxyproject/galaxy/commit/48664fa2fe7f43ee667e9fa4ece5… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Ensure all BLAST datatype contributors in CONTRIBUTORS.md Commit: ce5ceeb29b134a84cf577f0bf2244011ac0cdfe4 https://github.com/galaxyproject/galaxy/commit/ce5ceeb29b134a84cf577f0bf224… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M CONTRIBUTORS.md Log Message: ----------- Give my work email address as well. My Galaxy work to date has been while employed at The James Hutton Institute (UK). Commit: 17783cec36f4bf0d3b79137842dad52a64f80da2 https://github.com/galaxyproject/galaxy/commit/17783cec36f4bf0d3b79137842da… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py Log Message: ----------- Tweak testing installing BLAST datatypes from Tool Shed This is a short term pragmatic solution for the planned return of the BLAST datatypes to the main Galaxy distribution. Long term an additional test using an alternative Tool Shed defined datatype may be needed. Commit: 7fe47735209e43501e6116453a2fd961e5934429 https://github.com/galaxyproject/galaxy/commit/7fe47735209e43501e6116453a2f… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/datatypes/blast.py Log Message: ----------- Clearer error message if BLAST XML header too long Commit: 4159770ed9d173a2a3b45f7615aa764be9e99188 https://github.com/galaxyproject/galaxy/commit/4159770ed9d173a2a3b45f7615aa… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/datatypes/blast.py Log Message: ----------- Explicitly label blast.py as MIT licensed. Edward Kirton's contributions were made under the MIT license while this code was developed outside of the main Galaxy Project and distributed via the Galaxy Tool Shed). We have not been able to contact him to authorise re-licensing under the main Galaxy Project's license instead. Commit: b5ba9605e56b8a8c8a827c6bd83208314ab8ccf0 https://github.com/galaxyproject/galaxy/commit/b5ba9605e56b8a8c8a827c6bd832… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/datatypes/blast.py Log Message: ----------- Mark BLAST XML with EDAM ontology terms. As per Herve Menager, EDAM format should be 3331 and data 0857 (sequence search results). Commit: 58b7b6cf15c57a9a42340baeb2131e42cc76d02d https://github.com/galaxyproject/galaxy/commit/58b7b6cf15c57a9a42340baeb213… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-11-05 (Sat, 05 Nov 2016) Changed paths: M CONTRIBUTORS.md M config/datatypes_conf.xml.sample M config/tool_data_table_conf.xml.sample A lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/tblastn_four_human_vs_rhodopsin.xml M test/shed_functional/functional/test_1140_simple_repository_dependency_multiple_owners.py A tool-data/blastdb.loc.sample A tool-data/blastdb_d.loc.sample A tool-data/blastdb_p.loc.sample Log Message: ----------- Merge pull request #2696 from peterjc/blast_datatypes Returning Blast datatypes to Galaxy core (work-in-progress) Compare: https://github.com/galaxyproject/galaxy/compare/b1892b7e30f9...58b7b6cf15c5

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[galaxyproject/galaxy] 66dec1: Add download_to_file function to galaxy.util
by GitHub 04 Nov '16

04 Nov '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 66dec1d580b426ad955db03608ec7da7eb5c5018 https://github.com/galaxyproject/galaxy/commit/66dec1d580b426ad955db03608ec… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-26 (Wed, 26 Oct 2016) Changed paths: M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M test/base/driver_util.py Log Message: ----------- Add download_to_file function to galaxy.util Use it in 2 places: - test/base/driver_util.py (thus adding timeout and chunking) - lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py where the total download timeout is substituted with the usual urllib timeout Commit: b1892b7e30f9e2a9be94bd8ee064c0f548525bfe https://github.com/galaxyproject/galaxy/commit/b1892b7e30f9e2a9be94bd8ee064… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-11-04 (Fri, 04 Nov 2016) Changed paths: M lib/galaxy/util/__init__.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M test/base/driver_util.py Log Message: ----------- Merge pull request #3100 from nsoranzo/followup_on_3013 Add download_to_file function to galaxy.util Compare: https://github.com/galaxyproject/galaxy/compare/37399049552d...b1892b7e30f9

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