Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 18977d4132556a0c2bd0348db510cf765d434e6a
https://github.com/galaxyproject/galaxy/commit/18977d4132556a0c2bd0348db510…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-09-29 (Fri, 29 Sep 2017)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Don't load hidden tools into the tool panel at all.
Commit: 2eed478545857ab2c3b4c958bc3e2c360656af42
https://github.com/galaxyproject/galaxy/commit/2eed478545857ab2c3b4c958bc3e…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-10-02 (Mon, 02 Oct 2017)
Changed paths:
M config/galaxy.ini.sample
M doc/source/admin/dependency_resolvers.rst
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Update conda channel order to sync with Bioconda
Commit: a5b7dce09fb690f09d25f1b806d3339bdf2171c9
https://github.com/galaxyproject/galaxy/commit/a5b7dce09fb690f09d25f1b806d3…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-10-02 (Mon, 02 Oct 2017)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Remove _ensure_conda_context() function
and make conda_context argument mandatory in functions/methods.
This should help making sure the correct context (e.g. channels)
is used for all Conda operations.
Also remove unused is_target_available() function.
Conflicts:
lib/galaxy/tools/deps/conda_util.py
Commit: 3551386a1ac667e0d2f7c6e82256d180aa5100f7
https://github.com/galaxyproject/galaxy/commit/3551386a1ac667e0d2f7c6e82256…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-10-02 (Mon, 02 Oct 2017)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
Log Message:
-----------
Override channel list on the command line instead of modifying condarc
The way we were modifying condarc in the ensure_channels_configured()
method was broken because we were appending the missing channels at the
end, so the final order may not be the one specified in
conda_ensure_channels .
Also:
- not modifying the user condarc is a much better approach
- overriding the channel list on the command line will make debugging
easier
Commit: 04a572e509e875414b07e73c295f1c4bb37c1e0c
https://github.com/galaxyproject/galaxy/commit/04a572e509e875414b07e73c295f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-10-02 (Mon, 02 Oct 2017)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Merge pull request #4726 from natefoo/panel-hidden-fix
[17.09] If the newest version of a tool is hidden, load the newest older version, if any, into the tool panel
Commit: 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071
https://github.com/galaxyproject/galaxy/commit/81ece2551cea27cbd0e718ef5b7a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-10-02 (Mon, 02 Oct 2017)
Changed paths:
M config/galaxy.ini.sample
M doc/source/admin/dependency_resolvers.rst
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Merge pull request #4731 from nsoranzo/release_17.05_backport_4409
[17.05] Backport #4409
Commit: 280dc48c386f41c850ae3bbf9971979296b5abbc
https://github.com/galaxyproject/galaxy/commit/280dc48c386f41c850ae3bbf9971…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-10-02 (Mon, 02 Oct 2017)
Log Message:
-----------
Merge branch 'release_17.05' into release_17.09
Commit: 3d87afbb4174be1068aa701ca4d36d3b3f89591c
https://github.com/galaxyproject/galaxy/commit/3d87afbb4174be1068aa701ca4d3…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-10-02 (Mon, 02 Oct 2017)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Merge branch 'release_17.09' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/068c61a310e6...3d87afbb4174
Branch: refs/heads/release_17.09
Home: https://github.com/galaxyproject/galaxy
Commit: 2eed478545857ab2c3b4c958bc3e2c360656af42
https://github.com/galaxyproject/galaxy/commit/2eed478545857ab2c3b4c958bc3e…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-10-02 (Mon, 02 Oct 2017)
Changed paths:
M config/galaxy.ini.sample
M doc/source/admin/dependency_resolvers.rst
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Update conda channel order to sync with Bioconda
Commit: a5b7dce09fb690f09d25f1b806d3339bdf2171c9
https://github.com/galaxyproject/galaxy/commit/a5b7dce09fb690f09d25f1b806d3…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-10-02 (Mon, 02 Oct 2017)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Remove _ensure_conda_context() function
and make conda_context argument mandatory in functions/methods.
This should help making sure the correct context (e.g. channels)
is used for all Conda operations.
Also remove unused is_target_available() function.
Conflicts:
lib/galaxy/tools/deps/conda_util.py
Commit: 3551386a1ac667e0d2f7c6e82256d180aa5100f7
https://github.com/galaxyproject/galaxy/commit/3551386a1ac667e0d2f7c6e82256…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-10-02 (Mon, 02 Oct 2017)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
Log Message:
-----------
Override channel list on the command line instead of modifying condarc
The way we were modifying condarc in the ensure_channels_configured()
method was broken because we were appending the missing channels at the
end, so the final order may not be the one specified in
conda_ensure_channels .
Also:
- not modifying the user condarc is a much better approach
- overriding the channel list on the command line will make debugging
easier
Commit: 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071
https://github.com/galaxyproject/galaxy/commit/81ece2551cea27cbd0e718ef5b7a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-10-02 (Mon, 02 Oct 2017)
Changed paths:
M config/galaxy.ini.sample
M doc/source/admin/dependency_resolvers.rst
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Merge pull request #4731 from nsoranzo/release_17.05_backport_4409
[17.05] Backport #4409
Commit: 280dc48c386f41c850ae3bbf9971979296b5abbc
https://github.com/galaxyproject/galaxy/commit/280dc48c386f41c850ae3bbf9971…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-10-02 (Mon, 02 Oct 2017)
Log Message:
-----------
Merge branch 'release_17.05' into release_17.09
Compare: https://github.com/galaxyproject/galaxy/compare/04a572e509e8...280dc48c386f
Branch: refs/heads/release_17.05
Home: https://github.com/galaxyproject/galaxy
Commit: 2eed478545857ab2c3b4c958bc3e2c360656af42
https://github.com/galaxyproject/galaxy/commit/2eed478545857ab2c3b4c958bc3e…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-10-02 (Mon, 02 Oct 2017)
Changed paths:
M config/galaxy.ini.sample
M doc/source/admin/dependency_resolvers.rst
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Update conda channel order to sync with Bioconda
Commit: a5b7dce09fb690f09d25f1b806d3339bdf2171c9
https://github.com/galaxyproject/galaxy/commit/a5b7dce09fb690f09d25f1b806d3…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-10-02 (Mon, 02 Oct 2017)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Remove _ensure_conda_context() function
and make conda_context argument mandatory in functions/methods.
This should help making sure the correct context (e.g. channels)
is used for all Conda operations.
Also remove unused is_target_available() function.
Conflicts:
lib/galaxy/tools/deps/conda_util.py
Commit: 3551386a1ac667e0d2f7c6e82256d180aa5100f7
https://github.com/galaxyproject/galaxy/commit/3551386a1ac667e0d2f7c6e82256…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-10-02 (Mon, 02 Oct 2017)
Changed paths:
M lib/galaxy/tools/deps/conda_util.py
Log Message:
-----------
Override channel list on the command line instead of modifying condarc
The way we were modifying condarc in the ensure_channels_configured()
method was broken because we were appending the missing channels at the
end, so the final order may not be the one specified in
conda_ensure_channels .
Also:
- not modifying the user condarc is a much better approach
- overriding the channel list on the command line will make debugging
easier
Commit: 81ece2551cea27cbd0e718ef5b7a2fe8d4abd071
https://github.com/galaxyproject/galaxy/commit/81ece2551cea27cbd0e718ef5b7a…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-10-02 (Mon, 02 Oct 2017)
Changed paths:
M config/galaxy.ini.sample
M doc/source/admin/dependency_resolvers.rst
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
Log Message:
-----------
Merge pull request #4731 from nsoranzo/release_17.05_backport_4409
[17.05] Backport #4409
Compare: https://github.com/galaxyproject/galaxy/compare/cfabe37d6954...81ece2551cea