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:
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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:
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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:
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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:
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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:
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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:
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Merge pull request #790 from erasche/gie-docker-launch
Refactor GIE Launching to use -P
Compare: https://github.com/galaxyproject/galaxy/compare/0fefff07b34c...6d3ea7ee0086
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:
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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:
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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:
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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:
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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
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:
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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:
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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:
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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
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:
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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:
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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:
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Merge pull request #784 from jmchilton/sniff_test
Test case to prevent regression of #753.
Compare: https://github.com/galaxyproject/galaxy/compare/a90a4fcebaee...38823c61db7b