Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 47339bf1f33b52fade0db00a1af23eba34648da5
https://github.com/galaxyproject/galaxy/commit/47339bf1f33b52fade0db00a1af2…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M lib/tool_shed/galaxy_install/install_manager.py
Log Message:
-----------
Catch specific exception type
Also remove unused variable
Commit: a033a5821ad11fbe0465b01984c97e591785623c
https://github.com/galaxyproject/galaxy/commit/a033a5821ad11fbe0465b01984c9…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-05-23 (Tue, 23 May 2017)
Changed paths:
M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
Log Message:
-----------
Allow empty <environment_variable>
Presently trying to install a ToolShed tool dependency defined as
<tool_dependency>
<set_environment version="1.0">
<environment_variable name="MYVAR" action="set_to"></environment_variable>
</set_environment>
</tool_dependency>
results in EnvManager.create_env_var_dict() returning None, which in turn
causes the dependency silently not being installed with this error in the
logs:
tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler DEBUG 2017-05-23 10:08:23,798 Error setting environment for tool dependency: local variable 'tool_dependency' referenced before assignment
Commit: e4de203c7da50aee3a95edacaf7f00d79b1ac416
https://github.com/galaxyproject/galaxy/commit/e4de203c7da50aee3a95edacaf7f…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-05-23 (Tue, 23 May 2017)
Changed paths:
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
Log Message:
-----------
Raise an exception if name or action are not defined
instead of silently skipping the <environment_variable> tool dependency
Commit: 2aec5dda9ad7b66b0da6de08873b919d472b0309
https://github.com/galaxyproject/galaxy/commit/2aec5dda9ad7b66b0da6de08873b…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-05-23 (Tue, 23 May 2017)
Changed paths:
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
Log Message:
-----------
Merge pull request #4105 from nsoranzo/ts_tool_dep_install_fixes
ToolShed tool dependency install fixes
Compare: https://github.com/galaxyproject/galaxy/compare/1bc8ea69c950...2aec5dda9ad7
Branch: refs/heads/release_17.05
Home: https://github.com/galaxyproject/galaxy
Commit: 9ec6c13fa9196b87e30ed5a97769526b1c4a0cd0
https://github.com/galaxyproject/galaxy/commit/9ec6c13fa9196b87e30ed5a97769…
Author: Bjoern Gruening <bjoern.gruening(a)gmail.com>
Date: 2017-05-21 (Sun, 21 May 2017)
Changed paths:
M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/mol_to_smi_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml
Log Message:
-----------
update openbabel to version 2.4.1
Commit: 0b3e29199f33ad2f8ec0db3c9a750b4b16fc9415
https://github.com/galaxyproject/galaxy/commit/0b3e29199f33ad2f8ec0db3c9a75…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/cml_to_smi_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_cml_converter.xml
M lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/mol_to_smi_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_cml_converter.xml
M lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml
M lib/galaxy/datatypes/converters/smi_to_mol_converter.xml
M lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml
M lib/galaxy/datatypes/converters/smi_to_smi_converter.xml
Log Message:
-----------
Merge pull request #4094 from bgruening/openbabel_update
[17.05] Open Babel update for datatype converters
Compare: https://github.com/galaxyproject/galaxy/compare/15556c0a71eb...0b3e29199f33
Branch: refs/heads/release_17.05
Home: https://github.com/galaxyproject/galaxy
Commit: d1ce1a623772d19f5fe9039c81e47fc08e2624e7
https://github.com/galaxyproject/galaxy/commit/d1ce1a623772d19f5fe9039c81e4…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
A doc/source/releases/17.05.rst
M doc/source/releases/17.05_announce.rst
A doc/source/releases/17.09_announce.rst
Log Message:
-----------
initial version of RN
Commit: 4cb13b2404e4562c3d79e8707640624514fed3d5
https://github.com/galaxyproject/galaxy/commit/4cb13b2404e4562c3d79e8707640…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M doc/source/releases/index.rst
Log Message:
-----------
add 17.05 to the release list
Commit: 5aaf95e0459bc2331492df9423d2cfe9121ff22b
https://github.com/galaxyproject/galaxy/commit/5aaf95e0459bc2331492df9423d2…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M doc/source/releases/_thanks.rst
M doc/source/releases/older_releases.rst
Log Message:
-----------
fix links to wiki/hub
Commit: 56874e163086b89d97dae17d59afa004777936bd
https://github.com/galaxyproject/galaxy/commit/56874e163086b89d97dae17d59af…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M doc/source/releases/17.05.rst
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
rn improvements
Commit: c8250ae68aea09fb7a1f15109aa5f28027b50966
https://github.com/galaxyproject/galaxy/commit/c8250ae68aea09fb7a1f15109aa5…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
add new options from galaxy.ini diff
Commit: f0570a20a8aab422aa6e3674a5aed98803d7dd89
https://github.com/galaxyproject/galaxy/commit/f0570a20a8aab422aa6e3674a5ae…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
link to proper release-bound sample config
Commit: c459cd66ba7ebb5fbd0bb49557eabca4bd39433b
https://github.com/galaxyproject/galaxy/commit/c459cd66ba7ebb5fbd0bb49557ea…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-17 (Wed, 17 May 2017)
Changed paths:
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
add new datatypes section to the announce
Commit: f9f206ca45e21a72c96ddaa7f0b2f0751ffb7950
https://github.com/galaxyproject/galaxy/commit/f9f206ca45e21a72c96ddaa7f0b2…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
M doc/source/releases/17.05.rst
M doc/source/releases/17.05_announce.rst
Log Message:
-----------
polish release notes, add links to tutorials
Commit: 15556c0a71eb7bbdf33f35158239b4a243441510
https://github.com/galaxyproject/galaxy/commit/15556c0a71eb7bbdf33f35158239…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-05-22 (Mon, 22 May 2017)
Changed paths:
A doc/source/releases/17.05.rst
M doc/source/releases/17.05_announce.rst
A doc/source/releases/17.09_announce.rst
M doc/source/releases/_thanks.rst
M doc/source/releases/index.rst
M doc/source/releases/older_releases.rst
Log Message:
-----------
Merge pull request #4075 from martenson/17.05_release_notes
[17.05] release notes
Compare: https://github.com/galaxyproject/galaxy/compare/f94fa8edbe12...15556c0a71eb