Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 47b9eb47ddd64d770791556f18fedceaf3a705ec
https://github.com/galaxyproject/galaxy/commit/47b9eb47ddd64d770791556f18fe…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-02-02 (Tue, 02 Feb 2016)
Changed paths:
A .ci/first_startup.sh
M .travis.yml
M tox.ini
Log Message:
-----------
Add tox startup test and build matrix for travis-ci.
Commit: 4176bc9115b94eba30c6ad9c7a1bf08823a3791b
https://github.com/galaxyproject/galaxy/commit/4176bc9115b94eba30c6ad9c7a1b…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-02-02 (Tue, 02 Feb 2016)
Changed paths:
M .travis.yml
Log Message:
-----------
Move first_startup to last position
Commit: 3d4ddc438eb8e7e8822a2b0b05820098140ad6f3
https://github.com/galaxyproject/galaxy/commit/3d4ddc438eb8e7e8822a2b0b0582…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-02-02 (Tue, 02 Feb 2016)
Changed paths:
M .travis.yml
Log Message:
-----------
Add py27-unit tests on osx
Commit: 84b783027d68beb4d2f83ca21311d1ee3ea64042
https://github.com/galaxyproject/galaxy/commit/84b783027d68beb4d2f83ca21311…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-02-02 (Tue, 02 Feb 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/style/less/base.less
M lib/galaxy/config.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/util/__init__.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M scripts/common_startup.sh
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
M static/style/blue/base.css
M templates/user/info.mako
M templates/user/username.mako
Log Message:
-----------
Merge remote-tracking branch 'galaxy/dev' into HEAD
Commit: faeedd6f824f5d5def7839d2e72248f6e38e4aef
https://github.com/galaxyproject/galaxy/commit/faeedd6f824f5d5def7839d2e722…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-02-08 (Mon, 08 Feb 2016)
Changed paths:
A .ci/first_startup.sh
M .travis.yml
M tox.ini
Log Message:
-----------
Merge pull request #1649 from mvdbeek/add_startup_test
Add tox startup (run.sh) test and test on OS X and linux
Compare: https://github.com/galaxyproject/galaxy/compare/75f1b58ecb8a...faeedd6f824f
Branch: refs/heads/release_16.01
Home: https://github.com/galaxyproject/galaxy
Commit: ada39dea6ab68be543f53feb7a30e97167d96013
https://github.com/galaxyproject/galaxy/commit/ada39dea6ab68be543f53feb7a30…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
Log Message:
-----------
handle correctly application/json pased in POST
Commit: 530501c682be85b595bd8115bc2fc0ebc53f57a0
https://github.com/galaxyproject/galaxy/commit/530501c682be85b595bd8115bc2f…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/libraries.py
Log Message:
-----------
fix setting library permissions to accept JSON correctly
Commit: 5dd839960e1ca5170b528c4c88ad8965eebde08b
https://github.com/galaxyproject/galaxy/commit/5dd839960e1ca5170b528c4c88ad…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/libraries.py
Log Message:
-----------
unify api for library creation; support POST with url params
Commit: edd8b222acac34cd2e35e768ab1cbd888b2fc824
https://github.com/galaxyproject/galaxy/commit/edd8b222acac34cd2e35e768ab1c…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/libraries.py
Log Message:
-----------
catch value errors from id decoding
Commit: 0398aafb1cf0aa0863d0867d20dd79a09bc2fb85
https://github.com/galaxyproject/galaxy/commit/0398aafb1cf0aa0863d0867d20dd…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/libraries.py
Log Message:
-----------
fix updating library API to not require payload
and to properly handle optional params
Commit: 4b51be57d114d840112970baccb979ec1876663b
https://github.com/galaxyproject/galaxy/commit/4b51be57d114d840112970baccb9…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/libraries.py
Log Message:
-----------
allow specifying DELETE params in JSON
Commit: c288b43627d3da925c5fe4b2fd0ebd5a7bc752b2
https://github.com/galaxyproject/galaxy/commit/c288b43627d3da925c5fe4b2fd0e…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/folders.py
Log Message:
-----------
allow creating folders with JSON payload
Commit: 7867f3e0835a2cbd99658ad25debd9be278300f2
https://github.com/galaxyproject/galaxy/commit/7867f3e0835a2cbd99658ad25deb…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M client/galaxy/scripts/mvc/library/library-folder-view.js
M lib/galaxy/webapps/galaxy/api/folders.py
M static/maps/mvc/library/library-folder-view.js.map
M static/scripts/mvc/library/library-folder-view.js
Log Message:
-----------
accept json as input for setting permissions;
fix inconsistency by leveraging role_manager
Commit: a4c2098da010d79a70a9425e8ccb6c1e69807442
https://github.com/galaxyproject/galaxy/commit/a4c2098da010d79a70a9425e8ccb…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/folders.py
Log Message:
-----------
allow PATCHing with payload in urlparams
Commit: b46636a53f579fc6ffa63fbca888196bb0ff99f6
https://github.com/galaxyproject/galaxy/commit/b46636a53f579fc6ffa63fbca888…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/libraries.py
Log Message:
-----------
remove deletion of the payload dict item
it is not necessary and the key does not have to exist
Commit: 170c83e6c283e97b1e399bc122ee94ddb8cb34b4
https://github.com/galaxyproject/galaxy/commit/170c83e6c283e97b1e399bc122ee…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/folders.py
M lib/galaxy/webapps/galaxy/api/libraries.py
Log Message:
-----------
fix unused imports and unused vars
Commit: 134d792c1fcfba5d09e2937074c3263792bea991
https://github.com/galaxyproject/galaxy/commit/134d792c1fcfba5d09e2937074c3…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-05 (Fri, 05 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/libraries.py
Log Message:
-----------
delete the 'payload' if it is in kwd so it is not supplied twice
Commit: e7b6b4b13bd93a8520942c94d0ed28d110af261b
https://github.com/galaxyproject/galaxy/commit/e7b6b4b13bd93a8520942c94d0ed…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-05 (Fri, 05 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/libraries.py
Log Message:
-----------
Revert "delete the 'payload' if it is in kwd so it is not supplied twice"
This reverts commit 134d792c1fcfba5d09e2937074c3263792bea991.
Commit: 5301269fbb54753e75969ecd446b8cb74c6093b6
https://github.com/galaxyproject/galaxy/commit/5301269fbb54753e75969ecd446b…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-05 (Fri, 05 Feb 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/folders.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/libraries.py
Log Message:
-----------
update docs of the data libraries API
Commit: ef6bd90f20394f6fb74b1bdedbd0f94ecb752018
https://github.com/galaxyproject/galaxy/commit/ef6bd90f20394f6fb74b1bdedbd0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-02-08 (Mon, 08 Feb 2016)
Changed paths:
M client/galaxy/scripts/mvc/library/library-folder-view.js
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/folders.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/libraries.py
M static/maps/mvc/library/library-folder-view.js.map
M static/scripts/mvc/library/library-folder-view.js
Log Message:
-----------
Merge pull request #1641 from martenson/libraries-load-handle-payload
[16.01] libraries: handle correctly application/json pased in POST
Compare: https://github.com/galaxyproject/galaxy/compare/c693b69b3444...ef6bd90f2039
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 1e79c8c77e29f0aa5e6377d77ffa68d808ca4c89
https://github.com/galaxyproject/galaxy/commit/1e79c8c77e29f0aa5e6377d77ffa…
Author: Mark Einon <mark.einon(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/wrappers.py
Log Message:
-----------
Optionally pass dataset lists as a single file within tool wrappers
This change introduces an extra boolean XML attribute 'pass_as_file', that when
used with an input parameter already having the 'multiple=True' attribute, passes
the dataset list of files to the wrapped program as a single file containing a
list of the dataset files.
Commit: 27618a319d9c3bac01484bad80494f4423c04673
https://github.com/galaxyproject/galaxy/commit/27618a319d9c3bac01484bad8049…
Author: Mark Einon <mark.einon(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/wrappers.py
Log Message:
-----------
[Trivial] Whitespace fixes to please pylint
Commit: 66350fb87100a8986a95c28f9b532564c98f0034
https://github.com/galaxyproject/galaxy/commit/66350fb87100a8986a95c28f9b53…
Author: Mark Einon <mark.einon(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/wrappers.py
A test/functional/tools/paths_as_file.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Modify pass_as_file to apply to all Multiple parameters and add test case
Change the pass_as_file XML attribute to a cheetah method call, and
apply to all paramter types that can have Multiple=True set -
those given in DatasetListWrappers and DatasetCollectionWrappers.
Test case and modification suggestion provided by John Chilton
<jmchilton(a)gmail.com>
Commit: 75f1b58ecb8a4e60fd9f3bbcbc6b9501005b903d
https://github.com/galaxyproject/galaxy/commit/75f1b58ecb8a4e60fd9f3bbcbc6b…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-05 (Fri, 05 Feb 2016)
Changed paths:
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/wrapped.py
M lib/galaxy/tools/wrappers.py
A test/functional/tools/paths_as_file.xml
M test/functional/tools/samples_tool_conf.xml
Log Message:
-----------
Merge pull request #1658 from einon/pass_lists_as_file
Optionally pass dataset lists as a single file within tool wrappers
Compare: https://github.com/galaxyproject/galaxy/compare/dfceb5c144de...75f1b58ecb8a
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 61f168d34b748da0994be2d0d1c8c77af27c4520
https://github.com/galaxyproject/galaxy/commit/61f168d34b748da0994be2d0d1c8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M client/galaxy/scripts/mvc/tours.js
M static/maps/mvc/tours.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tours.js
Log Message:
-----------
A slightly different check for Galaxy object definition that doesn't assume a window-attached Galaxy context, only a parent. Minor cleanup.
Commit: 33ebeb801d235af58a6e1152056d52e9ee5bfac6
https://github.com/galaxyproject/galaxy/commit/33ebeb801d235af58a6e1152056d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.js
M static/maps/layout/menu.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/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/layout/menu.js
Log Message:
-----------
Use backbone routing for a tours URL, since there's no serverside endpoint.
Commit: ab5f1536171dba6fc2f8afaae9c0154d46e1dd5b
https://github.com/galaxyproject/galaxy/commit/ab5f1536171dba6fc2f8afaae9c0…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
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:
-----------
Clientside routing for tour kickoff, swapping from ?tour_id=foo approach.
Commit: dfceb5c144de556e10659a8d876237188bd4595f
https://github.com/galaxyproject/galaxy/commit/dfceb5c144de556e10659a8d8762…
Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com>
Date: 2016-02-04 (Thu, 04 Feb 2016)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/onload.js
M static/maps/layout/menu.js.map
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/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/layout/menu.js
M static/scripts/mvc/tours.js
M static/scripts/onload.js
Log Message:
-----------
Merge pull request #1671 from dannon/tour_fixes_and_cleanup
Tour improvements and bugfixes
Compare: https://github.com/galaxyproject/galaxy/compare/d93f095c7f56...dfceb5c144de
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 8cee212708f4de75c4bf066ac1dec0752bea0a5d
https://github.com/galaxyproject/galaxy/commit/8cee212708f4de75c4bf066ac1de…
Author: y.hoogstrate(a)erasmusmc.nl <y.hoogstrate(a)erasmusmc.nl>
Date: 2016-02-02 (Tue, 02 Feb 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-input.js
Log Message:
-----------
Fixes <param argument="--set" /> not working when help="" is not set
Commit: 09911084f3b424d4822d4b5baed7fa3ca1a0a3b9
https://github.com/galaxyproject/galaxy/commit/09911084f3b424d4822d4b5baed7…
Author: y.hoogstrate(a)erasmusmc.nl <y.hoogstrate(a)erasmusmc.nl>
Date: 2016-02-02 (Tue, 02 Feb 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-input.js
Log Message:
-----------
Fixes <param argument="--set" /> not working when help="" is not set (indentation)
Commit: d7dd9f9040be7a66e414322a67e15bea1b93a9f6
https://github.com/galaxyproject/galaxy/commit/d7dd9f9040be7a66e414322a67e1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-02-03 (Wed, 03 Feb 2016)
Changed paths:
M static/maps/mvc/form/form-input.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/form/form-input.js
Log Message:
-----------
Rebuild client stuff for #1650.
Commit: d93f095c7f56c85c871ef82f532c68e12d3a3318
https://github.com/galaxyproject/galaxy/commit/d93f095c7f56c85c871ef82f532c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-02-03 (Wed, 03 Feb 2016)
Changed paths:
M client/galaxy/scripts/mvc/form/form-input.js
M static/maps/mvc/form/form-input.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/form/form-input.js
Log Message:
-----------
Merge remote-tracking branch 'jmchilton/param_argument_fix' into dev
Conflicts:
static/scripts/bundled/analysis.bundled.js
static/scripts/bundled/analysis.bundled.js.map
static/scripts/bundled/libs.bundled.js
static/scripts/bundled/libs.bundled.js.map
Compare: https://github.com/galaxyproject/galaxy/compare/d97e8bbbbce8...d93f095c7f56
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 17a1683a383d7f375b77371548ff7d349a561a96
https://github.com/galaxyproject/galaxy/commit/17a1683a383d7f375b77371548ff…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-02-01 (Mon, 01 Feb 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Warn on optional select test parameter.
Commit: ccdb027d38428a38d79b4272fadb076b7f428825
https://github.com/galaxyproject/galaxy/commit/ccdb027d38428a38d79b4272fadb…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-02-01 (Mon, 01 Feb 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Prevent optional test parameters in conditionals
Commit: 6fa7f1e1edda25ec36f2373148af223493924803
https://github.com/galaxyproject/galaxy/commit/6fa7f1e1edda25ec36f2373148af…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-02-01 (Mon, 01 Feb 2016)
Changed paths:
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
Log Message:
-----------
Bump pysam to new 0.8.4+gx1.
Commit: 508ebea63f2376b5a3b452148e4a6d3c18366b3b
https://github.com/galaxyproject/galaxy/commit/508ebea63f2376b5a3b452148e4a…
Author: Aysam Guerler <aysam.guerler(a)gmail.com>
Date: 2016-02-01 (Mon, 01 Feb 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #8 from jmchilton/fix_optional_001
Warn on optional select test parameter.
Commit: ba9ad97c40bd994e0dc51888ef235cf3b434168a
https://github.com/galaxyproject/galaxy/commit/ba9ad97c40bd994e0dc51888ef23…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-02-02 (Tue, 02 Feb 2016)
Changed paths:
M test-data/3.bam
Log Message:
-----------
Fix 3.bam @PG header to use : instead of = as a key:value separator. See commentary in https://github.com/galaxyproject/galaxy/pull/1638 for more details.
Commit: 39eb262219beca9ec6b849b49c0430d834cfd2ae
https://github.com/galaxyproject/galaxy/commit/39eb262219beca9ec6b849b49c04…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-02-02 (Tue, 02 Feb 2016)
Changed paths:
M test-data/3.bam
Log Message:
-----------
More fixes to 3.bam to make it valid stripped out secondary HD header and duplicated sequences chr10-16
Commit: 66f20e7df91074e07cbade57b20deb68cb840a55
https://github.com/galaxyproject/galaxy/commit/66f20e7df91074e07cbade57b20d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-02-02 (Tue, 02 Feb 2016)
Changed paths:
M lib/galaxy/datatypes/binary.py
Log Message:
-----------
Fix method signature of bam.set_meta to include a positional argument which is now required.
Commit: d6325c5039f28062a2cf49d00c091d83a92865c3
https://github.com/galaxyproject/galaxy/commit/d6325c5039f28062a2cf49d00c09…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-02-02 (Tue, 02 Feb 2016)
Changed paths:
M lib/galaxy/visualization/data_providers/genome.py
Log Message:
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Update data providers pysam.AlignmentFile usage
Commit: a95827751f463f35c67e76f84127f850972244c5
https://github.com/galaxyproject/galaxy/commit/a95827751f463f35c67e76f84127…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-02-02 (Tue, 02 Feb 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
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Merge pull request #1637 from guerler/fix_optional_001
[16.01] Prevent optional test parameters in conditionals
Commit: 45f523f9229f6d943e3a65042b8cad0276a0a7d7
https://github.com/galaxyproject/galaxy/commit/45f523f9229f6d943e3a65042b8c…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2016-02-03 (Wed, 03 Feb 2016)
Changed paths:
M client/galaxy/scripts/layout/page.js
M static/maps/layout/page.js.map
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/layout/page.js
Log Message:
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fix show_welcome_with_login = True
Commit: b5d1c7721ee2f8ad1095e52d4e710b998f92945d
https://github.com/galaxyproject/galaxy/commit/b5d1c7721ee2f8ad1095e52d4e71…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-03 (Wed, 03 Feb 2016)
Changed paths:
M client/galaxy/scripts/layout/page.js
M static/maps/layout/page.js.map
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/layout/page.js
Log Message:
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Merge pull request #1664 from bgruening/release_16.01
fix `show_welcome_with_login = True`
Commit: cd3f3b330db34e294e78374e8e8b32300c66f36e
https://github.com/galaxyproject/galaxy/commit/cd3f3b330db34e294e78374e8e8b…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-02-03 (Wed, 03 Feb 2016)
Changed paths:
M lib/galaxy/datatypes/binary.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/visualization/data_providers/genome.py
M test-data/3.bam
Log Message:
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Merge pull request #1638 from dannon/pysam_84_update
Pysam 84 update [16.01]
Commit: 246870c459cffd48a0fe7b4963e674638298e620
https://github.com/galaxyproject/galaxy/commit/246870c459cffd48a0fe7b4963e6…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-02-03 (Wed, 03 Feb 2016)
Changed paths:
M client/galaxy/scripts/layout/page.js
M lib/galaxy/datatypes/binary.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/tools/__init__.py
M lib/galaxy/visualization/data_providers/genome.py
M static/maps/layout/page.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/page.js
M test-data/3.bam
Log Message:
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Merge branch 'release_16.01' into dev
Commit: d97e8bbbbce862eb6b4f8f5732cd0baa029e9e20
https://github.com/galaxyproject/galaxy/commit/d97e8bbbbce862eb6b4f8f5732cd…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-02-03 (Wed, 03 Feb 2016)
Changed paths:
M client/galaxy/scripts/layout/page.js
M lib/galaxy/datatypes/binary.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/tools/__init__.py
M lib/galaxy/visualization/data_providers/genome.py
M static/maps/layout/page.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/page.js
M test-data/3.bam
Log Message:
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Merge pull request #1667 from natefoo/dev
Merge release_16.01 to dev
Compare: https://github.com/galaxyproject/galaxy/compare/b82efd937504...d97e8bbbbce8