galaxy-commits May 2017

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[galaxyproject/galaxy] 3332df: [17.05] Fix setting up explicit container resoluti...
by GitHub 16 May '17

16 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3332dfb6717e9bd368341e0bc0aa51d3b53fa861 https://github.com/galaxyproject/galaxy/commit/3332dfb6717e9bd368341e0bc0aa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-04 (Thu, 04 May 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/util/plugin_config.py Log Message: ----------- [17.05] Fix setting up explicit container resolution from a container resolution config file. Commit: f26e358321481500d0f993e0d7b2be9bdd1047b8 https://github.com/galaxyproject/galaxy/commit/f26e358321481500d0f993e0d7b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M lib/galaxy/jobs/rule_helper.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Fix docker_dispatch dynamic destination rule for container resolvers. Commit: a9faa4873e4509a60822019afe3faa4cab3f8336 https://github.com/galaxyproject/galaxy/commit/a9faa4873e4509a60822019afe3f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Do not attempt to use mulled containers if tool requires legacy Galaxy environment. Commit: 04bb1e85cd16a04d6968c8d10755bd5e142831b1 https://github.com/galaxyproject/galaxy/commit/04bb1e85cd16a04d6968c8d10755… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M client/galaxy/scripts/mvc/upload/collection/collection-view.js M static/maps/mvc/upload/collection/collection-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/bundled/login.bundled.js.map M static/scripts/mvc/upload/collection/collection-view.js Log Message: ----------- [17.05] Fix FTP upload of multiple files in collection uploader. Commit: aa1e4cea148ba6a1683d905704191e64ee64a46c https://github.com/galaxyproject/galaxy/commit/aa1e4cea148ba6a1683d90570419… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M client/galaxy/scripts/mvc/upload/collection/collection-view.js M static/maps/mvc/upload/collection/collection-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/bundled/login.bundled.js.map M static/scripts/mvc/upload/collection/collection-view.js Log Message: ----------- Merge pull request #4058 from jmchilton/upload_ftp_fix [17.05] Fix FTP upload of multiple files in collection uploader. Commit: 0bafd683f152f28a193ee39a415018e4a8952767 https://github.com/galaxyproject/galaxy/commit/0bafd683f152f28a193ee39a4150… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-12 (Fri, 12 May 2017) Changed paths: M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/util/plugin_config.py Log Message: ----------- Merge pull request #4020 from jmchilton/fix_explicit_container_resolver_from_config [17.05] Fix setting up explicit container resolution... Commit: 185c76605f2d0da1d8e261b9b3b3a626b8ba6226 https://github.com/galaxyproject/galaxy/commit/185c76605f2d0da1d8e261b9b3b3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-12 (Fri, 12 May 2017) Changed paths: M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge pull request #4033 from jmchilton/dispatch_fix [17.05] Fixes for containerized job executions. Commit: 5e880815ade8756964017a446c6ceaa5cbb72f1a https://github.com/galaxyproject/galaxy/commit/5e880815ade8756964017a446c6c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-05-14 (Sun, 14 May 2017) Changed paths: M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M test/functional/webhooks/trans_object/config/trans_object.yaml Log Message: ----------- Use galaxy.root by default Commit: 88c0635ef70d8054b50dcbfae2788a9cfa7bd973 https://github.com/galaxyproject/galaxy/commit/88c0635ef70d8054b50dcbfae278… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-05-14 (Sun, 14 May 2017) Changed paths: M doc/source/admin/special_topics/webhooks.rst Log Message: ----------- Link has already rotted Commit: 6dd145ed1a97263eb9cca42f26613e28b22f177d https://github.com/galaxyproject/galaxy/commit/6dd145ed1a97263eb9cca42f2661… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-05-14 (Sun, 14 May 2017) Changed paths: M doc/source/admin/special_topics/webhooks.rst Log Message: ----------- Try and document a bit Commit: bd83608a2fb9ac6e8ec0391ab803f569e134d4fa https://github.com/galaxyproject/galaxy/commit/bd83608a2fb9ac6e8ec0391ab803… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M static/maps/mvc/grid/grid-template.js.map M static/scripts/mvc/grid/grid-template.js Log Message: ----------- Fix global grid action events Commit: d3427a1344d165cf6b76b3e2ef4c2113f5ea1916 https://github.com/galaxyproject/galaxy/commit/d3427a1344d165cf6b76b3e2ef4c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: 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/bundled/login.bundled.js.map Log Message: ----------- Rebuild Commit: 6614e94a4953a8352515edded517d060cd6265c7 https://github.com/galaxyproject/galaxy/commit/6614e94a4953a8352515edded517… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M doc/source/admin/special_topics/webhooks.rst M test/functional/webhooks/trans_object/config/trans_object.yaml Log Message: ----------- Merge pull request #4065 from erasche/fix-4064 [17.05] Correct webhooks to use Galaxy.root and be compatible with proxy_prefix Commit: 5eadd4842dcd2aedcc6a496d9bcaecd8048e4ead https://github.com/galaxyproject/galaxy/commit/5eadd4842dcd2aedcc6a496d9bca… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/upload/collection/collection-view.js M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M doc/source/admin/special_topics/webhooks.rst M lib/galaxy/jobs/rule_helper.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/container_resolvers/explicit.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/util/plugin_config.py M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/upload/collection/collection-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.map M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/upload/collection/collection-view.js M test/functional/webhooks/trans_object/config/trans_object.yaml Log Message: ----------- Merge branch 'release_17.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/18349b17b25e...5eadd4842dcd

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[galaxyproject/usegalaxy-playbook] eedfea: Update MTS
by GitHub 16 May '17

16 May '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: eedfea43fdbb2fe0a0e31d1dd077341f632f6b87 https://github.com/galaxyproject/usegalaxy-playbook/commit/eedfea43fdbb2fe0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M env/toolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update MTS

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[galaxyproject/galaxy] e19499: added missing parameter to function ensure_install...
by GitHub 16 May '17

16 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e1949962543f91f917894594140d73a91eb809f2 https://github.com/galaxyproject/galaxy/commit/e1949962543f91f917894594140d… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-05-10 (Wed, 10 May 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- added missing parameter to function ensure_installed Commit: 3895e95eb9adffdaeb0a9fb2051052ab38eca791 https://github.com/galaxyproject/galaxy/commit/3895e95eb9adffdaeb0a9fb20510… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-05-10 (Wed, 10 May 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- ensure_installed is now iterative instead of recursive Commit: 616c8916dd501ed00ee4d26b225abd0a03bc4fe6 https://github.com/galaxyproject/galaxy/commit/616c8916dd501ed00ee4d26b225a… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-05-10 (Wed, 10 May 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- version with no repetition at all Commit: f669b645f0f9fa67c679a7b2a56c88ecb33000c5 https://github.com/galaxyproject/galaxy/commit/f669b645f0f9fa67c679a7b2a56c… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- Set timeout for aquiring lock to 5min Commit: 18349b17b25e3059f5cde5d2440832747561b4d7 https://github.com/galaxyproject/galaxy/commit/18349b17b25e3059f5cde5d24408… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M lib/galaxy/tools/deps/installable.py Log Message: ----------- Merge pull request #4049 from bernt-matthias/dev Do not recurse in ensure_installed() Compare: https://github.com/galaxyproject/galaxy/compare/ff30262cd2b8...18349b17b25e

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[galaxyproject/usegalaxy-playbook] ad99d8: Finish renaming galaxyprojectdotorg -> galaxyproje...
by GitHub 16 May '17

16 May '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ad99d8528a1b4eaa650edf3783ccd81cfa835e42 https://github.com/galaxyproject/usegalaxy-playbook/commit/ad99d8528a1b4eaa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M README.md M env/common/tools.yml M env/common/update_shed.yml M env/main/group_vars/galaxyservers/vars.yml M env/main/group_vars/galaxystagingservers.yml M env/main/group_vars/pulsarservers/vars.yml M env/main/group_vars/webservers.yml M env/test/group_vars/galaxyservers/vars.yml M env/test/group_vars/pulsarservers/vars.yml M env/test/group_vars/webservers/vars.yml M env/testtoolshed/group_vars/toolshedservers/vars.yml M env/toolshed/group_vars/toolshedservers/vars.yml M roles/galaxyproject.galaxy/README.md M roles/galaxyproject.galaxy/defaults/main.yml M roles/galaxyproject.galaxy/handlers/main.yml M roles/galaxyproject.galaxy/tasks/main.yml M roles/galaxyproject.galaxy_toolshed/README.md M roles/galaxyproject.galaxy_toolshed/defaults/main.yml M roles/galaxyproject.galaxy_toolshed/handlers/main.yml M roles/galaxyproject.galaxy_toolshed/tasks/main.yml M roles/galaxyproject.interactive_environments/README.md M roles/galaxyproject.interactive_environments/defaults/main.yml M roles/galaxyproject.interactive_environments/handlers/main.yml M roles/galaxyproject.interactive_environments/tasks/main.yml M roles/galaxyproject.nginx/README.md M roles/galaxyproject.nginx/defaults/main.yml M roles/galaxyproject.nginx/handlers/main.yml M roles/galaxyproject.nginx/tasks/main.yml M roles/galaxyproject.proftpd/README.md M roles/galaxyproject.proftpd/defaults/main.yml M roles/galaxyproject.proftpd/handlers/main.yml M roles/galaxyproject.proftpd/tasks/debian.yml M roles/galaxyproject.proftpd/tasks/galaxy_auth.yml M roles/galaxyproject.proftpd/tasks/main.yml M roles/galaxyproject.proftpd/tasks/redhat.yml M roles/galaxyproject.proftpd/tasks/tls.yml M roles/galaxyproject.proftpd/tests/test.yml M roles/galaxyproject.proftpd/vars/main.yml M roles/galaxyproject.pulsar/README.md M roles/galaxyproject.pulsar/defaults/main.yml M roles/galaxyproject.pulsar/tasks/main.yml Log Message: ----------- Finish renaming galaxyprojectdotorg -> galaxyproject

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[galaxyproject/usegalaxy-playbook] e24a4f: Reorganize Main and MTS for new playbook structure...
by GitHub 16 May '17

16 May '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e24a4fee0cb63c1151a583a38bbabf69afdf0e7c https://github.com/galaxyproject/usegalaxy-playbook/commit/e24a4fee0cb63c11… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-12 (Fri, 12 May 2017) Changed paths: M README.md R common/docker/galaxy-installer/Dockerfile.main R common/docker/galaxy-installer/Dockerfile.test R common/docker/galaxy-installer/run_main.sh R common/docker/galaxy-installer/run_test.sh R common/docker/galaxy-update/Dockerfile R common/docker/galaxy-update/condarc R common/group_vars/all.yml R common/group_vars/all_debian_based_hosts.yml R common/group_vars/redhat_dbservers.yml R common/group_vars/webservers.yml R common/host_vars/galaxy-db-01.tacc.utexas.edu.yml R common/inventory R common/secret_vars/ssl.yml R common/secret_vars/supervisorusers.yml R common/secret_vars/trellocardcreatorservers.yml R common_infrastructure.yml R ec2.yml A env/common/files/galaxy/dynamic_rules/jetstream.py A env/common/files/galaxy/dynamic_rules/single_dynamic_memory.py A env/common/files/galaxy/static/welcome_img/GCC2017EarlyReg.png A env/common/files/galaxy/static/welcome_img/ISMBECCB2017Tutorial.png M env/common/group_vars/toolshedwebservers.yml M env/common/templates/galaxy/static/welcome.html.j2 A env/common/tools.yml M env/common/update_shed.yml A env/main/_inc_config_post_tasks.yml A env/main/_inc_restart.yml A env/main/_inc_snapshot.yml A env/main/_inc_static.yml A env/main/config.yml A env/main/files/galaxy/config/builds.txt A env/main/files/galaxy/config/data_manager_conf.xml A env/main/files/galaxy/config/disposable_email_blacklist.conf A env/main/files/galaxy/config/job_metrics_conf.xml A env/main/files/galaxy/config/job_resource_params_conf.xml A env/main/files/galaxy/config/nagios_tool_conf.xml A env/main/files/galaxy/config/object_store_conf.xml A env/main/files/galaxy/config/pulsar_jetstream.yml A env/main/files/galaxy/config/pulsar_jetstream_actions.yml A env/main/files/galaxy/config/pulsar_stampede_actions.yml A env/main/files/galaxy/config/tool_conf.xml A env/main/files/galaxy/config/tool_data_table_conf.xml A env/main/files/galaxy/config/tool_sheds_conf.xml A env/main/files/galaxy/config/ucsc_build_sites.txt A env/main/files/galaxy/dynamic_rules/bridges_select.py A env/main/files/galaxy/dynamic_rules/multi_dynamic_walltime.py A env/main/files/galaxy/dynamic_rules/nvc_dynamic_memory.py A env/main/files/galaxy/dynamic_rules/reserved.py A env/main/files/galaxy/error A env/main/files/galaxy/galaxy_version.yml A env/main/files/galaxy/nagios/echo_main_bridges.xml A env/main/files/galaxy/nagios/echo_main_cluster.xml A env/main/files/galaxy/nagios/echo_main_jetstream_iu.xml A env/main/files/galaxy/nagios/echo_main_jetstream_tacc.xml A env/main/files/galaxy/nagios/echo_main_stampede.xml A env/main/files/galaxy/nagios/echo_main_w1_handler0.xml A env/main/files/galaxy/nagios/echo_main_w1_handler1.xml A env/main/files/galaxy/nagios/echo_main_w1_handler2.xml A env/main/files/galaxy/nagios/echo_main_w2_handler0.xml A env/main/files/galaxy/nagios/echo_main_w2_handler1.xml A env/main/files/galaxy/nagios/echo_main_w2_handler2.xml A env/main/files/galaxy/static A env/main/files/galaxy/tool_list.yaml A env/main/files/galaxy/var/integrated_tool_panel.xml A env/main/files/galaxy/var/migrated_tools_conf.xml A env/main/files/galaxy/var/shed_data_manager_conf.xml A env/main/files/galaxy/var/shed_tool_conf.xml A env/main/files/galaxy/var/shed_tool_data_table_conf.xml A env/main/files/pulsar A env/main/files/ssl A env/main/group_vars/all.yml A env/main/group_vars/dbservers/vars.yml A env/main/group_vars/dbservers/vault.yml A env/main/group_vars/ftpservers/vars.yml A env/main/group_vars/ftpservers/vault.yml A env/main/group_vars/galaxyjobservers.yml A env/main/group_vars/galaxyservers/vars.yml A env/main/group_vars/galaxyservers/vault.yml A env/main/group_vars/galaxystagingservers.yml A env/main/group_vars/galaxywebservers.yml A env/main/group_vars/pulsarservers/vars.yml A env/main/group_vars/pulsarservers/vault.yml A env/main/group_vars/sslservers A env/main/group_vars/supervisorservers/vars.yml A env/main/group_vars/supervisorservers/vault.yml A env/main/group_vars/webservers.yml A env/main/host_vars/br005.bridges.psc.edu.yml A env/main/host_vars/galaxy-web-03.tacc.utexas.edu.yml A env/main/host_vars/galaxy-web-04.tacc.utexas.edu.yml A env/main/host_vars/galaxy-web-05.tacc.utexas.edu.yml A env/main/host_vars/jetstream-iu0.galaxyproject.org.yml A env/main/host_vars/jetstream-tacc0.galaxyproject.org.yml A env/main/host_vars/login5.stampede.tacc.utexas.edu.yml A env/main/inventory A env/main/pulsar.yml A env/main/restart.yml A env/main/snapshot.yml A env/main/stack.yml A env/main/static.yml A env/main/templates/galaxy/config/build_sites.yml.j2 A env/main/templates/galaxy/config/galaxy.ini.j2 A env/main/templates/galaxy/config/job_conf.xml.j2 A env/main/templates/galaxy/config/reports.ini.j2 A env/main/templates/galaxy/config/uwsgi.ini.j2 A env/main/templates/galaxy/static A env/main/templates/nginx/galaxy_bx.j2 A env/main/templates/nginx/usegalaxy.j2 A env/main/templates/nginx/usegalaxy_rewrites.conf.j2 A env/main/templates/nginx/usegalaxy_staging.j2 A env/main/templates/pulsar A env/main/templates/supervisor A env/main/update.yml R env/test/files/galaxy/dynamic_rules/jetstream.py R env/test/files/galaxy/dynamic_rules/single_dynamic_memory.py M env/test/group_vars/galaxyservers/vars.yml M env/test/group_vars/pulsarservers/vars.yml M env/test/inventory M env/test/templates/galaxy/config/galaxy.ini.j2 M env/test/templates/nginx/galaxy_test.j2 M env/testtoolshed/group_vars/toolshedservers/vars.yml A env/toolshed/files/ssl A env/toolshed/group_vars/sslservers A env/toolshed/group_vars/toolsheddbservers.yml A env/toolshed/group_vars/toolshedservers/common_vars.yml A env/toolshed/group_vars/toolshedservers/common_vault.yml A env/toolshed/group_vars/toolshedservers/vars.yml A env/toolshed/group_vars/toolshedservers/vault.yml A env/toolshed/group_vars/toolshedwebservers.yml A env/toolshed/inventory A env/toolshed/stack.yml A env/toolshed/templates/nginx/toolshed.j2 A env/toolshed/templates/supervisor/toolshed.j2 A env/toolshed/update.yml R files/galaxy/common/config/disposable_email_blacklist.conf R files/galaxy/common/config/pulsar_jetstream_actions.yml R files/galaxy/common/dynamic_rules/bridges_select.py R files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py R files/galaxy/common/dynamic_rules/nvc_dynamic_memory.py R files/galaxy/common/dynamic_rules/reserved.py R files/galaxy/common/error/413/index.html R files/galaxy/common/error/502/index.shtml R files/galaxy/common/error/content_bg.png R files/galaxy/common/error/error_message_icon.png R files/galaxy/common/error/masthead_bg.png R files/galaxy/common/static/terms.html R 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templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 R templates/galaxy/usegalaxy.org/config/reports.ini.j2 R templates/galaxy/usegalaxy.org/config/uwsgi.ini.j2 R templates/galaxy/usegalaxy.org/static R templates/nginx/galaxy_bx.j2 R templates/nginx/usegalaxy.j2 R templates/nginx/usegalaxy_rewrites.conf.j2 R templates/nginx/usegalaxy_staging.j2 R templates/supervisor/galaxy.j2 R templates/supervisor/galaxy_group.j2 R templates/supervisor/galaxy_handler.j2 R templates/supervisor/galaxy_impersonate.j2 R templates/supervisor/galaxy_reports.j2 R tools.yml R toolshed_infrastructure.yml Log Message: ----------- Reorganize Main and MTS for new playbook structure. Not deployed yet.

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[galaxyproject/galaxy] 9d48c3: Add some test tools for collection job failures.
by GitHub 16 May '17

16 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9d48c34a095035bed26b724b767b7ee284b0dd69 https://github.com/galaxyproject/galaxy/commit/9d48c34a095035bed26b724b767b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-09 (Tue, 09 May 2017) Changed paths: A test/functional/tools/collection_creates_dynamic_nested_fail.xml A test/functional/tools/collection_creates_list_fail.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add some test tools for collection job failures. xref #4032 These at least verify that jobs are properly failing whether they use dynamic dataset collection or not. In the case of pre-determinable list structures - they properly go red and expose the problems to the user (try running test/functional/tools/collection_creates_list_fail.xml manually). In the case of dynamic dataset collections - this does not occur though - all the resulting datasets are indeed green. Commit: 96a219840c54b879838d4cf6c45dc96f76bfce54 https://github.com/galaxyproject/galaxy/commit/96a219840c54b879838d4cf6c45d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M test/functional/tools/collection_creates_list_fail.xml Log Message: ----------- add indentation to for cycle content Commit: ff30262cd2b8a851e31599b421f7a3acfd3f87d1 https://github.com/galaxyproject/galaxy/commit/ff30262cd2b8a851e31599b421f7… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: A test/functional/tools/collection_creates_dynamic_nested_fail.xml A test/functional/tools/collection_creates_list_fail.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #4044 from jmchilton/collection_job_failure_tests Add some test tools for collection job failures. Compare: https://github.com/galaxyproject/galaxy/compare/6218e99fee2a...ff30262cd2b8

1 0

[galaxyproject/galaxy] a00f7f: Insert admin app, redirect controller
by GitHub 16 May '17

16 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a00f7f65136418a55b0b6cb4aeec9553b186e30c https://github.com/galaxyproject/galaxy/commit/a00f7f65136418a55b0b6cb4aeec… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: A client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/apps/history-panel.js A client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/apps/panels/history-panel.js A client/galaxy/scripts/apps/panels/tool-panel.js R client/galaxy/scripts/apps/tool-panel.js M client/webpack.config.js M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin.py 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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Insert admin app, redirect controller Commit: 6d19f595964403a9f6e65368ff644bafed6fc34c https://github.com/galaxyproject/galaxy/commit/6d19f595964403a9f6e65368ff64… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Prepare model structure for categories Commit: ee676aef4251cca9f7edd9bcd18d059b0857fbbc https://github.com/galaxyproject/galaxy/commit/ee676aef4251cca9f7edd9bcd18d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add tool shed related menu items Commit: dcf177f2123b7bcb3996b1b2be0ce18b939afad8 https://github.com/galaxyproject/galaxy/commit/dcf177f2123b7bcb3996b1b2be0c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add all admin panel links Commit: d131e1bd6cab451e97cf754c19eb1a19825a6dd8 https://github.com/galaxyproject/galaxy/commit/d131e1bd6cab451e97cf754c19eb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Convert definitions into collection Commit: b92099611c2199d55b6397a27f1bd93db975b02f https://github.com/galaxyproject/galaxy/commit/b92099611c2199d55b6397a27f1b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Remove debug statement Commit: 25eb8850971520b367a272166521a6fa56e7b44c https://github.com/galaxyproject/galaxy/commit/25eb8850971520b367a272166521… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/managers/configuration.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add additional properties Commit: e64c195ffc1b43c79baefcab42b9ae6906c0c804 https://github.com/galaxyproject/galaxy/commit/e64c195ffc1b43c79baefcab42b9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Load initial page Commit: 7de2b6b6ed6676b5cbe105e2970512506c89f77a https://github.com/galaxyproject/galaxy/commit/7de2b6b6ed6676b5cbe105e29705… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/webapps/galaxy/controllers/admin.py M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add conditions and additional attributes Commit: 2c3b4993cddea5f3a5d2e78a1e9bd6c4cc796283 https://github.com/galaxyproject/galaxy/commit/2c3b4993cddea5f3a5d2e78a1e9b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: R templates/webapps/galaxy/admin/index.mako Log Message: ----------- Remove admin index mako Commit: 0423dbc890fdfd67f6182c0ce825f43464e983f7 https://github.com/galaxyproject/galaxy/commit/0423dbc890fdfd67f6182c0ce825… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: 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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Pack scripts Commit: f01c20fc7de459f787cc9ef45e8812b18c3d7ff2 https://github.com/galaxyproject/galaxy/commit/f01c20fc7de459f787cc9ef45e88… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/style/less/ui.less 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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/style/blue/base.css Log Message: ----------- Fix style Commit: 866ddb4bcce355a36237762a34e68af863e87829 https://github.com/galaxyproject/galaxy/commit/866ddb4bcce355a36237762a34e6… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: 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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map Log Message: ----------- Repack scripts Commit: 8ab70efd00fb531659bad13066c79b599fb368f0 https://github.com/galaxyproject/galaxy/commit/8ab70efd00fb531659bad13066c7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Fix style Commit: b51da23c10c4673ba729ace4e2fad2afb49aa200 https://github.com/galaxyproject/galaxy/commit/b51da23c10c4673ba729ace4e2fa… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M client/galaxy/style/less/ui.less M static/style/blue/base.css Log Message: ----------- Remove unused css attribute Commit: 2399df09cc20033ceb1e25c80ca257e4746f61da https://github.com/galaxyproject/galaxy/commit/2399df09cc20033ceb1e25c80ca2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/layout/panel.js M static/maps/layout/panel.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Remove unused parts, comments Commit: fe59e3aeb477a1a441287c49af918abea0aa5791 https://github.com/galaxyproject/galaxy/commit/fe59e3aeb477a1a441287c49af91… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M client/galaxy/style/less/ui.less M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css Log Message: ----------- Fix overlapping css tags Commit: d2f9cee31b8e6c9ca729e6e27575285d8a8e7c76 https://github.com/galaxyproject/galaxy/commit/d2f9cee31b8e6c9ca729e6e27575… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove unused import Commit: b2b84a8e62ecd6365c0f3cfdaa5df013bd5aac59 https://github.com/galaxyproject/galaxy/commit/b2b84a8e62ecd6365c0f3cfdaa5d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M client/galaxy/scripts/mvc/tours.js M config/plugins/tours/core.history.yaml M lib/galaxy/managers/datasets.py M static/maps/mvc/tours.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tours.js M templates/show_params.mako Log Message: ----------- Merge branch 'dev' into admin_app Commit: 5ece2f0a53c0721a39d49991dcdcd24f84ca3a61 https://github.com/galaxyproject/galaxy/commit/5ece2f0a53c0721a39d49991dcdc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M client/galaxy/scripts/apps/admin.js Log Message: ----------- Remove spaces Commit: a476db0253d601360b6d6db321c806586f52a507 https://github.com/galaxyproject/galaxy/commit/a476db0253d601360b6d6db321c8… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/panels/admin-panel.js M lib/galaxy/web/base/controller.py M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add active view attribute, add monitoring ids Commit: 220fff9e9bf6fb88977f0f2d8a08436d264b17ef https://github.com/galaxyproject/galaxy/commit/220fff9e9bf6fb88977f0f2d8a08… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M client/galaxy/scripts/apps/panels/admin-panel.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Add localization support for admin panel labels Commit: fc69a85100bdfafe3f3106f7941205aaba64c01d https://github.com/galaxyproject/galaxy/commit/fc69a85100bdfafe3f3106f79412… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M client/galaxy/scripts/nls/locale.js M static/maps/nls/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/locale.js Log Message: ----------- add new translatable strings to the locale file Commit: 6218e99fee2a813376855d12b1d9849c2d280ef8 https://github.com/galaxyproject/galaxy/commit/6218e99fee2a813376855d12b1d9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: A client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/apps/history-panel.js A client/galaxy/scripts/apps/panels/admin-panel.js A client/galaxy/scripts/apps/panels/history-panel.js A client/galaxy/scripts/apps/panels/tool-panel.js R client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/layout/panel.js M client/galaxy/scripts/nls/locale.js M client/galaxy/style/less/ui.less M client/webpack.config.js M lib/galaxy/managers/configuration.py M lib/galaxy/web/base/controller.py M lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/admin.py M static/maps/layout/panel.js.map M static/maps/mvc/tours.js.map M static/maps/nls/locale.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/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/tours.js M static/scripts/nls/locale.js M static/style/blue/base.css R templates/webapps/galaxy/admin/index.mako Log Message: ----------- Merge pull request #4067 from guerler/admin_app Add admin app Compare: https://github.com/galaxyproject/galaxy/compare/3da8eb0d1384...6218e99fee2a

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[galaxyproject/galaxy] 5e8808: Use galaxy.root by default
by GitHub 15 May '17

15 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 5e880815ade8756964017a446c6ceaa5cbb72f1a https://github.com/galaxyproject/galaxy/commit/5e880815ade8756964017a446c6c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-05-14 (Sun, 14 May 2017) Changed paths: M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M test/functional/webhooks/trans_object/config/trans_object.yaml Log Message: ----------- Use galaxy.root by default Commit: 88c0635ef70d8054b50dcbfae2788a9cfa7bd973 https://github.com/galaxyproject/galaxy/commit/88c0635ef70d8054b50dcbfae278… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-05-14 (Sun, 14 May 2017) Changed paths: M doc/source/admin/special_topics/webhooks.rst Log Message: ----------- Link has already rotted Commit: 6dd145ed1a97263eb9cca42f26613e28b22f177d https://github.com/galaxyproject/galaxy/commit/6dd145ed1a97263eb9cca42f2661… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-05-14 (Sun, 14 May 2017) Changed paths: M doc/source/admin/special_topics/webhooks.rst Log Message: ----------- Try and document a bit Commit: 6614e94a4953a8352515edded517d060cd6265c7 https://github.com/galaxyproject/galaxy/commit/6614e94a4953a8352515edded517… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M config/plugins/webhooks/demo/search/config/searchover.yaml M config/plugins/webhooks/demo/tool_list/config/tool_list.yml M doc/source/admin/special_topics/webhooks.rst M test/functional/webhooks/trans_object/config/trans_object.yaml Log Message: ----------- Merge pull request #4065 from erasche/fix-4064 [17.05] Correct webhooks to use Galaxy.root and be compatible with proxy_prefix Compare: https://github.com/galaxyproject/galaxy/compare/d3427a1344d1...6614e94a4953

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[galaxyproject/galaxy] bd8360: Fix global grid action events
by GitHub 15 May '17

15 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: bd83608a2fb9ac6e8ec0391ab803f569e134d4fa https://github.com/galaxyproject/galaxy/commit/bd83608a2fb9ac6e8ec0391ab803… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M static/maps/mvc/grid/grid-template.js.map M static/scripts/mvc/grid/grid-template.js Log Message: ----------- Fix global grid action events Commit: d3427a1344d165cf6b76b3e2ef4c2113f5ea1916 https://github.com/galaxyproject/galaxy/commit/d3427a1344d165cf6b76b3e2ef4c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: 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/bundled/login.bundled.js.map Log Message: ----------- Rebuild Compare: https://github.com/galaxyproject/galaxy/compare/185c76605f2d...d3427a1344d1

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[galaxyproject/galaxy] 9df2b4: Don't try to get the file name of purged files
by GitHub 15 May '17

15 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9df2b4b8f7601a5682c46ee8bb223903f884be5c https://github.com/galaxyproject/galaxy/commit/9df2b4b8f7601a5682c46ee8bb22… Author: dpryan79 <dpryan79(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M lib/galaxy/managers/datasets.py M templates/show_params.mako Log Message: ----------- Don't try to get the file name of purged files Commit: 3da8eb0d1384bdc95f84b1894f941c16a26de164 https://github.com/galaxyproject/galaxy/commit/3da8eb0d1384bdc95f84b1894f94… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-15 (Mon, 15 May 2017) Changed paths: M lib/galaxy/managers/datasets.py M templates/show_params.mako Log Message: ----------- Merge pull request #4066 from dpryan79/handle_purged_files Don't try to get the file name of purged files Compare: https://github.com/galaxyproject/galaxy/compare/3a9df376975d...3da8eb0d1384

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