Branch: refs/heads/release_16.01
Home: https://github.com/galaxyproject/galaxy
Commit: 04af1ae1c609c0b73afabaf2aeb58110043847e6
https://github.com/galaxyproject/galaxy/commit/04af1ae1c609c0b73afabaf2aeb5…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2016-02-03 (Wed, 03 Feb 2016)
Changed paths:
M scripts/common_startup.sh
Log Message:
-----------
Always use the python hashlib for verifying the virtualenv download in
common_startup.sh rather than attempting to use sha256sum. Older
versions of coreutils (such as in RHEL 6) did not include the --strict
argument to sha256sum.
Commit: 2641f0af9ac84f91ea0cf3e849b6e8348da8909d
https://github.com/galaxyproject/galaxy/commit/2641f0af9ac84f91ea0cf3e849b6…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-02-03 (Wed, 03 Feb 2016)
Changed paths:
M scripts/common_startup.sh
Log Message:
-----------
Merge pull request #1668 from natefoo/venv-checksum
[16.01] Always use the python hashlib method for verifying the virtualenv download
Compare: https://github.com/galaxyproject/galaxy/compare/cd3f3b330db3...2641f0af9ac8
Branch: refs/heads/release_16.01
Home: https://github.com/galaxyproject/galaxy
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: 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:
-----------
Update data providers pysam.AlignmentFile usage
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:
-----------
Merge pull request #1638 from dannon/pysam_84_update
Pysam 84 update [16.01]
Compare: https://github.com/galaxyproject/galaxy/compare/b5d1c7721ee2...cd3f3b330db3
Branch: refs/heads/release_16.01
Home: https://github.com/galaxyproject/galaxy
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:
-----------
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:
-----------
Merge pull request #1664 from bgruening/release_16.01
fix `show_welcome_with_login = True`
Compare: https://github.com/galaxyproject/galaxy/compare/a95827751f46...b5d1c7721ee2
Branch: refs/heads/dev
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: 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.
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: 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.
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
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 …
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: 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
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 {}
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: 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: 85eccba79151a545af1e7aa07f24cece9c5398bd
https://github.com/galaxyproject/galaxy/commit/85eccba79151a545af1e7aa07f24…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-02-02 (Tue, 02 Feb 2016)
Changed paths:
M templates/user/info.mako
M templates/user/username.mako
Log Message:
-----------
Public name is mandatory not optional, update help text.
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.
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.
Commit: 6635e91170b310beafe629bc2956607234c41cb0
https://github.com/galaxyproject/galaxy/commit/6635e91170b310beafe629bc2956…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-02-02 (Tue, 02 Feb 2016)
Changed paths:
M scripts/common_startup.sh
Log Message:
-----------
Bump gx pip version to fix OSX platform issues.
Commit: 05e68addbe846a8f39cd1192285f936df166bf35
https://github.com/galaxyproject/galaxy/commit/05e68addbe846a8f39cd1192285f…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-02-02 (Tue, 02 Feb 2016)
Changed paths:
M scripts/common_startup.sh
Log Message:
-----------
Merge pull request #1652 from dannon/pip_bump
[16.01] Bump gx pip version to fix OSX platform issues.
Commit: 39aff8457201fc383d49cc8e90798795b7923189
https://github.com/galaxyproject/galaxy/commit/39aff8457201fc383d49cc8e9079…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-02-02 (Tue, 02 Feb 2016)
Changed paths:
M templates/user/info.mako
M templates/user/username.mako
Log Message:
-----------
Merge pull request #1655 from jmchilton/public-name-fixes
[16.01] Public name is mandatory not optional, update help text.
Commit: a8be2222ebb448ebac5996a2a9a042d0d618344f
https://github.com/galaxyproject/galaxy/commit/a8be2222ebb448ebac5996a2a9a0…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
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/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 branch 'release_16.01' into dev
Conflicts:
static/scripts/bundled/analysis.bundled.js
static/scripts/bundled/analysis.bundled.js.map
static/scripts/bundled/libs.bundled.js.map
static/style/blue/base.css
Commit: 1d6208f9ae317b1d10aed49cdcd2c9f653c9c8b8
https://github.com/galaxyproject/galaxy/commit/1d6208f9ae317b1d10aed49cdcd2…
Author: Dannon Baker <dannon.baker(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/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 pull request #1656 from nsoranzo/merge_16.01_into_dev
Merge 16.01 into dev.
Compare: https://github.com/galaxyproject/galaxy/compare/a5c4e0402547...1d6208f9ae31