galaxy-commits March 2016

galaxy-commits@lists.galaxyproject.org

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208 discussions

[galaxyproject/usegalaxy-playbook] c8444d: Undo change to Main's version
by GitHub 21 Mar '16

21 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c8444d60798041b93fc3b451ef89973ff9039db1 https://github.com/galaxyproject/usegalaxy-playbook/commit/c8444d60798041b9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M production/group_vars/all.yml Log Message: ----------- Undo change to Main's version Commit: 19f8ce2bcef0e7e7a9f108d0bd98112e8733a6fb https://github.com/galaxyproject/usegalaxy-playbook/commit/19f8ce2bcef0e7e7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Update the location of libdrmaa.so on Test and Main Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/5a4d97470ad4...…

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[galaxyproject/usegalaxy-playbook] 3f3a83: Update main's tools.
by GitHub 21 Mar '16

21 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 3f3a83376728469a8274d6f2c82e2a5400aed23f https://github.com/galaxyproject/usegalaxy-playbook/commit/3f3a83376728469a… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml M production/group_vars/all.yml Log Message: ----------- Update main's tools. Commit: 3c83d6def60c4352d1c6b61bbd4822853376ee83 https://github.com/galaxyproject/usegalaxy-playbook/commit/3c83d6def60c4352… Author: Dave Bouvier <dabe(a)bx.psu.edu> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_data_manager_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Update main, adding deeptools and gemini. Commit: 271f965cfd1e61a501d5773d27db29c8b61bdb36 https://github.com/galaxyproject/usegalaxy-playbook/commit/271f965cfd1e61a5… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: A files/galaxy/common/static/welcome_img/GCC2016OralAbstracts.png A files/galaxy/common/static/welcome_img/GCC2016ScholarshipsInternational.png A files/galaxy/common/static/welcome_img/RDF2GraphGalaxy.png M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_data_manager_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M galaxy.yml M galaxy_configs.yml M production/files/interactive_environments/plugins/.ansible_ie_role_current_version M production/files/interactive_environments/proxy/.ansible_ie_role_current_version M production/group_vars/galaxyservers.yml M production/group_vars/toolshedservers.yml M production/host_vars/galaxy-web-01.tacc.utexas.edu.yml M production/secret_vars/galaxyservers.yml M production/secret_vars/toolshedservers.yml M roles/galaxyprojectdotorg.galaxy/README.md M roles/galaxyprojectdotorg.galaxy/defaults/main.yml M roles/galaxyprojectdotorg.galaxy/meta/.galaxy_install_info M roles/galaxyprojectdotorg.galaxy/tasks/dependencies.yml M roles/galaxyprojectdotorg.galaxy/tasks/main.yml R roles/supervisor/defaults/main.yml R roles/supervisor/handlers/main.yml R roles/supervisor/tasks/main.yml R roles/supervisor/templates/centos.init.j2 R roles/supervisor/templates/debian.init.j2 R roles/supervisor/templates/redhat.init.j2 R roles/supervisor/templates/supervisord.conf.j2 R roles/supervisor/templates/systemd.init.j2 R roles/supervisor/templates/ubuntu.init.j2 M stage/group_vars/all.yml M stage/group_vars/galaxyservers.yml M stage/group_vars/toolshedservers.yml M stage/secret_vars/galaxyservers.yml M stage/secret_vars/toolshedservers.yml M templates/galaxy/common/static/welcome.html.j2 M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 R templates/supervisor/galaxy.conf.j2 A templates/supervisor/galaxy.j2 A templates/supervisor/galaxy_datamanager.j2 R templates/supervisor/galaxy_group.conf.j2 A templates/supervisor/galaxy_group.j2 R templates/supervisor/galaxy_impersonate.conf.j2 A templates/supervisor/galaxy_impersonate.j2 R templates/supervisor/galaxy_installer.conf.j2 A templates/supervisor/galaxy_installer.j2 R templates/supervisor/galaxy_reports.conf.j2 A templates/supervisor/galaxy_reports.j2 R templates/supervisor/testtoolshed.conf.j2 A templates/supervisor/testtoolshed.j2 R templates/supervisor/toolshed.conf.j2 A templates/supervisor/toolshed.j2 Log Message: ----------- Merge remote-tracking branch. Commit: 5a4d97470ad45725e9c2892eac71d63cdf9f1600 https://github.com/galaxyproject/usegalaxy-playbook/commit/5a4d97470ad45725… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_data_manager_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml M production/group_vars/all.yml Log Message: ----------- Merge pull request #17 from davebx/update_main Update main's tools Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/5b12e0782f98...…

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[galaxyproject/galaxy] 2efd9c: Fix #1721.
by GitHub 21 Mar '16

21 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 2efd9c2687d2ca818520249cdb3484e781659069 https://github.com/galaxyproject/galaxy/commit/2efd9c2687d2ca818520249cdb34… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix #1721. TODO: write test... Commit: 377ccbe23b717f9c8cb0d571de9f0d6da08a1ee8 https://github.com/galaxyproject/galaxy/commit/377ccbe23b717f9c8cb0d571de9f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1967 from jmchilton/fix_optional_numeric_params [16.01] Fix #1721. Compare: https://github.com/galaxyproject/galaxy/compare/5f5f0af5cd5e...377ccbe23b71

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[galaxyproject/galaxy] e4e92e: Fix typo: send-->sent
by GitHub 21 Mar '16

21 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e4e92e55ab1df5d0e2847d19e3381cc2cd5db37b https://github.com/galaxyproject/galaxy/commit/e4e92e55ab1df5d0e2847d19e338… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js 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/tool/tool-form-workflow.js Log Message: ----------- Fix typo: send-->sent Commit: 67e6ced2118b41627a51d5c9dbd0f4e303e88158 https://github.com/galaxyproject/galaxy/commit/67e6ced2118b41627a51d5c9dbd0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-workflow.js 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/tool/tool-form-workflow.js Log Message: ----------- Merge pull request #1965 from blankenberg/typo-dev Fix typo: send-->sent Compare: https://github.com/galaxyproject/galaxy/compare/162f6d49af20...67e6ced2118b

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[galaxyproject/galaxy] 5df783: Do not use "is not" to compare strings.
by GitHub 21 Mar '16

21 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5df78304246243488629838fad6635b6211036b0 https://github.com/galaxyproject/galaxy/commit/5df78304246243488629838fad66… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Do not use "is not" to compare strings. http://stackoverflow.com/questions/1504717/why-does-comparing-strings-in-py… Commit: 162f6d49af20900b18940845bcf65de5960244f2 https://github.com/galaxyproject/galaxy/commit/162f6d49af20900b18940845bcf6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1963 from jmchilton/str_comp Do not use "is not" to compare strings. Compare: https://github.com/galaxyproject/galaxy/compare/058c644d8853...162f6d49af20

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[galaxyproject/galaxy] d5c52c: Fixing error in run.sh script
by GitHub 21 Mar '16

21 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d5c52cadfd0007338d4c89f505ff272e9acae9f9 https://github.com/galaxyproject/galaxy/commit/d5c52cadfd0007338d4c89f505ff… Author: Kyle Ellrott <kellrott(a)gmail.com> Date: 2016-03-20 (Sun, 20 Mar 2016) Changed paths: M run.sh Log Message: ----------- Fixing error in run.sh script Commit: 058c644d8853232ee12dbbc8edce3cdf2ab595b8 https://github.com/galaxyproject/galaxy/commit/058c644d8853232ee12dbbc8edce… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M run.sh Log Message: ----------- Merge pull request #1954 from kellrott/dev Fixing error in run.sh script Compare: https://github.com/galaxyproject/galaxy/compare/c0f5ae88a711...058c644d8853

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[galaxyproject/galaxy] 50e5b0: libraries: also show folder items paginator at the...
by GitHub 21 Mar '16

21 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 50e5b08d7c375202aa39a69453d7eb6271078adf https://github.com/galaxyproject/galaxy/commit/50e5b08d7c375202aa39a69453d7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/less/library.less M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.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/library/library-foldertoolbar-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- libraries: also show folder items paginator at the bottom of the items Commit: c0f5ae88a7110d65946c780e68d5116e8e6a5e95 https://github.com/galaxyproject/galaxy/commit/c0f5ae88a7110d65946c780e68d5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-folder-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M client/galaxy/style/less/library.less M static/maps/mvc/library/library-folder-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.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/library/library-foldertoolbar-view.js M static/style/blue/base.css M static/style/blue/library.css Log Message: ----------- Merge pull request #1962 from martenson/better-library-paging libraries: also show folder items paginator at the bottom of the items Compare: https://github.com/galaxyproject/galaxy/compare/5ead8a95d11a...c0f5ae88a711

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[galaxyproject/galaxy] 1e9b0e: add molecule datatypes, like PDB and some cheminfo...
by GitHub 21 Mar '16

21 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1e9b0e6dbd89f40660ce00198d88803837239e48 https://github.com/galaxyproject/galaxy/commit/1e9b0e6dbd89f40660ce00198d88… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2016-03-20 (Sun, 20 Mar 2016) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml A lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml A lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml A lib/galaxy/datatypes/converters/cml_to_smi_converter.xml A lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml A lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml A lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml A lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml A lib/galaxy/datatypes/converters/mol_to_smi_converter.xml A lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml A lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml A lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml A lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml A lib/galaxy/datatypes/converters/smi_to_cml_converter.xml A lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol_converter.xml A lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/smi_to_smi_converter.xml A lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/5e5z.pdb A lib/galaxy/datatypes/test/drugbank_drugs.cml A lib/galaxy/datatypes/test/drugbank_drugs.inchi A lib/galaxy/datatypes/test/drugbank_drugs.mol2 A lib/galaxy/datatypes/test/drugbank_drugs.sdf A lib/galaxy/datatypes/test/drugbank_drugs.smi A lib/galaxy/datatypes/test/q.fps Log Message: ----------- add molecule datatypes, like PDB and some cheminformatic ones Commit: c8cb4280c18a6a2dcbc3c86395d19a8e511c7a60 https://github.com/galaxyproject/galaxy/commit/c8cb4280c18a6a2dcbc3c86395d1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Fix datatype sniff test to use sample and revert molecule registry hacks. Commit: df719c83b67a67a8f6d574cf4a6232f627341121 https://github.com/galaxyproject/galaxy/commit/df719c83b67a67a8f6d574cf4a62… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Merge pull request #9 from jmchilton/chemical_datatypes Fix datatype sniff test to use sample and revert molecule registry ha… Commit: 5ead8a95d11a18e8155ccf40bfd46511909ece80 https://github.com/galaxyproject/galaxy/commit/5ead8a95d11a18e8155ccf40bfd4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/cml_to_inchi_converter.xml A lib/galaxy/datatypes/converters/cml_to_mol2_converter.xml A lib/galaxy/datatypes/converters/cml_to_sdf_converter.xml A lib/galaxy/datatypes/converters/cml_to_smi_converter.xml A lib/galaxy/datatypes/converters/inchi_to_cml_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/inchi_to_mol_converter.xml A lib/galaxy/datatypes/converters/inchi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/inchi_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol2_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol2_to_mol_converter.xml A lib/galaxy/datatypes/converters/mol2_to_sdf_converter.xml A lib/galaxy/datatypes/converters/mol2_to_smi_converter.xml A lib/galaxy/datatypes/converters/mol_to_cml_converter.xml A lib/galaxy/datatypes/converters/mol_to_inchi_converter.xml A lib/galaxy/datatypes/converters/mol_to_mol2_converter.xml A lib/galaxy/datatypes/converters/mol_to_smi_converter.xml A lib/galaxy/datatypes/converters/sdf_to_cml_converter.xml A lib/galaxy/datatypes/converters/sdf_to_inchi_converter.xml A lib/galaxy/datatypes/converters/sdf_to_mol2_converter.xml A lib/galaxy/datatypes/converters/sdf_to_smi_converter.xml A lib/galaxy/datatypes/converters/smi_to_cml_converter.xml A lib/galaxy/datatypes/converters/smi_to_inchi_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol2_converter.xml A lib/galaxy/datatypes/converters/smi_to_mol_converter.xml A lib/galaxy/datatypes/converters/smi_to_sdf_converter.xml A lib/galaxy/datatypes/converters/smi_to_smi_converter.xml A lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/test/5e5z.pdb A lib/galaxy/datatypes/test/drugbank_drugs.cml A lib/galaxy/datatypes/test/drugbank_drugs.inchi A lib/galaxy/datatypes/test/drugbank_drugs.mol2 A lib/galaxy/datatypes/test/drugbank_drugs.sdf A lib/galaxy/datatypes/test/drugbank_drugs.smi A lib/galaxy/datatypes/test/q.fps Log Message: ----------- Merge pull request #1941 from bgruening/chemical_datatypes add chemical datatypes Compare: https://github.com/galaxyproject/galaxy/compare/b71ab68862d7...5ead8a95d11a

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[galaxyproject/galaxy] d3c6df: Improve logging and retry for another TS test...
by GitHub 21 Mar '16

21 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d3c6dfc2d83dd6f5d41ea524667fb753f95b3ee5 https://github.com/galaxyproject/galaxy/commit/d3c6dfc2d83dd6f5d41ea524667f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M test/tool_shed/functional/test_0490_export_import_repositories.py Log Message: ----------- Improve logging and retry for another TS test... ... I thought there was only one transiently failing tool shed test but there appears to be two. Commit: b71ab68862d71ea3df0cd0326425e79ecd9ed10b https://github.com/galaxyproject/galaxy/commit/b71ab68862d71ea3df0cd0326425… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M test/tool_shed/functional/test_0490_export_import_repositories.py Log Message: ----------- Merge pull request #1961 from jmchilton/more_aggressive_retry Improve logging and retry for another TS test... Compare: https://github.com/galaxyproject/galaxy/compare/901cab12cb12...b71ab68862d7

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[galaxyproject/usegalaxy-playbook] 5b12e0: update Test
by GitHub 21 Mar '16

21 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5b12e0782f98239eda31f2403f7e99f8d3f13dad https://github.com/galaxyproject/usegalaxy-playbook/commit/5b12e0782f98239e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-21 (Mon, 21 Mar 2016) Changed paths: M stage/group_vars/all.yml Log Message: ----------- update Test

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galaxy-commits March 2016