- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 4f1383: Forgot how XML comments work
by GitHub 02 Feb '16

02 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4f13837697316045c5b77c57fc34714532b0ecb1 https://github.com/galaxyproject/usegalaxy-playbook/commit/4f13837697316045… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/datatypes_conf.xml.j2 Log Message: ----------- Forgot how XML comments work

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[galaxyproject/galaxy] afc5f2: Fix: Use dependency resolvers if any config exists...
by GitHub 02 Feb '16

02 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: afc5f2a45399c474d86f1530a62afe280a0eb3be https://github.com/galaxyproject/galaxy/commit/afc5f2a45399c474d86f1530a62a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Fix: Use dependency resolvers if any config exists. This way resolvers like the Module resolver work even if tool_dependency_dir is not set. Commit: 916ddb575f40c445a47cf91a58aad00bf9360ae8 https://github.com/galaxyproject/galaxy/commit/916ddb575f40c445a47cf91a58aa… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M lib/galaxy/config.py Log Message: ----------- Merge pull request #1648 from jmchilton/dependencies_conf [16.01] Fix use_tool_dependencies for non-default dependency_resolver_conf files. Compare: https://github.com/galaxyproject/galaxy/compare/e4e48941a617...916ddb575f40

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[galaxyproject/galaxy] 50ea46: Change python print() format to be backward compat...
by GitHub 02 Feb '16

02 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 50ea4694af82ac33eaac1ddc9ca8aee1e71e1f00 https://github.com/galaxyproject/galaxy/commit/50ea4694af82ac33eaac1ddc9ca8… Author: Mark Einon <mark.einon(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M scripts/binary_compatibility.py Log Message: ----------- Change python print() format to be backward compatible with older versions In python versions prior to 3.1, the print("{}", .format(x)) form throws an error, use the more compatible print("{0}", .format(x)) form instead. Commit: e4e48941a6174a148cde06ef2218ef6480568716 https://github.com/galaxyproject/galaxy/commit/e4e48941a6174a148cde06ef2218… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-02 (Tue, 02 Feb 2016) Changed paths: M scripts/binary_compatibility.py Log Message: ----------- Merge pull request #1651 from jmchilton/backport_print_fix [16.01] Backport print fix. Compare: https://github.com/galaxyproject/galaxy/compare/9170865dfbe0...e4e48941a617

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[galaxyproject/galaxy] e9d7d6: Export info required to re-run an exported workflo...
by GitHub 01 Feb '16

01 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e9d7d6f1be49aedd44b1ada0bf92e5ee7a14a638 https://github.com/galaxyproject/galaxy/commit/e9d7d6f1be49aedd44b1ada0bf92… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Export info required to re-run an exported workflow. Commit: 3e267124ad5454ac69c91aef59064d81b7e74140 https://github.com/galaxyproject/galaxy/commit/3e267124ad5454ac69c91aef5906… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #1636 from mvdbeek/add_repo_info_to_wf_export Export toolshed repository information for workflow portability Compare: https://github.com/galaxyproject/galaxy/compare/f3b7dd56f766...3e267124ad54

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[galaxyproject/galaxy] 062711: Lint optional handling on conditional test paramet...
by GitHub 01 Feb '16

01 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0627116e112e2a250e5d3db9867224bdfc1fbed0 https://github.com/galaxyproject/galaxy/commit/0627116e112e2a250e5d3db98672… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/tools/linters/inputs.py Log Message: ----------- Lint optional handling on conditional test parameters. Commit: f3b7dd56f766fdae9cdb8bd552fd29866d3ad81a https://github.com/galaxyproject/galaxy/commit/f3b7dd56f766fdae9cdb8bd552fd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/tools/linters/inputs.py Log Message: ----------- Merge pull request #1639 from jmchilton/lint_test_params Lint optional handling on conditional test parameters. Compare: https://github.com/galaxyproject/galaxy/compare/c8d05e2fb704...f3b7dd56f766

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[galaxyproject/galaxy] a10a4a: attempt to fix suite outside of tool panel.
by GitHub 01 Feb '16

01 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a10a4a1b8478a3a89830fb9d61ebe721a33c13cd https://github.com/galaxyproject/galaxy/commit/a10a4a1b8478a3a89830fb9d61eb… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- attempt to fix suite outside of tool panel. Commit: cda1ee8be65db00d659809a4c383e7c614ca31dc https://github.com/galaxyproject/galaxy/commit/cda1ee8be65db00d659809a4c383… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- also save integrated tool panel Commit: c8d05e2fb7049a1938c403569ee01b0377d86733 https://github.com/galaxyproject/galaxy/commit/c8d05e2fb7049a1938c403569ee0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- Merge pull request #1601 from mvdbeek/fix_outside_tool_panel Fix installation of repository suites outside of tool panel section Compare: https://github.com/galaxyproject/galaxy/compare/e0d0bcd4e4cb...c8d05e2fb704

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[galaxyproject/galaxy] 7ebc3e: Remove unnecessary variable and assignment of job ...
by GitHub 01 Feb '16

01 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7ebc3eb0601f6a3f3509db586f28e65a85605740 https://github.com/galaxyproject/galaxy/commit/7ebc3eb0601f6a3f3509db586f28… Author: Mark Einon <mark.einon(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Remove unnecessary variable and assignment of job command Commit: e0d0bcd4e4cb00f84a998e5a29b98ba05982defe https://github.com/galaxyproject/galaxy/commit/e0d0bcd4e4cb00f84a998e5a29b9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #1616 from einon/job_code_tweaks Remove unnecessary variable and assignment of job command Compare: https://github.com/galaxyproject/galaxy/compare/41a3a1676245...e0d0bcd4e4cb

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[galaxyproject/galaxy] f05c95: Remove unvalidated values
by GitHub 01 Feb '16

01 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f05c9518be52ecaa9cb13885aeec3f57054e976a https://github.com/galaxyproject/galaxy/commit/f05c9518be52ecaa9cb13885aeec… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py Log Message: ----------- Remove unvalidated values Commit: 89ba002475695d09542dbe85886c6d69e6f54307 https://github.com/galaxyproject/galaxy/commit/89ba002475695d09542dbe85886c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Remove late validation handling Commit: 49026134443e49c81d5b071817bb7a018357f945 https://github.com/galaxyproject/galaxy/commit/49026134443e49c81d5b071817bb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/util/dbkeys.py Log Message: ----------- Use bunch instead of trans Commit: 12f2571d975ca89548259e1322882e87dbb5b17e https://github.com/galaxyproject/galaxy/commit/12f2571d975ca89548259e132288… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Use self.app in tools Commit: 52b6881f017e38ea5969c5adb70b5c83d6753cd3 https://github.com/galaxyproject/galaxy/commit/52b6881f017e38ea5969c5adb70b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Revise history handling Commit: 34f46c98c7bdace6af9126b44534fd41c9121002 https://github.com/galaxyproject/galaxy/commit/34f46c98c7bdace6af9126b44534… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Remove comments Commit: 7eb6cc7b8247689d1bfef12c99a9514610bbd0bb https://github.com/galaxyproject/galaxy/commit/7eb6cc7b8247689d1bfef12c99a9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Revise validate signature Commit: a272bff066516019ca74ee0012b2ae6fe02c21bc https://github.com/galaxyproject/galaxy/commit/a272bff066516019ca74ee0012b2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Use consistently other_values Commit: 550102915866ab4448a3e8a070437c80772320da https://github.com/galaxyproject/galaxy/commit/550102915866ab4448a3e8a07043… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Revise validate signature Commit: 4b6172299e2adc4edd117c505e5c7ddcde38c24b https://github.com/galaxyproject/galaxy/commit/4b6172299e2adc4edd117c505e5c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/work/context.py Log Message: ----------- Use workcontext Commit: eaf02029d43620db309e2860d4502e0f830bc2a9 https://github.com/galaxyproject/galaxy/commit/eaf02029d43620db309e2860d450… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix remaining self.app, use workcontext app Commit: 5a72480719055ac4a6d04ff690f69d5a118b5c81 https://github.com/galaxyproject/galaxy/commit/5a72480719055ac4a6d04ff690f6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix dataset selection Commit: 7cc505019d2b2af938b61efe0e00bd25a13af91b https://github.com/galaxyproject/galaxy/commit/7cc505019d2b2af938b61efe0e00… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/util/dbkeys.py Log Message: ----------- Use sa_session of workcontext Commit: b56574115fa9ae32f2d4703f0b257991ad2f4c26 https://github.com/galaxyproject/galaxy/commit/b56574115fa9ae32f2d4703f0b25… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/util/dbkeys.py Log Message: ----------- Fix trans usage Commit: 93dbf742b36b614bacbb7a806431532567203b70 https://github.com/galaxyproject/galaxy/commit/93dbf742b36b614bacbb7a806431… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/evaluation.py Log Message: ----------- Reinsert last validation Commit: 7c69227c8cde400df37f5e9390fdd88e51f64f2a https://github.com/galaxyproject/galaxy/commit/7c69227c8cde400df37f5e9390fd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix db_builds Commit: 269ce36d3f5212b2d98315a67b25cc6db5a3429c https://github.com/galaxyproject/galaxy/commit/269ce36d3f5212b2d98315a67b25… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/workflow/modules.py Log Message: ----------- Fix check params Commit: 3acdee5143586d0224f896d2bfc5c085e3409349 https://github.com/galaxyproject/galaxy/commit/3acdee5143586d0224f896d2bfc5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py Log Message: ----------- Show validation error for workflow step preparation Commit: b38479c4a49efcf2c56e400b56d1da4f5eb4a02d https://github.com/galaxyproject/galaxy/commit/b38479c4a49efcf2c56e400b56d1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/work/context.py M lib/galaxy/workflow/extract.py Log Message: ----------- Remove unvalidated value handling in workflow extraction Commit: 6939c99f1bb06532e5c4cb4c2a4ef936075b4569 https://github.com/galaxyproject/galaxy/commit/6939c99f1bb06532e5c4cb4c2a4e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/extract.py Log Message: ----------- Remove more unvalidated value hacks Commit: 539ddd4d90bda5400c3006ab4c574bebd353d280 https://github.com/galaxyproject/galaxy/commit/539ddd4d90bda5400c3006ab4c57… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/evaluation.py Log Message: ----------- Remove optional parameter from request context initialization Commit: cc2cfe8d6adb264df41e18b4c33781712bb12cbb https://github.com/galaxyproject/galaxy/commit/cc2cfe8d6adb264df41e18b4c337… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Use request context instead of trans in to_json Commit: a7117574268ab907fb27483a485d5d9e501b7e5e https://github.com/galaxyproject/galaxy/commit/a7117574268ab907fb27483a485d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/validation.py Log Message: ----------- Remove unused error handler, error is handled consistently through full validation Commit: 0ca9c7027b5ee3cd8ba433a4e8bc3e5ad57a5d7f https://github.com/galaxyproject/galaxy/commit/0ca9c7027b5ee3cd8ba433a4e8bc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/workflow/extract.py Log Message: ----------- Use request context in handle inputs Commit: 193c5293d9552d53a2358254fa2a25b236a31511 https://github.com/galaxyproject/galaxy/commit/193c5293d9552d53a2358254fa2a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M tools/data_source/upload.xml Log Message: ----------- Remove invalid validator from upload.xml Commit: 0fc8726414bfedcc234d7c4738ebff3a1b37e3d4 https://github.com/galaxyproject/galaxy/commit/0fc8726414bfedcc234d7c4738eb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Fix prefixed_label concatenation Commit: 0521644bb37336f31577c8bd73ac1fef6c936016 https://github.com/galaxyproject/galaxy/commit/0521644bb37336f31577c8bd73ac… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix select validator Commit: 8bd4cabdde922f23c06c64f95f50ea4d81caa940 https://github.com/galaxyproject/galaxy/commit/8bd4cabdde922f23c06c64f95f50… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/workflow/modules.py Log Message: ----------- Use request context for parameter helper Commit: b3f3f81a7d0d221e4a698dbd9a586a92cd6662af https://github.com/galaxyproject/galaxy/commit/b3f3f81a7d0d221e4a698dbd9a58… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Remove unused to_html helper Commit: 8b6e4c9f2584d5768926836ee08607aeae0bb501 https://github.com/galaxyproject/galaxy/commit/8b6e4c9f2584d5768926836ee086… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/grouping.py Log Message: ----------- Remove unused filter value helper Commit: 27df773c5a8823fff2d0dd68a8bd162147336bed https://github.com/galaxyproject/galaxy/commit/27df773c5a8823fff2d0dd68a8bd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Always display discarded datasets on rerun Commit: f8e3fa51f4b2fbaab54becd869ede40e43c5067a https://github.com/galaxyproject/galaxy/commit/f8e3fa51f4b2fbaab54becd869ed… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_select_parameters.py M test/unit/tools_support.py Log Message: ----------- Apply suggested fixes, fix test cases Commit: 72370b251723eac746bd1720a85df539cd96e78a https://github.com/galaxyproject/galaxy/commit/72370b251723eac746bd1720a85d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Fix paused workflow step resubmission Commit: 41a3a1676245284fa01e9697bd91710244ddde83 https://github.com/galaxyproject/galaxy/commit/41a3a1676245284fa01e9697bd91… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dynamic_options.py M lib/galaxy/tools/parameters/grouping.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/work/context.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/modules.py M templates/webapps/galaxy/workflow/editor_tool_form.mako M templates/webapps/galaxy/workflow/run.mako M test/unit/tools/test_data_parameters.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_execution.py M test/unit/tools/test_select_parameters.py M test/unit/tools_support.py M tools/data_source/upload.xml Log Message: ----------- Merge pull request #1572 from guerler/fix_unvalidated_008 Fix parameter validation Compare: https://github.com/galaxyproject/galaxy/compare/dacb91907af7...41a3a1676245

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[galaxyproject/galaxy] 30cceb: remove forgotten util.params that fails when POSTi...
by GitHub 01 Feb '16

01 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 30ccebfb0c8ef0809bbd3f1d2d64be5ac23bb3a2 https://github.com/galaxyproject/galaxy/commit/30ccebfb0c8ef0809bbd3f1d2d64… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- remove forgotten util.params that fails when POSTing a payload{} dict (because it cannot sanitize dict in dict) Commit: 9170865dfbe0f8588ec47449e683236e5ba92a39 https://github.com/galaxyproject/galaxy/commit/9170865dfbe0f8588ec47449e683… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Merge pull request #1634 from martenson/remove-utilparams [16.01] libraries: remove forgotten util.params that fails when POSTing a payload {} Compare: https://github.com/galaxyproject/galaxy/compare/ee4f58ce7d6a...9170865dfbe0

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[galaxyproject/galaxy] 618189: Fix default option for repeats
by GitHub 01 Feb '16

01 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 61818948a163602b3c135937d053fe42c46bb4d2 https://github.com/galaxyproject/galaxy/commit/61818948a163602b3c135937d053… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M static/maps/mvc/form/form-section.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/form/form-section.js Log Message: ----------- Fix default option for repeats Commit: ee4f58ce7d6a81477e5e4fc3e544e5da909f1198 https://github.com/galaxyproject/galaxy/commit/ee4f58ce7d6a81477e5e4fc3e544… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M static/maps/mvc/form/form-section.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/form/form-section.js Log Message: ----------- Merge pull request #1635 from guerler/fix_repeat_default_001 [16.01] Fix default option for repeats Compare: https://github.com/galaxyproject/galaxy/compare/ade18b3cd23c...ee4f58ce7d6a

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[galaxyproject/galaxy] 2eb686: datalibs: introduce folder management; fix various...
by GitHub 01 Feb '16

01 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2eb6868955ccf13c71802fd9a42db3bb3b859d05 https://github.com/galaxyproject/galaxy/commit/2eb6868955ccf13c71802fd9a42d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/style/less/library.less M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- datalibs: introduce folder management; fix various glitches; refactor Commit: 88ed6e93e84abe155292fc0ffbf21efd4043a9c9 https://github.com/galaxyproject/galaxy/commit/88ed6e93e84abe155292fc0ffbf2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/folder_contents.py Log Message: ----------- extend API to show folder.description and dataset.message Commit: 11c5259f46b7d1774ecbee89e2459efa32b30099 https://github.com/galaxyproject/galaxy/commit/11c5259f46b7d1774ecbee89e245… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folderrow-view.js M static/maps/mvc/library/library-folderrow-view.js.map M static/scripts/mvc/library/library-folderrow-view.js Log Message: ----------- fix librarydataset model detection; always show dataset.message and folder.description Commit: 17dcff96011f740d7e60ef09e451844ed39ea398 https://github.com/galaxyproject/galaxy/commit/17dcff96011f740d7e60ef09e451… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- datalib: show nice size after undeleting dataset Commit: cb1010682d5117737c62303aecfce0193088c8db https://github.com/galaxyproject/galaxy/commit/cb1010682d5117737c62303aecfc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/folder_contents.py Log Message: ----------- remove abundant dict update Commit: dacb91907af7a885518d79f311e9e3115d3e87e5 https://github.com/galaxyproject/galaxy/commit/dacb91907af7a885518d79f311e9… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folderlist-view.js M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/scripts/mvc/library/library-libraryrow-view.js M client/galaxy/style/less/library.less M lib/galaxy/webapps/galaxy/api/folder_contents.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M static/maps/mvc/library/library-folderlist-view.js.map M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/maps/mvc/library/library-libraryrow-view.js.map M static/scripts/mvc/library/library-folderlist-view.js M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js M static/scripts/mvc/library/library-libraryrow-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Merge pull request #1562 from martenson/datalibs_better_foldermanagement datalibs: introduce folder management; fix various glitches; refactor Compare: https://github.com/galaxyproject/galaxy/compare/962fdc0eba0c...dacb91907af7

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[galaxyproject/usegalaxy-playbook] 376328: Update datatypes_conf.xml on Test
by GitHub 01 Feb '16

01 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 37632872d6b7ed9b805fa08fbf0dc0639daaccb3 https://github.com/galaxyproject/usegalaxy-playbook/commit/37632872d6b7ed9b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/datatypes_conf.xml.j2 Log Message: ----------- Update datatypes_conf.xml on Test Commit: 37e7fcf578fc182e1fee943be0d244c0c53678b1 https://github.com/galaxyproject/usegalaxy-playbook/commit/37e7fcf578fc182e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M stage/files/interactive_environments/plugins/.ansible_ie_role_current_version M stage/files/interactive_environments/proxy/.ansible_ie_role_current_version Log Message: ----------- Mutable configs (+ ie clone version I forgot to commit) on Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/d8c80fd42dd5...…

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[galaxyproject/galaxy] 981f90: Attempt to fix transiently failing test due to obj...
by GitHub 01 Feb '16

01 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 981f904c3f8a501ffabaf7b83538151070bd8a21 https://github.com/galaxyproject/galaxy/commit/981f904c3f8a501ffabaf7b83538… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/util/__init__.py Log Message: ----------- Attempt to fix transiently failing test due to object store makedirs call. Failing test - https://jenkins.galaxyproject.org/job/docker-api/2421/testReport/junit/api.…. If you look at the actual source code for os.makedirs - it does inconsistently handle errno.EEXIST - this is probably a better approach than raw os.makedirs for most cases. xref #1617 Commit: ade18b3cd23c54c347d38585736d32da5fccc4dd https://github.com/galaxyproject/galaxy/commit/ade18b3cd23c54c347d38585736d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M lib/galaxy/objectstore/__init__.py M lib/galaxy/util/__init__.py Log Message: ----------- Merge pull request #1623 from jmchilton/makedirs [16.01] Attempt to fix transiently failing test due to objectstore makedirs … Compare: https://github.com/galaxyproject/galaxy/compare/44336b289bd5...ade18b3cd23c

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[galaxyproject/galaxy] 399e0c: Disable individual file metadata changes in upload
by GitHub 01 Feb '16

01 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 399e0ced6dd51733ee45c03ac558856e952706d4 https://github.com/galaxyproject/galaxy/commit/399e0ced6dd51733ee45c03ac558… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/default/default-row.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/upload/default/default-row.js Log Message: ----------- Disable individual file metadata changes in upload Commit: 962fdc0eba0c3436e034df3068b61e3eaa811c8f https://github.com/galaxyproject/galaxy/commit/962fdc0eba0c3436e034df3068b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-01 (Mon, 01 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js M static/maps/mvc/upload/default/default-row.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/upload/default/default-row.js Log Message: ----------- Merge pull request #1625 from guerler/fix_upload_000 Disable individual file metadata changes in upload Compare: https://github.com/galaxyproject/galaxy/compare/3deb005e99c6...962fdc0eba0c

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[galaxyproject/galaxy] bf5bf7: Tour cleanup, remove a few globals.
by GitHub 29 Jan '16

29 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf5bf73e827337f3481fcbd8c6e1a34ffc0058ea https://github.com/galaxyproject/galaxy/commit/bf5bf73e827337f3481fcbd8c6e1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M static/maps/mvc/tours.js.map M static/maps/onload.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js M static/scripts/onload.js Log Message: ----------- Tour cleanup, remove a few globals. Commit: f8e6a55ab7a9048cdf1dbb87f7393e4535d43e03 https://github.com/galaxyproject/galaxy/commit/f8e6a55ab7a9048cdf1dbb87f739… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M client/galaxy/scripts/onload.js M static/maps/onload.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/onload.js Log Message: ----------- Swap to standard url parsing function from our js utils. Commit: 3deb005e99c609a9c5cee60b301027c4f6ec0df4 https://github.com/galaxyproject/galaxy/commit/3deb005e99c609a9c5cee60b3010… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/scripts/onload.js M static/maps/mvc/tours.js.map M static/maps/onload.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/mvc/tours.js M static/scripts/onload.js Log Message: ----------- Merge pull request #1621 from dannon/tour_cleanup Tour cleanup, remove a few globals. Compare: https://github.com/galaxyproject/galaxy/compare/76624949bc31...3deb005e99c6

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[galaxyproject/galaxy] 4ae49f: Fix module/step border style in workflow canvas
by GitHub 29 Jan '16

29 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 4ae49fbfec952a2087a9cf3f9b9940f86fd05220 https://github.com/galaxyproject/galaxy/commit/4ae49fbfec952a2087a9cf3f9b99… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css Log Message: ----------- Fix module/step border style in workflow canvas Commit: 44336b289bd5ba7d9911bf1c1fcc0a604fda7358 https://github.com/galaxyproject/galaxy/commit/44336b289bd5ba7d9911bf1c1fcc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M client/galaxy/style/less/base.less M static/style/blue/base.css Log Message: ----------- Merge pull request #1620 from guerler/fix_module_border_000 [16.01] Fix module/step border style in workflow canvas Compare: https://github.com/galaxyproject/galaxy/compare/81535c5778b7...44336b289bd5

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[galaxyproject/galaxy] 28c4b4: Various improvements to the heartbeat:
by GitHub 29 Jan '16

29 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 28c4b49e8de240bde1fe4acefac32cbcc516afc4 https://github.com/galaxyproject/galaxy/commit/28c4b49e8de240bde1fe4acefac3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/util/heartbeat.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Various improvements to the heartbeat: - Dump on `SIGUSR1` - Configurable dump period (including "no periodic dump, signal only") - Default log filename now includes server_name so logs do not clobber eachother - Configurable/templateable log filename - Catch more sleeping threads - Use write() instead of print Commit: 148b4099bff3ed54f97a0c20c8b4f46e64969989 https://github.com/galaxyproject/galaxy/commit/148b4099bff3ed54f97a0c20c8b4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/app.py Log Message: ----------- Move heartbeat import to the global imports, do not attempt to register a None signal handler Commit: 76624949bc31555d7142b5e7476d3e60e5d08fa7 https://github.com/galaxyproject/galaxy/commit/76624949bc31555d7142b5e7476d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/util/heartbeat.py M lib/galaxy/workflow/scheduling_manager.py Log Message: ----------- Merge pull request #1614 from natefoo/heartbeat-improvements Various improvements to the heartbeat Compare: https://github.com/galaxyproject/galaxy/compare/670a5f2c85fe...76624949bc31

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[galaxyproject/galaxy] cb09c3: Fix line wrapping for peek of tabular files.
by GitHub 29 Jan '16

29 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: cb09c35a07e3b9f8ca7e4eb5e8d37ffacdee6253 https://github.com/galaxyproject/galaxy/commit/cb09c35a07e3b9f8ca7e4eb5e8d3… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-01-13 (Wed, 13 Jan 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Fix line wrapping for peek of tabular files. Commit: 81535c5778b70001bfeb3da5690eba6426ea4638 https://github.com/galaxyproject/galaxy/commit/81535c5778b70001bfeb3da5690e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-29 (Fri, 29 Jan 2016) Changed paths: M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/tabular.py Log Message: ----------- Merge pull request #1500 from blankenberg/peek-fix [16.01] Fix line wrapping for peek of tabular files. Compare: https://github.com/galaxyproject/galaxy/compare/685fd1560e98...81535c5778b7

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[galaxyproject/usegalaxy-playbook] d8c80f: Update Test and Main
by GitHub 28 Jan '16

28 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d8c80fd42dd5a3e9c1cc8c5c7681689b0a7386d8 https://github.com/galaxyproject/usegalaxy-playbook/commit/d8c80fd42dd5a3e9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M production/group_vars/all.yml M stage/group_vars/all.yml Log Message: ----------- Update Test and Main

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[galaxyproject/galaxy] 390c1f: Always install a specific version of Galaxy pip in...
by GitHub 28 Jan '16

28 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 390c1fc275ba7128f22f533b0b512b0bc517e521 https://github.com/galaxyproject/galaxy/commit/390c1fc275ba7128f22f533b0b51… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Always install a specific version of Galaxy pip in common_startup.sh. Commit: 46471d61e4349bba2d0c702de18f91a5b201bb66 https://github.com/galaxyproject/galaxy/commit/46471d61e4349bba2d0c702de18f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- pip < 1.6 cannot parse requirement specifiers to the `install` command that contain a `+` in the version. For these older versions, directly install the wheel or install from the sdist. Technically 1.4 and later can install wheels, but in testing, only 1.5+ was able to install them properly with their scripts. The new heredoc execute and redirect syntax is Bourne-compatible. pip --pre is no longer necessary since the Galaxy pip version is no longer a development version of pip. Commit: 60062b020dc2b753e5b8f034272e0b982b8c2f6f https://github.com/galaxyproject/galaxy/commit/60062b020dc2b753e5b8f034272e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- pip 1.6 -> 6.0, thanks @nsoranzo Commit: 685fd1560e98e6d885d6cf627b691d2228807974 https://github.com/galaxyproject/galaxy/commit/685fd1560e98e6d885d6cf627b69… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #1595 from natefoo/fix-pip-wheel-version [16.01] Always install a specific version of Galaxy pip in common_startup.sh. Compare: https://github.com/galaxyproject/galaxy/compare/27685377f629...685fd1560e98

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[galaxyproject/ansible-galaxy]
by GitHub 28 Jan '16

28 Jan '16

Branch: refs/tags/0.6.2 Home: https://github.com/galaxyproject/ansible-galaxy

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[galaxyproject/ansible-galaxy] 3f8e11: Fix pip at 8.0.0
by GitHub 28 Jan '16

28 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 3f8e1140b73629dd4cbf1c326533493e0bc80fb5 https://github.com/galaxyproject/ansible-galaxy/commit/3f8e1140b73629dd4cbf… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-01-24 (Sun, 24 Jan 2016) Changed paths: M tasks/dependencies.yml Log Message: ----------- Fix pip at 8.0.0 Commit: 001cf5a411cea597229c7e9bae10aff86c4e7c55 https://github.com/galaxyproject/ansible-galaxy/commit/001cf5a411cea597229c… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-01-25 (Mon, 25 Jan 2016) Changed paths: M defaults/main.yml M tasks/dependencies.yml Log Message: ----------- Make pip version confogurable. Commit: 9adce55fd265229089ae2709892ea7d2d8cff148 https://github.com/galaxyproject/ansible-galaxy/commit/9adce55fd265229089ae… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M defaults/main.yml M tasks/dependencies.yml Log Message: ----------- pip at version 8.0.2, no --pre. Commit: 6209af56b96b4b326b63c8c6a8a8282f81094ce5 https://github.com/galaxyproject/ansible-galaxy/commit/6209af56b96b4b326b63… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M defaults/main.yml M tasks/dependencies.yml Log Message: ----------- Merge pull request #9 from ARTbio/fix_pip_version Fix pip at 8.0.0 Compare: https://github.com/galaxyproject/ansible-galaxy/compare/2f4cbc0969fc...6209…

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[galaxyproject/galaxy] 33ba1f: Link from the 16.01 announcement to the Admin whee...
by GitHub 28 Jan '16

28 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 33ba1face9e1f1bf025f37dc4e508143972845dc https://github.com/galaxyproject/galaxy/commit/33ba1face9e1f1bf025f37dc4e50… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/releases/16.01_announce.rst Log Message: ----------- Link from the 16.01 announcement to the Admin wheels documentation, document the process of adding new wheels. Commit: 27685377f629c536e56189e795bc91bb8caf0736 https://github.com/galaxyproject/galaxy/commit/27685377f629c536e56189e795bc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/releases/16.01_announce.rst Log Message: ----------- Merge pull request #1612 from natefoo/admin-docs [16.01] Additional documentation regarding wheels Commit: 670a5f2c85fe153b79db1a37eb39f39ffa20b761 https://github.com/galaxyproject/galaxy/commit/670a5f2c85fe153b79db1a37eb39… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/releases/16.01_announce.rst Log Message: ----------- Merge branch 'release_16.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/9264d90ea471...670a5f2c85fe

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[galaxyproject/galaxy] a077b0: Remove recovery hack for REALLY old jobs.
by GitHub 28 Jan '16

28 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a077b04809ff4ce44a534bbf61151a904accd6a0 https://github.com/galaxyproject/galaxy/commit/a077b04809ff4ce44a534bbf6115… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-25 (Mon, 25 Jan 2016) Changed paths: M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Remove recovery hack for REALLY old jobs. No more upgrading Galaxy straight from 2012 to 2016. Commit: 9264d90ea471214b09666b82781acd49d84f19ec https://github.com/galaxyproject/galaxy/commit/9264d90ea471214b09666b82781a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Merge pull request #1574 from jmchilton/remove_old_job_hack Remove recovery hack for REALLY old jobs. Compare: https://github.com/galaxyproject/galaxy/compare/db221325dac1...9264d90ea471

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[galaxyproject/galaxy] 33ba1f: Link from the 16.01 announcement to the Admin whee...
by GitHub 28 Jan '16

28 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 33ba1face9e1f1bf025f37dc4e508143972845dc https://github.com/galaxyproject/galaxy/commit/33ba1face9e1f1bf025f37dc4e50… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/releases/16.01_announce.rst Log Message: ----------- Link from the 16.01 announcement to the Admin wheels documentation, document the process of adding new wheels. Commit: 27685377f629c536e56189e795bc91bb8caf0736 https://github.com/galaxyproject/galaxy/commit/27685377f629c536e56189e795bc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/releases/16.01_announce.rst Log Message: ----------- Merge pull request #1612 from natefoo/admin-docs [16.01] Additional documentation regarding wheels Compare: https://github.com/galaxyproject/galaxy/compare/f499ec0cabef...27685377f629

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