September 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 484578: Refactor to use -P
by GitHub 25 Sep '15

25 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 484578936bc7ee04c6b28cb848772a4b6ded2b03 https://github.com/galaxyproject/galaxy/commit/484578936bc7ee04c6b28cb84877… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Refactor to use -P This is a major refactoring to use the -P option of docker which should simplify some of our deployment like running docker containers on another host. In support of #372 Commit: 04c5e6864cc77fa1952d1acd88bac5df93f5ac44 https://github.com/galaxyproject/galaxy/commit/04c5e6864cc77fa1952d1acd88ba… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge branch 'gie-docker-cmd' into gie-docker-launch Commit: c9e9c95514e50f9a260b5ed342a715d2846fd4fe https://github.com/galaxyproject/galaxy/commit/c9e9c95514e50f9a260b5ed342a7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Correct small logic bugs, add logging Commit: a02df53f3356a03f3784070a4c50accfbc00187f https://github.com/galaxyproject/galaxy/commit/a02df53f3356a03f3784070a4c50… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/templates/ipython.mako Log Message: ----------- Correct IPython notebooks to new URL Commit: a5b296b8ecd262d58a17049f5a9aeeecb7649621 https://github.com/galaxyproject/galaxy/commit/a5b296b8ecd262d58a17049f5a9a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Include user email Fixes bgruening/docker-ipython-notebook#51 Commit: a76ba39321e71cab8a0ecd3a610bcd861827815c https://github.com/galaxyproject/galaxy/commit/a76ba39321e71cab8a0ecd3a610b… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Update against gie-docker-cmd Commit: 06a67c8c109dcf59425b53b80dcb5419f5e814af https://github.com/galaxyproject/galaxy/commit/06a67c8c109dcf59425b53b80dcb… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Add dynamic_proxy_prefix configuration Normally the proxy binds to :8800 and runs containers under :8800/ipython/... which is great... until you have an upstream proxy like apache wrapping that at the url FQDN/ipython and suddenly your cookies aren't available because they're specific to /galaxy. Thus, when an upstream proxy is in use, we correct the proxy's path to: with :8800/{cookie_path}/gie_proxy/ipython/... which behaves much more nicely with upstraem proxies. Commit: 5a2b1ec322f0808ba4e7925effe87a467f6b467a https://github.com/galaxyproject/galaxy/commit/5a2b1ec322f0808ba4e7925effe8… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge branch 'gie-docker-cmd' into gie-docker-launch Commit: 1d78033625259bc50413393422feab38116b8884 https://github.com/galaxyproject/galaxy/commit/1d78033625259bc50413393422fe… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Merge branch 'gie-docker-cmd' into gie-docker-launch Commit: b4bbd1c2f161959fabdb62962aa63fb630c1ca2d https://github.com/galaxyproject/galaxy/commit/b4bbd1c2f161959fabdb62962aa6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/templates/ipython.mako M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Make use of proxy path in appropriate places Commit: 4a4a7ca51b195ac9d9a718448d65c89c02ae118c https://github.com/galaxyproject/galaxy/commit/4a4a7ca51b195ac9d9a718448d65… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/rstudio/templates/rstudio.mako Log Message: ----------- Update URLs for rstudio Commit: e8eb46b65d76a2b7645aa325e321d135df02e802 https://github.com/galaxyproject/galaxy/commit/e8eb46b65d76a2b7645aa325e321… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Use a backport for check_output that is not part of python 2.6 Commit: d4d439f51ebd2343e111d912499f336778e590c5 https://github.com/galaxyproject/galaxy/commit/d4d439f51ebd2343e111d912499f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #10 from erasche/check_output_backport Use a backport for check_output that is not part of python 2.6 Commit: 5f15b0d94c4a9703315f96fe3ce63b9b3906ea84 https://github.com/galaxyproject/galaxy/commit/5f15b0d94c4a9703315f96fe3ce6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Replace backported one with just the code used Sorry bjoern, ripped out what you'd added and just used the code because the doctest was failing for some unknown reason and we didn't ever need to reuse the function, so ... easier this way Commit: 6d3ea7ee0086707bbf3f6d54cfa0ee1e2221341c https://github.com/galaxyproject/galaxy/commit/6d3ea7ee0086707bbf3f6d54cfa0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M config/galaxy.ini.sample M config/plugins/interactive_environments/ipython/templates/ipython.mako M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M lib/galaxy/config.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/web/proxy/__init__.py Log Message: ----------- Merge pull request #790 from erasche/gie-docker-launch Refactor GIE Launching to use -P Compare: https://github.com/galaxyproject/galaxy/compare/0fefff07b34c...6d3ea7ee0086

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[galaxyproject/galaxy] f935d2: Fix _JAVA_OPTIONS example in job_conf.xml.
by GitHub 25 Sep '15

25 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f935d27bdfb4ff66e841de2667a40d3d65c0175d https://github.com/galaxyproject/galaxy/commit/f935d27bdfb4ff66e841de2667a4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Fix _JAVA_OPTIONS example in job_conf.xml. Thanks detailed bug report by Damion Dooley (http://dev.list.galaxyproject.org/JAVA-OPTIONS-config-parameter-in-job-conf…) Commit: 0fefff07b34c2b16793a3ae1c68849119abfa244 https://github.com/galaxyproject/galaxy/commit/0fefff07b34c2b16793a3ae1c688… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-25 (Fri, 25 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Merge pull request #796 from jmchilton/java_opts_doc Fix _JAVA_OPTIONS example in job_conf.xml.sample_advanced Compare: https://github.com/galaxyproject/galaxy/compare/0428de04fba3...0fefff07b34c

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[galaxyproject/galaxy] b58c72: UI, datasets: Move support for rerunnable to datas...
by GitHub 24 Sep '15

24 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b58c7203d0b874ef2d266a96c33e44aabdec61ed https://github.com/galaxyproject/galaxy/commit/b58c7203d0b874ef2d266a96c33e… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/tools/tools-jobs.js Log Message: ----------- UI, datasets: Move support for rerunnable to dataset-li expansion; remove redundant listener set up Commit: e1aad977597996f0e60422ba8b3fdd0275cc56fe https://github.com/galaxyproject/galaxy/commit/e1aad977597996f0e60422ba8b3f… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M static/maps/mvc/dataset/dataset-li.js.map M static/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Fix to b58c720: add creating_job to info needed for re-run button Commit: 12ada39cdd17cb19bc16aa096a1d0984bac49e4e https://github.com/galaxyproject/galaxy/commit/12ada39cdd17cb19bc16aa096a1d… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M static/maps/mvc/dataset/dataset-li.js.map M static/scripts/mvc/dataset/dataset-li.js Log Message: ----------- Fix to b58c720: only request creating_job and rerunnable Commit: 0428de04fba3fa695304a2a42d396ad64c7beb50 https://github.com/galaxyproject/galaxy/commit/0428de04fba3fa695304a2a42d39… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/tools/tools-jobs.js Log Message: ----------- Merge pull request #793 from carlfeberhard/fix.rerun-details-take2 UI, datasets: Move support for rerunnable to dataset-li expansion; re… Compare: https://github.com/galaxyproject/galaxy/compare/ace8c8864b55...0428de04fba3

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[galaxyproject/galaxy] fa0c3a: Implement failing workflow test case.
by GitHub 24 Sep '15

24 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fa0c3a4bbc9995b0f20638984d0395b442c33c92 https://github.com/galaxyproject/galaxy/commit/fa0c3a4bbc9995b0f20638984d03… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M test/api/test_workflows.py M test/functional/tools/min_repeat.xml Log Message: ----------- Implement failing workflow test case. For galaxyproject/galaxy#776. Commit: 0e521fd39822f9488392ef0485a40ded3606f0f2 https://github.com/galaxyproject/galaxy/commit/0e521fd39822f9488392ef0485a4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Fix problem maintaining input maps when rescheduling workflows. Fixes #776. I suspect the problem has very little to do with dynamic output collections and in fact exhibits itself when workflow rescheduling occurs, it is just that workflow rescheduling is forced when using dynamic output collections. Commit: ace8c8864b552f3104774c45ca13a6f057545625 https://github.com/galaxyproject/galaxy/commit/ace8c8864b552f3104774c45ca13… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M lib/galaxy/workflow/run.py M test/api/test_workflows.py M test/functional/tools/min_repeat.xml Log Message: ----------- Merge pull request #795 from jmchilton/workflow_output_collect Regression test case and fix for #776 Compare: https://github.com/galaxyproject/galaxy/compare/7f3ee5b1670b...ace8c8864b55

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[galaxyproject/galaxy] 5810a8: Move manual_builds.txt to manual_builds.txt.sample...
by GitHub 24 Sep '15

24 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5810a853b0370d09a3f3eb9fc80e8e90bfe8c791 https://github.com/galaxyproject/galaxy/commit/5810a853b0370d09a3f3eb9fc80e… Author: Lance Parsons <lparsons(a)genomics.princeton.edu> Date: 2015-08-18 (Tue, 18 Aug 2015) Changed paths: M .gitignore M scripts/common_startup.sh R tool-data/shared/ucsc/manual_builds.txt A tool-data/shared/ucsc/manual_builds.txt.sample Log Message: ----------- Move manual_builds.txt to manual_builds.txt.sample to allow for customization Commit: 7f3ee5b1670b80ec2fa14943950eac7cfe5bbd76 https://github.com/galaxyproject/galaxy/commit/7f3ee5b1670b80ec2fa14943950e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M .gitignore M scripts/common_startup.sh R tool-data/shared/ucsc/manual_builds.txt A tool-data/shared/ucsc/manual_builds.txt.sample Log Message: ----------- Merge pull request #612 from lparsons/manual_builds Move manual_builds.txt to manual_builds.txt.sample Compare: https://github.com/galaxyproject/galaxy/compare/f0ea4be88477...7f3ee5b1670b

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[galaxyproject/galaxy] 52dfd5: Unify the docker command, command_inject, and comm...
by GitHub 24 Sep '15

24 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 52dfd589b986397852d6700a4ca8d8afa7235416 https://github.com/galaxyproject/galaxy/commit/52dfd589b986397852d6700a4ca8… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Unify the docker command, command_inject, and command_wrapper Commit: 56ac2c0f137523c320ca12c684579b75d4b76dfc https://github.com/galaxyproject/galaxy/commit/56ac2c0f137523c320ca12c68457… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Revert command inject and document rationale Commit: 175f89bdc8df1550d34bc5084df45185ef633057 https://github.com/galaxyproject/galaxy/commit/175f89bdc8df1550d34bc5084df4… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Hardcode defaults, per @jmchilton's comments Commit: 10af45012735603385ac076f7b517dfe70314484 https://github.com/galaxyproject/galaxy/commit/10af45012735603385ac076f7b51… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Move run into python from template Commit: d7bff96778b11a3ed2838103aea6cceca43bdfb4 https://github.com/galaxyproject/galaxy/commit/d7bff96778b11a3ed2838103aea6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Correct stupid mistake from lack of testing Commit: 1ad3308b49a6f5a25ef357300b47791987acbb22 https://github.com/galaxyproject/galaxy/commit/1ad3308b49a6f5a25ef357300b47… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Remove small formatting issue Commit: e8db8a1932ab058d83331b547d9ef6e6e49bb934 https://github.com/galaxyproject/galaxy/commit/e8db8a1932ab058d83331b547d9e… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Add docker_galaxy_temp_dir This is useful for if the normal tmp dir is located on NFS. In this case it's useful to override the temporary directory with an sshfs mount for example. Commit: b1d642a6ecd324c6c519fb391f7747a05d709bb7 https://github.com/galaxyproject/galaxy/commit/b1d642a6ecd324c6c519fb391f77… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample Log Message: ----------- Update ipython.ini.sample Commit: a7c1c53f5352323abdb422fc8a9557e16e3f7993 https://github.com/galaxyproject/galaxy/commit/a7c1c53f5352323abdb422fc8a95… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Update rstudio.ini.sample Commit: 03ee295e7be09d53f7c1c3ff03988e0e82aa254d https://github.com/galaxyproject/galaxy/commit/03ee295e7be09d53f7c1c3ff0398… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #9 from erasche/docker_galaxy_temp_dir Add docker_galaxy_temp_dir Commit: f0ea4be88477d1baf3d4793af3fa173ec431a418 https://github.com/galaxyproject/galaxy/commit/f0ea4be88477d1baf3d4793af3fa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #782 from erasche/gie-docker-cmd Unify the docker command, command_inject, and command_wrapper Compare: https://github.com/galaxyproject/galaxy/compare/cc1d7a509cf7...f0ea4be88477

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[galaxyproject/galaxy] baf25e: Print has_metrics class name instead of object mem...
by GitHub 24 Sep '15

24 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: baf25e07b809d1f7ce0c1c7b6b9b5f8ab7011a24 https://github.com/galaxyproject/galaxy/commit/baf25e07b809d1f7ce0c1c7b6b9b… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Print has_metrics class name instead of object memory address. Commit: cc1d7a509cf75f49516c8e2a664cf81a15d1f7e9 https://github.com/galaxyproject/galaxy/commit/cc1d7a509cf75f49516c8e2a664c… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-24 (Thu, 24 Sep 2015) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #791 from nsoranzo/772_followup Print has_metrics class name instead of object memory address. Compare: https://github.com/galaxyproject/galaxy/compare/bf0ab52e75e7...cc1d7a509cf7

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[galaxyproject/galaxy] 61fda5: Add missing file from previous commit.
by GitHub 23 Sep '15

23 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 61fda5f23dce31da353bbee209c8cf260427a400 https://github.com/galaxyproject/galaxy/commit/61fda5f23dce31da353bbee209c8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: A test-data/1.RData Log Message: ----------- Add missing file from previous commit. Commit: bf0ab52e75e7a51f696262bc33b1d82ba4acd98c https://github.com/galaxyproject/galaxy/commit/bf0ab52e75e7a51f696262bc33b1… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: A test-data/1.RData Log Message: ----------- Merge pull request #787 from jmchilton/sniff_test Add missing file from #784 Compare: https://github.com/galaxyproject/galaxy/compare/38823c61db7b...bf0ab52e75e7

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[galaxyproject/galaxy] 3f3c1b: Pin IE versions
by GitHub 23 Sep '15

23 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 3f3c1b679bfef5dbd75d7c267d25fd2979f362d1 https://github.com/galaxyproject/galaxy/commit/3f3c1b679bfef5dbd75d7c267d25… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Pin IE versions Commit: 85df2f67c4988700232098d4dc08f2bc5148359d https://github.com/galaxyproject/galaxy/commit/85df2f67c4988700232098d4dc08… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample Log Message: ----------- Merge pull request #785 from erasche/pin-gie-images [release_15.07] pin GIE image versions Compare: https://github.com/galaxyproject/galaxy/compare/aff8c708a925...85df2f67c498

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[galaxyproject/galaxy] 19bc49: Binary sniffing; along with the registry forcing c...
by GitHub 23 Sep '15

23 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 19bc49d207a92288dc402900cfa0125b8da45111 https://github.com/galaxyproject/galaxy/commit/19bc49d207a92288dc402900cfa0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-22 (Tue, 22 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Binary sniffing; along with the registry forcing case insensitivity through lower() which was implemented a while back, the un/sniffable formats lists should as well. This resolves #753 Commit: aff8c708a925205332c4190e3ada5712dc04519e https://github.com/galaxyproject/galaxy/commit/aff8c708a925205332c4190e3ada… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #774 from dannon/stable_sniffers [15.07] Binary sniffing; along with the registry forcing case insensitivity t… Commit: ce16573897ca471e8fd431029ae19861439bce5c https://github.com/galaxyproject/galaxy/commit/ce16573897ca471e8fd431029ae1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge remote-tracking branch 'jmchilton/release_15.07' into sniff_test Commit: 684be5f6a5c4ac91d6df2c5ec4f1e2866a538965 https://github.com/galaxyproject/galaxy/commit/684be5f6a5c4ac91d6df2c5ec4f1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M test/api/helpers.py M test/api/test_tools.py M test/base/test_data.py M test/base/twilltestcase.py Log Message: ----------- Functional test to verify RData is not decompressed in upload process. Commit: 38823c61db7b3d43c620752dc215dc5af6f76576 https://github.com/galaxyproject/galaxy/commit/38823c61db7b3d43c620752dc215… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-23 (Wed, 23 Sep 2015) Changed paths: M lib/galaxy/datatypes/binary.py M test/api/helpers.py M test/api/test_tools.py M test/base/test_data.py M test/base/twilltestcase.py Log Message: ----------- Merge pull request #784 from jmchilton/sniff_test Test case to prevent regression of #753. Compare: https://github.com/galaxyproject/galaxy/compare/a90a4fcebaee...38823c61db7b

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