- galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook] 3851a8: Infrastructure for new Galaxy job handler VMs
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 3851a8ed924a2fc746938727a1d4f9788aaa6397 https://github.com/galaxyproject/infrastructure-playbook/commit/3851a8ed924… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: A roles/cvmfs/files/cvmfs_wipecache.centos_7 A taccenv/group_vars/slurmclients.yml M taccenv/inventory M taccenv/playbook.yml A taccenv/secret_group_vars/slurmclients.yml A taccenv/templates/slurm/slurm.conf.j2 Log Message: ----------- Infrastructure for new Galaxy job handler VMs

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[galaxyproject/galaxy] 87d623: Improve startup scripts
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 87d6239c362397824f6d145b56d564dfb3d4b774 https://github.com/galaxyproject/galaxy/commit/87d6239c362397824f6d145b56d5… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M run.sh M scripts/common_startup.sh Log Message: ----------- Improve startup scripts Fix errors reported by shellcheck Commit: f174c8bd4296a7fa74d23af39cb8d0523a69aa4f https://github.com/galaxyproject/galaxy/commit/f174c8bd4296a7fa74d23af39cb8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M run.sh M scripts/common_startup.sh Log Message: ----------- Merge pull request #2765 from nsoranzo/run_sh Improve startup scripts Compare: https://github.com/galaxyproject/galaxy/compare/ac5ce47888e0...f174c8bd4296

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[galaxyproject/infrastructure-playbook] d8dec9: Allow jenkins on slaves to log in to the starforge...
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d8dec916e7b50acf2973e1f5081eac8e305758cf https://github.com/galaxyproject/infrastructure-playbook/commit/d8dec916e7b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M galaxyenv/secret_group_vars/all.yml Log Message: ----------- Allow jenkins on slaves to log in to the starforge builder

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[galaxyproject/galaxy] 893047: Rephrase comment
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 89304762a21c0122659ba08a719813d7790e7a7b https://github.com/galaxyproject/galaxy/commit/89304762a21c0122659ba08a7198… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Rephrase comment Commit: a9e04331de9ba972be9d394da32439fb3054707c https://github.com/galaxyproject/galaxy/commit/a9e04331de9ba972be9d394da324… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M .ci/first_startup.sh Log Message: ----------- Ensure EXIT_CODE is set. Kill Galaxy for local testing Also properly initialise $i and use POSIX syntax Commit: 4b86f6137f132eb640424194766383f39fa18f32 https://github.com/galaxyproject/galaxy/commit/4b86f6137f132eb6404241947663… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M .ci/first_startup.sh M config/galaxy.ini.sample Log Message: ----------- Merge pull request #2773 from nsoranzo/release_16.07_followup_for_2759 [16.07] Small followup for #2759 Commit: ac5ce47888e006279e94d242b8bb55b32edae529 https://github.com/galaxyproject/galaxy/commit/ac5ce47888e006279e94d242b8bb… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M .ci/first_startup.sh M config/galaxy.ini.sample Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/b40e9938d68b...ac5ce47888e0

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[galaxyproject/galaxy] 0bf941: Minimally functional metadata file fetching via th...
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0bf9417fbaf56ff52edfa62458d9f66bada6a449 https://github.com/galaxyproject/galaxy/commit/0bf9417fbaf56ff52edfa62458d9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Minimally functional metadata file fetching via the API Commit: e219dfef95a565bee081ff89cb8110a860722bdd https://github.com/galaxyproject/galaxy/commit/e219dfef95a565bee081ff89cb81… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M lib/galaxy/managers/datasets.py Log Message: ----------- Add download url for metadata file. Commit: f87b08efa0d0d2c127eab88cf31233df3e867ec1 https://github.com/galaxyproject/galaxy/commit/f87b08efa0d0d2c127eab88cf312… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py Log Message: ----------- Consolidate usage of 'valid_chars' in the application. Commit: ce04973b20e3c21a274f8f3560b1d2086d0d410c https://github.com/galaxyproject/galaxy/commit/ce04973b20e3c21a274f8f3560b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M lib/galaxy/managers/datasets.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Rename get_metadata_file route to just metadata_file. Thanks @carlfeberhard. Commit: c9ac723174ae7200230575b7101c91353744e319 https://github.com/galaxyproject/galaxy/commit/c9ac723174ae7200230575b7101c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py Log Message: ----------- Revert genomespace tool changes related to FILENAME_VALID_CHARS Commit: b40e9938d68b3d5d2d818e178ae24e9317ee3728 https://github.com/galaxyproject/galaxy/commit/b40e9938d68b3d5d2d818e178ae2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/neo4j.py M lib/galaxy/managers/datasets.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/datasets.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_importer.py Log Message: ----------- Merge pull request #2741 from dannon/expose_metadata_api Metadata file fetching via the API Compare: https://github.com/galaxyproject/galaxy/compare/49f58dd01771...b40e9938d68b

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[galaxyproject/galaxy] 893047: Rephrase comment
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 89304762a21c0122659ba08a719813d7790e7a7b https://github.com/galaxyproject/galaxy/commit/89304762a21c0122659ba08a7198… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Rephrase comment Commit: a9e04331de9ba972be9d394da32439fb3054707c https://github.com/galaxyproject/galaxy/commit/a9e04331de9ba972be9d394da324… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M .ci/first_startup.sh Log Message: ----------- Ensure EXIT_CODE is set. Kill Galaxy for local testing Also properly initialise $i and use POSIX syntax Commit: 4b86f6137f132eb640424194766383f39fa18f32 https://github.com/galaxyproject/galaxy/commit/4b86f6137f132eb6404241947663… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M .ci/first_startup.sh M config/galaxy.ini.sample Log Message: ----------- Merge pull request #2773 from nsoranzo/release_16.07_followup_for_2759 [16.07] Small followup for #2759 Compare: https://github.com/galaxyproject/galaxy/compare/a7be24e111de...4b86f6137f13

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[galaxyproject/galaxy] e29cf1: Add implicit conversions target extension to hda n...
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e29cf1b7ee669d602995afed43122c288aef785f https://github.com/galaxyproject/galaxy/commit/e29cf1b7ee669d602995afed4312… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-08-04 (Thu, 04 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Add implicit conversions target extension to hda name when listed as selection option Commit: 49f58dd017718ce16ee8314504ba8c52e70dcd48 https://github.com/galaxyproject/galaxy/commit/49f58dd017718ce16ee8314504ba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #2734 from guerler/add_implicit_conversion_info Add implicit conversions target extension to hda name when listed as selection option Compare: https://github.com/galaxyproject/galaxy/compare/4ffbedd844b0...49f58dd01771

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[galaxyproject/galaxy] 9d467d: enable conda_auto_init in sample, adjust wording
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9d467ddd5204deafb3a0dadae7813691e24c7c3c https://github.com/galaxyproject/galaxy/commit/9d467ddd5204deafb3a0dadae781… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/__init__.py Log Message: ----------- enable conda_auto_init in sample, adjust wording Commit: fd3c8753706491e1f6c261d58f42842bfe2757ec https://github.com/galaxyproject/galaxy/commit/fd3c8753706491e1f6c261d58f42… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix string substitution Commit: 730233f48a4ba64c338969036845b0d2aeea5035 https://github.com/galaxyproject/galaxy/commit/730233f48a4ba64c338969036845… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #15 from mvdbeek/fix_string_substitution Fix string substitution Commit: e35c6295694c4065fc880e00fabe43f0c1905748 https://github.com/galaxyproject/galaxy/commit/e35c6295694c4065fc880e00fabe… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M .ci/first_startup.sh Log Message: ----------- Extend startup time Commit: 702891e3efc79fa75ed8e7475e712760355d825c https://github.com/galaxyproject/galaxy/commit/702891e3efc79fa75ed8e7475e71… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M .ci/first_startup.sh Log Message: ----------- Merge pull request #16 from mvdbeek/fix_string_substitution Extend startup time Commit: a7be24e111de2c37c52af580c8a776ee0478ec92 https://github.com/galaxyproject/galaxy/commit/a7be24e111de2c37c52af580c8a7… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M .ci/first_startup.sh M config/galaxy.ini.sample M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #2759 from martenson/conda_config [16.07] install Conda at startup; enable conda_auto_init in sample conf Commit: 4ffbedd844b077b48c09092ed0d406ab73060148 https://github.com/galaxyproject/galaxy/commit/4ffbedd844b077b48c09092ed0d4… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M .ci/first_startup.sh M config/galaxy.ini.sample M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge branch 'release_16.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/13b8067d91f8...4ffbedd844b0

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[galaxyproject/galaxy] 9d467d: enable conda_auto_init in sample, adjust wording
by GitHub 11 Aug '16

11 Aug '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 9d467ddd5204deafb3a0dadae7813691e24c7c3c https://github.com/galaxyproject/galaxy/commit/9d467ddd5204deafb3a0dadae781… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/tools/deps/__init__.py Log Message: ----------- enable conda_auto_init in sample, adjust wording Commit: fd3c8753706491e1f6c261d58f42842bfe2757ec https://github.com/galaxyproject/galaxy/commit/fd3c8753706491e1f6c261d58f42… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix string substitution Commit: 730233f48a4ba64c338969036845b0d2aeea5035 https://github.com/galaxyproject/galaxy/commit/730233f48a4ba64c338969036845… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-09 (Tue, 09 Aug 2016) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #15 from mvdbeek/fix_string_substitution Fix string substitution Commit: e35c6295694c4065fc880e00fabe43f0c1905748 https://github.com/galaxyproject/galaxy/commit/e35c6295694c4065fc880e00fabe… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M .ci/first_startup.sh Log Message: ----------- Extend startup time Commit: 702891e3efc79fa75ed8e7475e712760355d825c https://github.com/galaxyproject/galaxy/commit/702891e3efc79fa75ed8e7475e71… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M .ci/first_startup.sh Log Message: ----------- Merge pull request #16 from mvdbeek/fix_string_substitution Extend startup time Commit: a7be24e111de2c37c52af580c8a776ee0478ec92 https://github.com/galaxyproject/galaxy/commit/a7be24e111de2c37c52af580c8a7… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-08-11 (Thu, 11 Aug 2016) Changed paths: M .ci/first_startup.sh M config/galaxy.ini.sample M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #2759 from martenson/conda_config [16.07] install Conda at startup; enable conda_auto_init in sample conf Compare: https://github.com/galaxyproject/galaxy/compare/9c03d4c16fad...a7be24e111de

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[galaxyproject/galaxy] 185924: Update python-ldap module
by GitHub 10 Aug '16

10 Aug '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 185924e45a5b413c50d3aae7e330677e34376c1b https://github.com/galaxyproject/galaxy/commit/185924e45a5b413c50d3aae7e330… Author: Anthony Bretaudeau <abretaud(a)irisa.fr> Date: 2016-08-05 (Fri, 05 Aug 2016) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Update python-ldap module Updating to the same version as galaxyproject/starforge#97 Commit: 13b8067d91f81d8e638b89aa44ea5ba0a053dbcc https://github.com/galaxyproject/galaxy/commit/13b8067d91f81d8e638b89aa44ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-08-10 (Wed, 10 Aug 2016) Changed paths: M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Merge pull request #2738 from abretaud/patch-1 Update python-ldap module Compare: https://github.com/galaxyproject/galaxy/compare/0052a1c3bba1...13b8067d91f8

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