galaxy-commits January 2018

galaxy-commits@lists.galaxyproject.org

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[galaxyproject/galaxy] a475c4: Strip vue.js from static/scripts/libs; this should...
by GitHub 05 Jan '18

05 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a475c4c3d4102aa2a6952a4642c13e545388b55a https://github.com/galaxyproject/galaxy/commit/a475c4c3d4102aa2a6952a4642c1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-05 (Fri, 05 Jan 2018) Changed paths: R static/scripts/libs/vue.js Log Message: ----------- Strip vue.js from static/scripts/libs; this should be used exclusively out of node_modules now (and probably got added back accidentally) Commit: 1266b691d881c36e4ad277a5c9eca36226bb7c53 https://github.com/galaxyproject/galaxy/commit/1266b691d881c36e4ad277a5c9ec… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-05 (Fri, 05 Jan 2018) Changed paths: R static/scripts/libs/vue.js Log Message: ----------- Merge pull request #5272 from dannon/vue_static_removal Strip vue.js from static/scripts/libs Compare: https://github.com/galaxyproject/galaxy/compare/1f592f6acead...1266b691d881

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[galaxyproject/galaxy] 2f6cc2: Copy element_identifier to resumed job
by GitHub 05 Jan '18

05 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2f6cc2238428b8cf855b3118bd59d94bcae20cdb https://github.com/galaxyproject/galaxy/commit/2f6cc2238428b8cf855b3118bd59… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-05 (Fri, 05 Jan 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M test/api/test_workflows.py Log Message: ----------- Copy element_identifier to resumed job This fixes #5269. Commit: 1f592f6acead8b56dab01c0ad6fecf9ba48879f7 https://github.com/galaxyproject/galaxy/commit/1f592f6acead8b56dab01c0ad6fe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-05 (Fri, 05 Jan 2018) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #5270 from mvdbeek/fix_element_identifier_job_resume Copy element_identifier to resumed job Compare: https://github.com/galaxyproject/galaxy/compare/310f5f4423e3...1f592f6acead

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[galaxyproject/galaxy] f6ed56: Clarify some FTP purging behaviors with tests.
by GitHub 05 Jan '18

05 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f6ed56897103e72048511c011941587c9c9cbed1 https://github.com/galaxyproject/galaxy/commit/f6ed56897103e72048511c011941… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-04 (Thu, 04 Jan 2018) Changed paths: M test/integration/test_upload_configuration_options.py Log Message: ----------- Clarify some FTP purging behaviors with tests. xref https://github.com/galaxyproject/galaxy/pull/5264#issuecomment-355373614 Commit: 310f5f4423e370867468bfccc3ef535b88947169 https://github.com/galaxyproject/galaxy/commit/310f5f4423e370867468bfccc3ef… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-05 (Fri, 05 Jan 2018) Changed paths: M test/integration/test_upload_configuration_options.py Log Message: ----------- Merge pull request #5266 from jmchilton/upload_test Clarify some FTP purging behaviors with tests. Compare: https://github.com/galaxyproject/galaxy/compare/be5b88ef6fb1...310f5f4423e3

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[galaxyproject/galaxy] 748364: Catch error when displaying broken BAM file
by GitHub 05 Jan '18

05 Jan '18

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 7483648b3e7ddfd5cc4d9ebfbf80a62ed741462c https://github.com/galaxyproject/galaxy/commit/7483648b3e7ddfd5cc4d9ebfbf80… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-01-02 (Tue, 02 Jan 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Catch error when displaying broken BAM file This should fix https://github.com/galaxyproject/galaxy/issues/5252. Commit: bdbc1a680e46c3853f47489b6e3649b596ce5c95 https://github.com/galaxyproject/galaxy/commit/bdbc1a680e46c3853f47489b6e36… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-04 (Thu, 04 Jan 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #5253 from mvdbeek/catch_pysam_errors_when_viewing_bam_files [17.09] Catch and display error when displaying broken BAM file Compare: https://github.com/galaxyproject/galaxy/compare/41ce472cf2a2...bdbc1a680e46

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[galaxyproject/galaxy] 3f75a2: Re-work upload clarification from #5206.
by GitHub 04 Jan '18

04 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3f75a2d3a63d524f64bdd908e5375fc9bf093f17 https://github.com/galaxyproject/galaxy/commit/3f75a2d3a63d524f64bdd908e537… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-04 (Thu, 04 Jan 2018) Changed paths: M lib/galaxy/tools/actions/upload_common.py M tools/data_source/upload.py Log Message: ----------- Re-work upload clarification from #5206. See post-merge discussion on that issue. Commit: be5b88ef6fb14644cd76812ee03ca9b339b27092 https://github.com/galaxyproject/galaxy/commit/be5b88ef6fb14644cd76812ee03c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-04 (Thu, 04 Jan 2018) Changed paths: M lib/galaxy/tools/actions/upload_common.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #5264 from jmchilton/upload_clarification_2ish Re-work upload clarification from #5206. Compare: https://github.com/galaxyproject/galaxy/compare/a8fe2e19f657...be5b88ef6fb1

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[galaxyproject/galaxy] a3b575: Add extra help output in Makefile for when Yarn is...
by GitHub 04 Jan '18

04 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a3b575644c66c57a836f12b5d3c1acc1d65354e2 https://github.com/galaxyproject/galaxy/commit/a3b575644c66c57a836f12b5d3c1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-03 (Wed, 03 Jan 2018) Changed paths: M Makefile Log Message: ----------- Add extra help output in Makefile for when Yarn isn't found. Commit: 57090c0e73fc171103c097aaa352a560255a7bf1 https://github.com/galaxyproject/galaxy/commit/57090c0e73fc171103c097aaa352… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-03 (Wed, 03 Jan 2018) Changed paths: M Makefile Log Message: ----------- Ugh, yern->yarn (was using yern to test the failure of the command, left in this debug switch...) Commit: a8fe2e19f6573f5a8cb988b0b6cb13dea68ae094 https://github.com/galaxyproject/galaxy/commit/a8fe2e19f6573f5a8cb988b0b6cb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-03 (Wed, 03 Jan 2018) Changed paths: M Makefile Log Message: ----------- Merge pull request #5262 from dannon/yarn_info_output Add extra help output in Makefile for when Yarn isn't found. Compare: https://github.com/galaxyproject/galaxy/compare/bb29444edf34...a8fe2e19f657

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[galaxyproject/galaxy] 45a25a: Rudimentary build checking for -dev only.
by GitHub 03 Jan '18

03 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 45a25a1b8bd182cc6dff2926974681ef1bf4fc6f https://github.com/galaxyproject/galaxy/commit/45a25a1b8bd182cc6dff29269746… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-04 (Mon, 04 Dec 2017) Changed paths: M .gitignore M client/package.json M scripts/common_startup.sh Log Message: ----------- Rudimentary build checking for -dev only. Commit: b57af28c9bcc349099ef39ebbf9187253223c74c https://github.com/galaxyproject/galaxy/commit/b57af28c9bcc349099ef39ebbf91… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-05 (Tue, 05 Dec 2017) Changed paths: M scripts/common_startup.sh Log Message: ----------- Elaborate on comment, todo Commit: cf662803cb9b55aadcbb2136c89b388d9b882299 https://github.com/galaxyproject/galaxy/commit/cf662803cb9b55aadcbb2136c89b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M client/README.md Log Message: ----------- Update client readme with specific ways to get help. Commit: c8b454b5328fec61dc05bd0d5fef615d9249be6c https://github.com/galaxyproject/galaxy/commit/c8b454b5328fec61dc05bd0d5fef… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-12-20 (Wed, 20 Dec 2017) Changed paths: M scripts/common_startup.sh Log Message: ----------- More descriptive help for the dev client build check. Commit: bb29444edf34ee01ad1a71e38bd92350c37c534b https://github.com/galaxyproject/galaxy/commit/bb29444edf34ee01ad1a71e38bd9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-03 (Wed, 03 Jan 2018) Changed paths: M .gitignore M client/README.md M client/package.json M scripts/common_startup.sh Log Message: ----------- Merge pull request #5128 from dannon/check_for_client_build Client build check Compare: https://github.com/galaxyproject/galaxy/compare/7b2bad0e21a5...bb29444edf34

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[galaxyproject/galaxy] 70941c: Update api quickstart doc to use default port, wit...
by GitHub 03 Jan '18

03 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 70941cc57bfcb903f591425b994320a05bbf4249 https://github.com/galaxyproject/galaxy/commit/70941cc57bfcb903f591425b9943… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-03 (Wed, 03 Jan 2018) Changed paths: M doc/source/api/quickstart.rst Log Message: ----------- Update api quickstart doc to use default port, with a little bit of extra guidance. Commit: 7b2bad0e21a551a6484904112fa59bba7bb73675 https://github.com/galaxyproject/galaxy/commit/7b2bad0e21a551a6484904112fa5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-03 (Wed, 03 Jan 2018) Changed paths: M doc/source/api/quickstart.rst Log Message: ----------- Merge pull request #5260 from dannon/api_quickstart_tweak Update api quickstart doc to use default port, with a little bit of extra guidance. Compare: https://github.com/galaxyproject/galaxy/compare/368b001e435a...7b2bad0e21a5

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[galaxyproject/galaxy] 9c7793: Adjust note about nginx enabled sites configuratio...
by GitHub 03 Jan '18

03 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9c7793651516eabe38818582aad474cbf5d5c37a https://github.com/galaxyproject/galaxy/commit/9c7793651516eabe38818582aad4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-03 (Wed, 03 Jan 2018) Changed paths: M doc/source/admin/special_topics/nginx.md Log Message: ----------- Adjust note about nginx enabled sites configuration Originally implemented by @scholtalbers in https://github.com/galaxyproject/galaxy-hub/pull/355. Commit: 368b001e435ad25e5027dc6f06e901c1c20893f3 https://github.com/galaxyproject/galaxy/commit/368b001e435ad25e5027dc6f06e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-03 (Wed, 03 Jan 2018) Changed paths: M doc/source/admin/special_topics/nginx.md Log Message: ----------- Merge pull request #5259 from jmchilton/nginx_docs_touchup Adjust note about nginx enabled sites configuration Compare: https://github.com/galaxyproject/galaxy/compare/11ca454c4db4...368b001e435a

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[galaxyproject/galaxy] 889e08: Make pam a conditional dependency
by GitHub 02 Jan '18

02 Jan '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 889e0839d4c32afa280fae12ef9a063a01653411 https://github.com/galaxyproject/galaxy/commit/889e0839d4c32afa280fae12ef9a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-01-02 (Tue, 02 Jan 2018) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Make pam a conditional dependency Commit: 11ca454c4db4b631b800cd7d724497b756082bf4 https://github.com/galaxyproject/galaxy/commit/11ca454c4db4b631b800cd7d7244… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-01-02 (Tue, 02 Jan 2018) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Merge pull request #5251 from nsoranzo/pam_conditional_dep Make pam a conditional dependency Compare: https://github.com/galaxyproject/galaxy/compare/75283c7b6c2d...11ca454c4db4

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galaxy-commits January 2018