Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 65a3a6dcf650a74a74d8de04e4ea2ca418960e7f
https://github.com/galaxyproject/galaxy/commit/65a3a6dcf650a74a74d8de04e4ea…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-04-25 (Mon, 25 Apr 2016)
Changed paths:
M config/tool_shed.ini.sample
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/webapps/tool_shed/model/mapping.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/util.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/utility_containers/__init__.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M templates/webapps/tool_shed/index.mako
M templates/webapps/tool_shed/repository/common.mako
M templates/webapps/tool_shed/repository/manage_repository.mako
R test/shed_functional/functional/test_0450_skip_tool_tests.py
Log Message:
-----------
Cleanup of the install and test framework.
The system to install and test repositories has been deprecated, and this commit removes the parts that would display the results.
Commit: cb1ca652f0fd3f3d9297a22474dfd7edb9b4c3b0
https://github.com/galaxyproject/galaxy/commit/cb1ca652f0fd3f3d9297a22474df…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-04-25 (Mon, 25 Apr 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/util.py
Log Message:
-----------
Remove imports that became unused.
Commit: 9242847a4f5d3d63a6ed44f68ec0e48b2a256ab1
https://github.com/galaxyproject/galaxy/commit/9242847a4f5d3d63a6ed44f68ec0…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2016-04-27 (Wed, 27 Apr 2016)
Changed paths:
M config/tool_shed.ini.sample
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/webapps/tool_shed/model/mapping.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/util.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/utility_containers/__init__.py
M lib/tool_shed/utility_containers/utility_container_manager.py
M templates/webapps/tool_shed/index.mako
M templates/webapps/tool_shed/repository/common.mako
M templates/webapps/tool_shed/repository/manage_repository.mako
R test/shed_functional/functional/test_0450_skip_tool_tests.py
Log Message:
-----------
Merge pull request #2249 from davebx/remove_ttr
Cleanup of the install and test framework.
Compare: https://github.com/galaxyproject/galaxy/compare/898588a4d571...9242847a4f5d
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 3e5505fa4de90cdb23f9fb1e00dcb4af6289521c
https://github.com/galaxyproject/galaxy/commit/3e5505fa4de90cdb23f9fb1e00dc…
Author: Iyad Kandalaft <ik(a)iyadk.com>
Date: 2016-03-26 (Sat, 26 Mar 2016)
Changed paths:
M config/datatypes_conf.xml.sample
A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
A lib/galaxy/datatypes/mothur.py
Log Message:
-----------
initial files by IyadKandalaft
Commit: f8a2dbd05a87782f5f0c30540ef463330d040589
https://github.com/galaxyproject/galaxy/commit/f8a2dbd05a87782f5f0c30540ef4…
Author: shiltemann <zazkia(a)gmail.com>
Date: 2016-03-26 (Sat, 26 Mar 2016)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
Log Message:
-----------
add mothur prefix
Commit: 8961d8bd3d52cdd1abeba6060a226192277dbc2d
https://github.com/galaxyproject/galaxy/commit/8961d8bd3d52cdd1abeba6060a22…
Author: shiltemann <zazkia(a)gmail.com>
Date: 2016-03-26 (Sat, 26 Mar 2016)
Changed paths:
M lib/galaxy/datatypes/mothur.py
Log Message:
-----------
use 'with open' throughout
Commit: 4311a4fbf84c073fbe01806ce7968c10cabfd00b
https://github.com/galaxyproject/galaxy/commit/4311a4fbf84c073fbe01806ce796…
Author: shiltemann <zazkia(a)gmail.com>
Date: 2016-03-26 (Sat, 26 Mar 2016)
Changed paths:
M lib/galaxy/datatypes/mothur.py
Log Message:
-----------
minor changes to list creations
Commit: 65dde43041b94fd7f04f47369cb3302514a3e997
https://github.com/galaxyproject/galaxy/commit/65dde43041b94fd7f04f47369cb3…
Author: shiltemann <zazkia(a)gmail.com>
Date: 2016-03-26 (Sat, 26 Mar 2016)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
remove sniffers for datatypes that were subclassed
Commit: 45bf09dad0c8b3db9c0f9973d9347932d108e172
https://github.com/galaxyproject/galaxy/commit/45bf09dad0c8b3db9c0f9973d934…
Author: shiltemann <s.hiltemann(a)erasmusmc.nl>
Date: 2016-03-30 (Wed, 30 Mar 2016)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/mothur.py
Log Message:
-----------
add mothur prefix to extension, update sniffers and sniffer order, subclass taxonomy datatypes
Commit: ef32ee15fd9ee7a61c018a7e22a3cae0cc498b87
https://github.com/galaxyproject/galaxy/commit/ef32ee15fd9ee7a61c018a7e22a3…
Author: shiltemann <s.hiltemann(a)erasmusmc.nl>
Date: 2016-03-30 (Wed, 30 Mar 2016)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/mothur.py
Log Message:
-----------
remove phylip datatype (not specific to mothur)
Commit: 6ac7ec56032e25e9f883421d5aba6d1e6165e2cc
https://github.com/galaxyproject/galaxy/commit/6ac7ec56032e25e9f883421d5aba…
Author: shiltemann <s.hiltemann(a)erasmusmc.nl>
Date: 2016-03-30 (Wed, 30 Mar 2016)
Changed paths:
M lib/galaxy/datatypes/mothur.py
Log Message:
-----------
make sniffers for otu and distmatrices stricter
Commit: c43235011bf211da96b4507b986850ccc59567f8
https://github.com/galaxyproject/galaxy/commit/c43235011bf211da96b4507b9868…
Author: shiltemann <s.hiltemann(a)erasmusmc.nl>
Date: 2016-03-30 (Wed, 30 Mar 2016)
Changed paths:
M lib/galaxy/datatypes/mothur.py
Log Message:
-----------
remove two unused classes
Commit: b833d385056f23dfb314e4c8162982374766e73d
https://github.com/galaxyproject/galaxy/commit/b833d385056f23dfb314e4c81629…
Author: shiltemann <s.hiltemann(a)erasmusmc.nl>
Date: 2016-03-30 (Wed, 30 Mar 2016)
Changed paths:
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
Log Message:
-----------
stop using deprecated 'interpreter'
Commit: f3820538d186a1143443e47e764ad8ddc001d27f
https://github.com/galaxyproject/galaxy/commit/f3820538d186a1143443e47e764a…
Author: shiltemann <s.hiltemann(a)erasmusmc.nl>
Date: 2016-03-31 (Thu, 31 Mar 2016)
Changed paths:
M lib/galaxy/datatypes/mothur.py
Log Message:
-----------
stylefixes
Commit: 31129e9d18b52eb9842a0ebbfe1eabbaedc73334
https://github.com/galaxyproject/galaxy/commit/31129e9d18b52eb9842a0ebbfe1e…
Author: shiltemann <s.hiltemann(a)erasmusmc.nl>
Date: 2016-03-31 (Thu, 31 Mar 2016)
Changed paths:
M config/datatypes_conf.xml.sample
Log Message:
-----------
subclass mothur.align
Commit: 43f7564365ac101bfd43c55b741b1543eed6457d
https://github.com/galaxyproject/galaxy/commit/43f7564365ac101bfd43c55b741b…
Author: shiltemann <s.hiltemann(a)erasmusmc.nl>
Date: 2016-03-31 (Thu, 31 Mar 2016)
Changed paths:
M lib/galaxy/datatypes/mothur.py
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.axes
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.filter
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.freq
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.lower.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.map
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.oligos
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.otu
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.pair.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.quan
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.ref.taxonomy
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.sabund
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.shared
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.square.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.axes
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.freq
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.lower.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.map
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.oligos
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.otu
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.pair.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.quan
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.ref.taxonomy
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.sabund
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.shared
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.square.dist
Log Message:
-----------
update sniffers and add doctests
Commit: a82a5b20ddd71e1a5180a15220e9aa000f307dbe
https://github.com/galaxyproject/galaxy/commit/a82a5b20ddd71e1a5180a15220e9…
Author: shiltemann <s.hiltemann(a)erasmusmc.nl>
Date: 2016-03-31 (Thu, 31 Mar 2016)
Changed paths:
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
M lib/galaxy/datatypes/mothur.py
Log Message:
-----------
stylefixes and updates set_metas
Commit: 3a74c774095c2d3967bba869e74cceaf94479f66
https://github.com/galaxyproject/galaxy/commit/3a74c774095c2d3967bba869e74c…
Author: shiltemann <zazkia(a)gmail.com>
Date: 2016-04-14 (Thu, 14 Apr 2016)
Changed paths:
M lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
M lib/galaxy/datatypes/mothur.py
Log Message:
-----------
add python optimisations
Commit: f56e81a996511869f4a068418ffcd104c1b0ccdc
https://github.com/galaxyproject/galaxy/commit/f56e81a996511869f4a068418ffc…
Author: shiltemann <zazkia(a)gmail.com>
Date: 2016-04-21 (Thu, 21 Apr 2016)
Changed paths:
M lib/galaxy/datatypes/mothur.py
Log Message:
-----------
allow for comment lines in Otu files
Commit: d47f8f577e358b4e7a71b15a905040e5d3b079d4
https://github.com/galaxyproject/galaxy/commit/d47f8f577e358b4e7a71b15a9050…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-04-27 (Wed, 27 Apr 2016)
Changed paths:
M lib/galaxy/datatypes/mothur.py
Log Message:
-----------
Fixup exception handling in mothur datatypes.
Commit: d73a86d3658ed2ff7815ba5bd57ae63e527d4381
https://github.com/galaxyproject/galaxy/commit/d73a86d3658ed2ff7815ba5bd57a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-04-27 (Wed, 27 Apr 2016)
Changed paths:
M lib/galaxy/datatypes/sniff.py
Log Message:
-----------
Add a sample sniff test for new Mothur datatype.
The existing sniffer tests with the mothur stuff tests the sniffers in isolation - this is more of an integration test that tests the sample datatype configuration for the newly added mothur stuff.
Commit: 04476160aa19f3ce5cbd345cd8b3073575ed327b
https://github.com/galaxyproject/galaxy/commit/04476160aa19f3ce5cbd345cd8b3…
Author: Saskia Hiltemann <shiltemann(a)users.noreply.github.com>
Date: 2016-04-27 (Wed, 27 Apr 2016)
Changed paths:
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/sniff.py
Log Message:
-----------
Merge pull request #1 from jmchilton/mothur_datatypes
Small tweaks to mothur dataytpes.
Commit: c72381c528a9ab0afc231f1d109c8f4e66860b2e
https://github.com/galaxyproject/galaxy/commit/c72381c528a9ab0afc231f1d109c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-04-27 (Wed, 27 Apr 2016)
Changed paths:
M config/datatypes_conf.xml.sample
A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.py
A lib/galaxy/datatypes/converters/ref_to_seq_taxonomy_converter.xml
A lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/sniff.py
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.axes
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.filter
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.freq
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.lower.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.map
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.oligos
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.otu
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.pair.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.quan
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.ref.taxonomy
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.sabund
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.shared
A lib/galaxy/datatypes/test/mothur_datatypetest_false.mothur.square.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.axes
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.filter
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.freq
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.lower.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.map
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.oligos
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.otu
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.pair.dist
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.quan
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.ref.taxonomy
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.sabund
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.shared
A lib/galaxy/datatypes/test/mothur_datatypetest_true.mothur.square.dist
Log Message:
-----------
Merge pull request #2038 from shiltemann/mothur_datatypes
Import mothur datatypes
Compare: https://github.com/galaxyproject/galaxy/compare/a7bcd69f9e6b...c72381c528a9
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: aaf09dc99b0dc2896cbba5d21c132e998f5126e7
https://github.com/galaxyproject/galaxy/commit/aaf09dc99b0dc2896cbba5d21c13…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-04-27 (Wed, 27 Apr 2016)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Generate metadata in separate conda environment
Galaxy supports generating metadata in a separate command (enable
beta_tool_command_isolation). This command has its own dependency resolution,
that may interfere with thedependency resolution of the actual tool, if the
same environment is being used. With this PR we create a new environment when
resolving metadata dependencies with conda, that will be active only for
metadata generation.
Commit: 5dd9d1bafcc4532fdb48b312a47e2f90b7178d80
https://github.com/galaxyproject/galaxy/commit/5dd9d1bafcc4532fdb48b312a47e…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-04-27 (Wed, 27 Apr 2016)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
Log Message:
-----------
Fix whitespace and comma use
Commit: a7bcd69f9e6b72279772cc9ca003408df830e881
https://github.com/galaxyproject/galaxy/commit/a7bcd69f9e6b72279772cc9ca003…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-04-27 (Wed, 27 Apr 2016)
Changed paths:
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Merge pull request #2253 from mvdbeek/conda-metadata-env
Generate metadata in separate conda environment
Compare: https://github.com/galaxyproject/galaxy/compare/8a3b5d3d3e36...a7bcd69f9e6b
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 4630c6417d4e2c0ec747df02d28578f9576bb2a4
https://github.com/galaxyproject/galaxy/commit/4630c6417d4e2c0ec747df02d285…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-04-27 (Wed, 27 Apr 2016)
Changed paths:
M lib/galaxy/tools/deps/__init__.py
Log Message:
-----------
Tool execution dependency resolution already contains the relevant
information for viewing dependency resolution attempts and warns when
the dependency isn't found (Null resolver). Pretty sure this was just a
stray extra debugging statement that got unintentionally left in, and
it's pretty chatty.
Commit: 8a3b5d3d3e36946f240b55de071b75e4c0fa2e07
https://github.com/galaxyproject/galaxy/commit/8a3b5d3d3e36946f240b55de071b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-04-27 (Wed, 27 Apr 2016)
Changed paths:
M lib/galaxy/tools/deps/__init__.py
Log Message:
-----------
Merge pull request #2254 from dannon/remove_dep_debugging
Tool execution dependency resolution already contains the relevant
Compare: https://github.com/galaxyproject/galaxy/compare/e2287e2c9dd6...8a3b5d3d3e36