galaxy-commits May 2017

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[galaxyproject/usegalaxy-playbook] fbd3d5: Rename roles due to name change in Ansible Galaxy
by GitHub 11 May '17

11 May '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fbd3d5ccb119814c8a42dc6e10d2007ac203da10 https://github.com/galaxyproject/usegalaxy-playbook/commit/fbd3d5ccb119814c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M env/common/config.yml M env/common/pulsar.yml M env/common/stack.yml M env/common/update.yml A roles/galaxyproject.galaxy/README.md A roles/galaxyproject.galaxy/defaults/main.yml A roles/galaxyproject.galaxy/files/errordocs/content_bg.png A roles/galaxyproject.galaxy/files/errordocs/error_message_icon.png A roles/galaxyproject.galaxy/files/errordocs/masthead_bg.png A roles/galaxyproject.galaxy/files/makepyc.py A roles/galaxyproject.galaxy/handlers/main.yml A roles/galaxyproject.galaxy/meta/.galaxy_install_info A roles/galaxyproject.galaxy/meta/main.yml A roles/galaxyproject.galaxy/tasks/clone.yml A roles/galaxyproject.galaxy/tasks/database.yml A roles/galaxyproject.galaxy/tasks/dependencies.yml A roles/galaxyproject.galaxy/tasks/download.yml A roles/galaxyproject.galaxy/tasks/errordocs.yml A roles/galaxyproject.galaxy/tasks/main.yml A roles/galaxyproject.galaxy/tasks/mutable_setup.yml A roles/galaxyproject.galaxy/tasks/static_setup.yml A roles/galaxyproject.galaxy/tasks/virtualenv.yml A roles/galaxyproject.galaxy/templates/errordocs/413/index.html.j2 A roles/galaxyproject.galaxy/templates/errordocs/502/index.shtml.j2 A roles/galaxyproject.galaxy/templates/galaxy.ini.j2 A roles/galaxyproject.galaxy_toolshed/README.md A roles/galaxyproject.galaxy_toolshed/defaults/main.yml A roles/galaxyproject.galaxy_toolshed/handlers/main.yml A roles/galaxyproject.galaxy_toolshed/meta/.galaxy_install_info A roles/galaxyproject.galaxy_toolshed/meta/main.yml A roles/galaxyproject.galaxy_toolshed/tasks/database.yml A roles/galaxyproject.galaxy_toolshed/tasks/main.yml A roles/galaxyproject.galaxy_toolshed/tasks/static_setup.yml A roles/galaxyproject.galaxy_toolshed/templates/tool_shed.ini.j2 A roles/galaxyproject.galaxy_toolshed/templates/user_info.xml.j2 A roles/galaxyproject.nginx/README.md A roles/galaxyproject.nginx/defaults/main.yml A roles/galaxyproject.nginx/handlers/main.yml A roles/galaxyproject.nginx/meta/.galaxy_install_info A roles/galaxyproject.nginx/meta/main.yml A roles/galaxyproject.nginx/tasks/apt.yml A roles/galaxyproject.nginx/tasks/main.yml A roles/galaxyproject.nginx/tasks/pkgin.yml A roles/galaxyproject.nginx/tasks/yum.yml A roles/galaxyproject.nginx/templates/epel-nginx.conf.j2 A roles/galaxyproject.nginx/templates/http_options.conf.j2 A roles/galaxyproject.nginx/templates/pkgin-nginx.conf.j2 A roles/galaxyproject.nginx/templates/ssl.conf.j2 A roles/galaxyproject.nginx/templates/supervisord.conf.j2 A roles/galaxyproject.nginx/vars/pkgin.yml A roles/galaxyproject.postgresql/.gitignore A roles/galaxyproject.postgresql/README.md A roles/galaxyproject.postgresql/defaults/main.yml A roles/galaxyproject.postgresql/files/get_repo_rpm_release.py A roles/galaxyproject.postgresql/handlers/main.yml A roles/galaxyproject.postgresql/meta/.galaxy_install_info A roles/galaxyproject.postgresql/meta/main.yml A roles/galaxyproject.postgresql/tasks/backup.yml A roles/galaxyproject.postgresql/tasks/debian.yml A roles/galaxyproject.postgresql/tasks/main.yml A roles/galaxyproject.postgresql/tasks/redhat.yml A roles/galaxyproject.postgresql/templates/20ansible_backup.conf.j2 A roles/galaxyproject.postgresql/templates/25ansible_postgresql.conf.j2 A roles/galaxyproject.postgresql/templates/archive_wal.sh.j2 A roles/galaxyproject.postgresql/templates/backup_working_wal.sh.j2 A roles/galaxyproject.postgresql/templates/pg_hba.conf.debian.j2 A roles/galaxyproject.postgresql/templates/pg_hba.conf.redhat.j2 A roles/galaxyproject.postgresql/templates/scheduled_backup.sh.j2 A roles/galaxyproject.postgresql/vars/debian.yml A roles/galaxyproject.postgresql/vars/main.yml A roles/galaxyproject.postgresql/vars/redhat.yml A roles/galaxyproject.proftpd/.travis.yml A roles/galaxyproject.proftpd/README.md A roles/galaxyproject.proftpd/defaults/main.yml A roles/galaxyproject.proftpd/handlers/main.yml A roles/galaxyproject.proftpd/meta/main.yml A roles/galaxyproject.proftpd/tasks/debian.yml A roles/galaxyproject.proftpd/tasks/galaxy_auth.yml A roles/galaxyproject.proftpd/tasks/main.yml A roles/galaxyproject.proftpd/tasks/redhat.yml A roles/galaxyproject.proftpd/tasks/tls.yml A roles/galaxyproject.proftpd/templates/galaxy_auth.conf.j2 A roles/galaxyproject.proftpd/templates/server.conf.j2 A roles/galaxyproject.proftpd/templates/tls.conf.j2 A roles/galaxyproject.proftpd/tests/inventory A roles/galaxyproject.proftpd/tests/test.yml A roles/galaxyproject.proftpd/vars/debian.yml A roles/galaxyproject.proftpd/vars/main.yml A roles/galaxyproject.proftpd/vars/redhat.yml A roles/galaxyproject.pulsar/README.md A roles/galaxyproject.pulsar/defaults/main.yml A roles/galaxyproject.pulsar/meta/.galaxy_install_info A roles/galaxyproject.pulsar/meta/main.yml A roles/galaxyproject.pulsar/tasks/main.yml A roles/galaxyproject.pulsar/templates/app.yml.j2 A roles/galaxyproject.pulsar/templates/job_managers.ini.j2 A roles/galaxyproject.pulsar/templates/job_metrics_conf.xml.j2 A roles/galaxyproject.pulsar/templates/local_env.sh.j2 A roles/galaxyproject.pulsar/templates/server.ini.j2 A roles/galaxyproject.tools/LICENSE A roles/galaxyproject.tools/README.md A roles/galaxyproject.tools/defaults/main.yml A roles/galaxyproject.tools/files/README.md A roles/galaxyproject.tools/files/dbkeys_list.yaml.sample A roles/galaxyproject.tools/files/install_tool_shed_tools.py A roles/galaxyproject.tools/files/tool_list.yaml A roles/galaxyproject.tools/files/tool_list.yaml.sample A roles/galaxyproject.tools/meta/.galaxy_install_info A roles/galaxyproject.tools/meta/main.yml A roles/galaxyproject.tools/tasks/main.yml A roles/galaxyproject.tools/tasks/tools.yml R roles/galaxyprojectdotorg.galaxy/README.md R roles/galaxyprojectdotorg.galaxy/defaults/main.yml R roles/galaxyprojectdotorg.galaxy/files/errordocs/content_bg.png R roles/galaxyprojectdotorg.galaxy/files/errordocs/error_message_icon.png R roles/galaxyprojectdotorg.galaxy/files/errordocs/masthead_bg.png R roles/galaxyprojectdotorg.galaxy/files/makepyc.py R roles/galaxyprojectdotorg.galaxy/handlers/main.yml R roles/galaxyprojectdotorg.galaxy/meta/.galaxy_install_info R roles/galaxyprojectdotorg.galaxy/meta/main.yml R roles/galaxyprojectdotorg.galaxy/tasks/clone.yml R roles/galaxyprojectdotorg.galaxy/tasks/database.yml R roles/galaxyprojectdotorg.galaxy/tasks/dependencies.yml R roles/galaxyprojectdotorg.galaxy/tasks/download.yml R roles/galaxyprojectdotorg.galaxy/tasks/errordocs.yml R roles/galaxyprojectdotorg.galaxy/tasks/main.yml R roles/galaxyprojectdotorg.galaxy/tasks/mutable_setup.yml R roles/galaxyprojectdotorg.galaxy/tasks/static_setup.yml R roles/galaxyprojectdotorg.galaxy/tasks/virtualenv.yml R roles/galaxyprojectdotorg.galaxy/templates/errordocs/413/index.html.j2 R roles/galaxyprojectdotorg.galaxy/templates/errordocs/502/index.shtml.j2 R roles/galaxyprojectdotorg.galaxy/templates/galaxy.ini.j2 R roles/galaxyprojectdotorg.galaxy_toolshed/README.md R roles/galaxyprojectdotorg.galaxy_toolshed/defaults/main.yml R roles/galaxyprojectdotorg.galaxy_toolshed/handlers/main.yml R roles/galaxyprojectdotorg.galaxy_toolshed/meta/.galaxy_install_info R roles/galaxyprojectdotorg.galaxy_toolshed/meta/main.yml R roles/galaxyprojectdotorg.galaxy_toolshed/tasks/database.yml R roles/galaxyprojectdotorg.galaxy_toolshed/tasks/main.yml R roles/galaxyprojectdotorg.galaxy_toolshed/tasks/static_setup.yml R roles/galaxyprojectdotorg.galaxy_toolshed/templates/tool_shed.ini.j2 R roles/galaxyprojectdotorg.galaxy_toolshed/templates/user_info.xml.j2 R roles/galaxyprojectdotorg.nginx/README.md R roles/galaxyprojectdotorg.nginx/defaults/main.yml R roles/galaxyprojectdotorg.nginx/handlers/main.yml R roles/galaxyprojectdotorg.nginx/meta/.galaxy_install_info R roles/galaxyprojectdotorg.nginx/meta/main.yml R roles/galaxyprojectdotorg.nginx/tasks/apt.yml R roles/galaxyprojectdotorg.nginx/tasks/main.yml R roles/galaxyprojectdotorg.nginx/tasks/pkgin.yml R roles/galaxyprojectdotorg.nginx/tasks/yum.yml R roles/galaxyprojectdotorg.nginx/templates/epel-nginx.conf.j2 R roles/galaxyprojectdotorg.nginx/templates/http_options.conf.j2 R roles/galaxyprojectdotorg.nginx/templates/pkgin-nginx.conf.j2 R roles/galaxyprojectdotorg.nginx/templates/ssl.conf.j2 R roles/galaxyprojectdotorg.nginx/templates/supervisord.conf.j2 R roles/galaxyprojectdotorg.nginx/vars/pkgin.yml R roles/galaxyprojectdotorg.postgresql/.gitignore R roles/galaxyprojectdotorg.postgresql/README.md R roles/galaxyprojectdotorg.postgresql/defaults/main.yml R roles/galaxyprojectdotorg.postgresql/files/get_repo_rpm_release.py R roles/galaxyprojectdotorg.postgresql/handlers/main.yml R roles/galaxyprojectdotorg.postgresql/meta/.galaxy_install_info R roles/galaxyprojectdotorg.postgresql/meta/main.yml R roles/galaxyprojectdotorg.postgresql/tasks/backup.yml R roles/galaxyprojectdotorg.postgresql/tasks/debian.yml R roles/galaxyprojectdotorg.postgresql/tasks/main.yml R roles/galaxyprojectdotorg.postgresql/tasks/redhat.yml R roles/galaxyprojectdotorg.postgresql/templates/20ansible_backup.conf.j2 R roles/galaxyprojectdotorg.postgresql/templates/25ansible_postgresql.conf.j2 R roles/galaxyprojectdotorg.postgresql/templates/archive_wal.sh.j2 R roles/galaxyprojectdotorg.postgresql/templates/backup_working_wal.sh.j2 R roles/galaxyprojectdotorg.postgresql/templates/pg_hba.conf.debian.j2 R roles/galaxyprojectdotorg.postgresql/templates/pg_hba.conf.redhat.j2 R roles/galaxyprojectdotorg.postgresql/templates/scheduled_backup.sh.j2 R roles/galaxyprojectdotorg.postgresql/vars/debian.yml R roles/galaxyprojectdotorg.postgresql/vars/main.yml R roles/galaxyprojectdotorg.postgresql/vars/redhat.yml R roles/galaxyprojectdotorg.proftpd/.travis.yml R roles/galaxyprojectdotorg.proftpd/README.md R roles/galaxyprojectdotorg.proftpd/defaults/main.yml R roles/galaxyprojectdotorg.proftpd/handlers/main.yml R roles/galaxyprojectdotorg.proftpd/meta/main.yml R roles/galaxyprojectdotorg.proftpd/tasks/debian.yml R roles/galaxyprojectdotorg.proftpd/tasks/galaxy_auth.yml R roles/galaxyprojectdotorg.proftpd/tasks/main.yml R roles/galaxyprojectdotorg.proftpd/tasks/redhat.yml R roles/galaxyprojectdotorg.proftpd/tasks/tls.yml R roles/galaxyprojectdotorg.proftpd/templates/galaxy_auth.conf.j2 R roles/galaxyprojectdotorg.proftpd/templates/server.conf.j2 R roles/galaxyprojectdotorg.proftpd/templates/tls.conf.j2 R roles/galaxyprojectdotorg.proftpd/tests/inventory R roles/galaxyprojectdotorg.proftpd/tests/test.yml R roles/galaxyprojectdotorg.proftpd/vars/debian.yml R roles/galaxyprojectdotorg.proftpd/vars/main.yml R roles/galaxyprojectdotorg.proftpd/vars/redhat.yml R roles/galaxyprojectdotorg.pulsar/README.md R roles/galaxyprojectdotorg.pulsar/defaults/main.yml R roles/galaxyprojectdotorg.pulsar/meta/.galaxy_install_info R roles/galaxyprojectdotorg.pulsar/meta/main.yml R roles/galaxyprojectdotorg.pulsar/tasks/main.yml R roles/galaxyprojectdotorg.pulsar/templates/app.yml.j2 R roles/galaxyprojectdotorg.pulsar/templates/job_managers.ini.j2 R roles/galaxyprojectdotorg.pulsar/templates/job_metrics_conf.xml.j2 R roles/galaxyprojectdotorg.pulsar/templates/local_env.sh.j2 R roles/galaxyprojectdotorg.pulsar/templates/server.ini.j2 R roles/galaxyprojectdotorg.tools/LICENSE R roles/galaxyprojectdotorg.tools/README.md R roles/galaxyprojectdotorg.tools/defaults/main.yml R roles/galaxyprojectdotorg.tools/files/README.md R roles/galaxyprojectdotorg.tools/files/dbkeys_list.yaml.sample R roles/galaxyprojectdotorg.tools/files/install_tool_shed_tools.py R roles/galaxyprojectdotorg.tools/files/tool_list.yaml R roles/galaxyprojectdotorg.tools/files/tool_list.yaml.sample R roles/galaxyprojectdotorg.tools/meta/.galaxy_install_info R roles/galaxyprojectdotorg.tools/meta/main.yml R roles/galaxyprojectdotorg.tools/tasks/main.yml R roles/galaxyprojectdotorg.tools/tasks/tools.yml Log Message: ----------- Rename roles due to name change in Ansible Galaxy

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[galaxyproject/usegalaxy-playbook] 385c2a: Update the interactive_environments role and stop ...
by GitHub 11 May '17

11 May '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 385c2a31d7eeb02186330226e50db80919f7b2ff https://github.com/galaxyproject/usegalaxy-playbook/commit/385c2a31d7eeb021… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M env/common/update.yml R env/test/files/interactive_environments/plugins/.ansible_ie_role_current_version R env/test/files/interactive_environments/plugins/bam_iobio/config/bam_iobio.ini.sample R env/test/files/interactive_environments/plugins/bam_iobio/config/bam_iobio.xml R env/test/files/interactive_environments/plugins/bam_iobio/static/js/bam_iobio.js R env/test/files/interactive_environments/plugins/bam_iobio/templates/bam_iobio.mako R env/test/files/interactive_environments/plugins/common/templates/ie.mako R env/test/files/interactive_environments/plugins/ethercalc/config/allowed_images.yml.sample R env/test/files/interactive_environments/plugins/ethercalc/config/ethercalc.ini.sample R env/test/files/interactive_environments/plugins/ethercalc/config/ethercalc.xml R env/test/files/interactive_environments/plugins/ethercalc/static/js/ethercalc.js R env/test/files/interactive_environments/plugins/ethercalc/templates/ethercalc.mako R env/test/files/interactive_environments/plugins/interactive_environments.dtd R env/test/files/interactive_environments/plugins/jupyter/config/allowed_images.yml.sample R env/test/files/interactive_environments/plugins/jupyter/config/jupyter.ini.sample R env/test/files/interactive_environments/plugins/jupyter/config/jupyter.xml R env/test/files/interactive_environments/plugins/jupyter/static/js/jupyter.js R env/test/files/interactive_environments/plugins/jupyter/templates/jupyter.mako R env/test/files/interactive_environments/plugins/neo/config/allowed_images.yml.sample R env/test/files/interactive_environments/plugins/neo/config/neo.ini.sample R env/test/files/interactive_environments/plugins/neo/config/neo.xml R env/test/files/interactive_environments/plugins/neo/static/js/neo.js R env/test/files/interactive_environments/plugins/neo/templates/neo.mako R env/test/files/interactive_environments/plugins/phinch/config/phinch.ini.sample R env/test/files/interactive_environments/plugins/phinch/config/phinch.xml R env/test/files/interactive_environments/plugins/phinch/static/js/phinch.js R env/test/files/interactive_environments/plugins/phinch/templates/phinch.mako R env/test/files/interactive_environments/plugins/rstudio/config/allowed_images.yml.sample R env/test/files/interactive_environments/plugins/rstudio/config/rstudio.ini.sample R env/test/files/interactive_environments/plugins/rstudio/config/rstudio.xml R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/base64.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/jsbn.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/prng4.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/rng.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/rsa.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio.big.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio.min.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/base64.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/jsbn.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/prng4.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/rng.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/rstudio/rsa.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/base64.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/jsbn.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/prng4.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/rng.js R env/test/files/interactive_environments/plugins/rstudio/static/js/crypto/wu/rsa.js R env/test/files/interactive_environments/plugins/rstudio/static/js/rstudio.js R env/test/files/interactive_environments/plugins/rstudio/templates/rstudio.mako R env/test/files/interactive_environments/proxy/.ansible_ie_role_current_version R env/test/files/interactive_environments/proxy/Dockerfile R env/test/files/interactive_environments/proxy/README.md R env/test/files/interactive_environments/proxy/lib/main.js R env/test/files/interactive_environments/proxy/lib/mapper.js R env/test/files/interactive_environments/proxy/lib/proxy.js R env/test/files/interactive_environments/proxy/package.json A roles/galaxyproject.interactive_environments/README.md A roles/galaxyproject.interactive_environments/defaults/main.yml A roles/galaxyproject.interactive_environments/handlers/main.yml A roles/galaxyproject.interactive_environments/meta/.galaxy_install_info A roles/galaxyproject.interactive_environments/meta/main.yml A roles/galaxyproject.interactive_environments/tasks/docker_ssl.yml A roles/galaxyproject.interactive_environments/tasks/install_dependencies.yml A roles/galaxyproject.interactive_environments/tasks/main.yml A roles/galaxyproject.interactive_environments/tasks/supervisor.yml A roles/galaxyproject.interactive_environments/tasks/synchronize_components.yml A roles/galaxyproject.interactive_environments/tasks/webserver_conf.yml A roles/galaxyproject.interactive_environments/templates/_prefix.j2 A roles/galaxyproject.interactive_environments/templates/config.ini.j2 A roles/galaxyproject.interactive_environments/templates/generic_apache.conf.j2 A roles/galaxyproject.interactive_environments/templates/generic_nginx.conf.j2 A roles/galaxyproject.interactive_environments/templates/jupyter_apache.conf.j2 A roles/galaxyproject.interactive_environments/templates/jupyter_nginx.conf.j2 A roles/galaxyproject.interactive_environments/templates/proxy_supervisor.conf.j2 R roles/galaxyprojectdotorg.interactive_environments/README.md R roles/galaxyprojectdotorg.interactive_environments/defaults/main.yml R roles/galaxyprojectdotorg.interactive_environments/handlers/main.yml R roles/galaxyprojectdotorg.interactive_environments/meta/.galaxy_install_info R roles/galaxyprojectdotorg.interactive_environments/meta/main.yml R roles/galaxyprojectdotorg.interactive_environments/tasks/docker_ssl.yml R roles/galaxyprojectdotorg.interactive_environments/tasks/extract_component.yml R roles/galaxyprojectdotorg.interactive_environments/tasks/install_dependencies.yml R roles/galaxyprojectdotorg.interactive_environments/tasks/main.yml R roles/galaxyprojectdotorg.interactive_environments/tasks/supervisor.yml R roles/galaxyprojectdotorg.interactive_environments/tasks/synchronize_components.yml R roles/galaxyprojectdotorg.interactive_environments/tasks/webserver_conf.yml R roles/galaxyprojectdotorg.interactive_environments/templates/_prefix.j2 R roles/galaxyprojectdotorg.interactive_environments/templates/config.ini.j2 R roles/galaxyprojectdotorg.interactive_environments/templates/generic_apache.conf.j2 R roles/galaxyprojectdotorg.interactive_environments/templates/generic_nginx.conf.j2 R roles/galaxyprojectdotorg.interactive_environments/templates/jupyter_apache.conf.j2 R roles/galaxyprojectdotorg.interactive_environments/templates/jupyter_nginx.conf.j2 R roles/galaxyprojectdotorg.interactive_environments/templates/proxy_supervisor.conf.j2 Log Message: ----------- Update the interactive_environments role and stop storing a copy of GIEs in the playbook Commit: c318d9a95c079d27c3c8ee72333d12c6dd52c4e2 https://github.com/galaxyproject/usegalaxy-playbook/commit/c318d9a95c079d27… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/69ea530df07a...…

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[galaxyproject/galaxy] a0c59d: Try activating conda environment again if previous...
by GitHub 11 May '17

11 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a0c59d8f05c011f6c7b002599ed09c3fe091c340 https://github.com/galaxyproject/galaxy/commit/a0c59d8f05c011f6c7b002599ed0… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Try activating conda environment again if previous activation failed Commit: c38c0276afb88ed5b1403ede53ae35247307890d https://github.com/galaxyproject/galaxy/commit/c38c0276afb88ed5b1403ede53ae… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-05-07 (Sun, 07 May 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Exit with error message when conda environemnt could not be activated (thx @nsoranzo). Commit: 9e6c1529929132414e240e306d2b244ef6853944 https://github.com/galaxyproject/galaxy/commit/9e6c1529929132414e240e306d2b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-08 (Mon, 08 May 2017) Changed paths: M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #4035 from mvdbeek/retry_conda_activation [17.05] Try activating conda environment again if previous activation failed Commit: ced568a9e5974d0a4944abce99a64f1b8eb6e6f6 https://github.com/galaxyproject/galaxy/commit/ced568a9e5974d0a4944abce99a6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-10 (Wed, 10 May 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M static/maps/mvc/dataset/dataset-li.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/dataset/dataset-li.js Log Message: ----------- Fix destructive tag rerender to be a simple replacement. Left the original template/render in place, we could refactor as this becomes more standardized. Commit: 650691c943c096ee15233c61e4459982b2c6928d https://github.com/galaxyproject/galaxy/commit/650691c943c096ee15233c61e445… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M static/maps/mvc/dataset/dataset-li.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/dataset/dataset-li.js Log Message: ----------- Merge pull request #4052 from dannon/1705_fix_tag_drag [17.05] Fix destructive tag rerender to be a simpler, more precise html replacement. Commit: 3e079a9f2c908e53413df0c4d77363995df8425f https://github.com/galaxyproject/galaxy/commit/3e079a9f2c908e53413df0c4d773… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M lib/galaxy/objectstore/s3.py Log Message: ----------- Fix for s3objectstore _clean_cache method, thanks to @zzsoni and @nsoranzo Commit: b7a66f182ef8607835665035e547e389d93237de https://github.com/galaxyproject/galaxy/commit/b7a66f182ef8607835665035e547… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M lib/galaxy/objectstore/s3.py Log Message: ----------- Merge pull request #4055 from dannon/s3_objs_fix [17.01] Fix for s3objectstore _clean_cache method Commit: 9940ae70309a56013200d3e30ced5bf9437c75c7 https://github.com/galaxyproject/galaxy/commit/9940ae70309a56013200d3e30ced… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M lib/galaxy/objectstore/s3.py Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Commit: 2eeabc00b19c26d8ebd1efd7e74d5c3b865e567e https://github.com/galaxyproject/galaxy/commit/2eeabc00b19c26d8ebd1efd7e74d… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/deps/resolvers/conda.py M static/maps/mvc/dataset/dataset-li.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/dataset/dataset-li.js Log Message: ----------- Merge branch 'release_17.05' into dev Conflicts: static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map Compare: https://github.com/galaxyproject/galaxy/compare/2f6d9590feec...2eeabc00b19c

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[galaxyproject/usegalaxy-playbook] ee705b: Update Main
by GitHub 11 May '17

11 May '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ee705bc05e7db9bf730bc94fbbad9dbbf4f92dbf https://github.com/galaxyproject/usegalaxy-playbook/commit/ee705bc05e7db9bf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M production/files/interactive_environments/plugins/.ansible_ie_role_current_version M production/files/interactive_environments/proxy/.ansible_ie_role_current_version M production/galaxy_version.yml Log Message: ----------- Update Main

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[galaxyproject/galaxy] 3e079a: Fix for s3objectstore _clean_cache method, thanks ...
by GitHub 11 May '17

11 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 3e079a9f2c908e53413df0c4d77363995df8425f https://github.com/galaxyproject/galaxy/commit/3e079a9f2c908e53413df0c4d773… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M lib/galaxy/objectstore/s3.py Log Message: ----------- Fix for s3objectstore _clean_cache method, thanks to @zzsoni and @nsoranzo Commit: b7a66f182ef8607835665035e547e389d93237de https://github.com/galaxyproject/galaxy/commit/b7a66f182ef8607835665035e547… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M lib/galaxy/objectstore/s3.py Log Message: ----------- Merge pull request #4055 from dannon/s3_objs_fix [17.01] Fix for s3objectstore _clean_cache method Commit: 9940ae70309a56013200d3e30ced5bf9437c75c7 https://github.com/galaxyproject/galaxy/commit/9940ae70309a56013200d3e30ced… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M lib/galaxy/objectstore/s3.py Log Message: ----------- Merge branch 'release_17.01' into release_17.05 Compare: https://github.com/galaxyproject/galaxy/compare/650691c943c0...9940ae70309a

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[galaxyproject/galaxy] 3e079a: Fix for s3objectstore _clean_cache method, thanks ...
by GitHub 11 May '17

11 May '17

Branch: refs/heads/release_17.01 Home: https://github.com/galaxyproject/galaxy Commit: 3e079a9f2c908e53413df0c4d77363995df8425f https://github.com/galaxyproject/galaxy/commit/3e079a9f2c908e53413df0c4d773… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M lib/galaxy/objectstore/s3.py Log Message: ----------- Fix for s3objectstore _clean_cache method, thanks to @zzsoni and @nsoranzo Commit: b7a66f182ef8607835665035e547e389d93237de https://github.com/galaxyproject/galaxy/commit/b7a66f182ef8607835665035e547… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M lib/galaxy/objectstore/s3.py Log Message: ----------- Merge pull request #4055 from dannon/s3_objs_fix [17.01] Fix for s3objectstore _clean_cache method Compare: https://github.com/galaxyproject/galaxy/compare/de46a0edba4c...b7a66f182ef8

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[galaxyproject/galaxy] e2d6b6: Initial commit for transforming mako files for wor...
by GitHub 11 May '17

11 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e2d6b6dc2c500027d4c4daf138d2ef5a9fee334f https://github.com/galaxyproject/galaxy/commit/e2d6b6dc2c500027d4c4daf138d2… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-04-09 (Sun, 09 Apr 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/layout/menu.js.map A static/maps/mvc/workflow/workflow.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/layout/menu.js A static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css Log Message: ----------- Initial commit for transforming mako files for workflow into plain javascript Commit: b7af4a3cf4acb7489f4e181b29997374f90cfce2 https://github.com/galaxyproject/galaxy/commit/b7af4a3cf4acb7489f4e181b2999… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-04-20 (Thu, 20 Apr 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/layout/menu.js.map M static/maps/mvc/workflow/workflow.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/layout/menu.js M static/scripts/mvc/workflow/workflow.js Log Message: ----------- Create new workflow Commit: a421eb54bf9ad62f4891275d9e60292e4022e60e https://github.com/galaxyproject/galaxy/commit/a421eb54bf9ad62f4891275d9e60… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-04-20 (Thu, 20 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow.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/workflow/workflow.js M static/style/blue/base.css Log Message: ----------- Show workflow information using workflow select list Commit: 07cdbd209c7454232fb6936125448abb2f62e948 https://github.com/galaxyproject/galaxy/commit/07cdbd209c7454232fb693612544… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/layout/menu.js.map M static/maps/mvc/workflow/workflow.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/layout/menu.js M static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css Log Message: ----------- Fixing the routing issue and showing the main workflow dashboard in the center panel Commit: 14f3697bce50ae4e898ff15e1b7ee3b9938eecc9 https://github.com/galaxyproject/galaxy/commit/14f3697bce50ae4e898ff15e1b7e… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M static/maps/mvc/workflow/workflow.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/workflow/workflow.js M static/style/blue/base.css Log Message: ----------- Adding actions dropdown for workflows Commit: 18f5b7d71c4c8718726394b57e8b478b54d1432d https://github.com/galaxyproject/galaxy/commit/18f5b7d71c4c8718726394b57e8b… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-04-25 (Tue, 25 Apr 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Redirecting to workflow list page once actions are over Commit: 26822859c13d19cc86185f68fe5145439d04af97 https://github.com/galaxyproject/galaxy/commit/26822859c13d19cc86185f68fe51… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M static/maps/mvc/workflow/workflow.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/workflow/workflow.js M static/style/blue/base.css Log Message: ----------- Adding shared workflow and congifure workflow options Commit: 9b13a87cdbdbae0542b289b25ece8458c4584aad https://github.com/galaxyproject/galaxy/commit/9b13a87cdbdbae0542b289b25ece… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-04-26 (Wed, 26 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/workflow/workflow.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/workflow/workflow.js M static/style/blue/base.css Log Message: ----------- Adding actions for shared workflows Commit: c72dc0c39a0d2333c1da24e44f71866e806f2fa6 https://github.com/galaxyproject/galaxy/commit/c72dc0c39a0d2333c1da24e44f71… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-04-27 (Thu, 27 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow.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/workflow/workflow.js M static/style/blue/base.css Log Message: ----------- Changing html structure a bit Commit: 89a32b77b3b9d9766244c0991f5497407ae1b9d2 https://github.com/galaxyproject/galaxy/commit/89a32b77b3b9d9766244c0991f54… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M static/maps/mvc/workflow/workflow.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/workflow/workflow.js M static/style/blue/base.css Log Message: ----------- Updating html and js structure and adding font awesome icons Commit: a625901664a1ccde9988aa758a3dd8fca387ab47 https://github.com/galaxyproject/galaxy/commit/a625901664a1ccde9988aa758a3d… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-04-28 (Fri, 28 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/workflow/workflow.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/workflow/workflow.js M static/style/blue/base.css Log Message: ----------- Adding view action for shared workflow and fixing font-family for buttons Commit: 5630a5c7eb4e25e14a6e6173c1a46d7ce0babde6 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M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-color-picker.js M client/galaxy/scripts/mvc/ui/ui-misc.js M client/galaxy/scripts/mvc/ui/ui-options.js M client/galaxy/scripts/mvc/ui/ui-select-content.js M client/galaxy/scripts/mvc/ui/ui-table.js A client/galaxy/scripts/mvc/user/user-custom-builds.js M client/galaxy/scripts/mvc/user/user-preferences.js M client/galaxy/scripts/mvc/workflow/workflow-forms.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/style/less/ui.less M client/package.json M client/webpack.config.js A config/containers_conf.yml.sample M config/datatypes_conf.xml.sample M config/galaxy.ini.sample M config/openid_conf.xml.sample M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js M config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako M config/plugins/interactive_environments/rstudio/config/allowed_images.yml.sample M config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M config/plugins/interactive_environments/rstudio/templates/rstudio.mako M config/plugins/tours/core.galaxy_ui.yaml M config/plugins/tours/core.history.yaml A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js A config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map M config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js M 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doc/source/admin/special_topics/index.rst A doc/source/admin/special_topics/performance_tracking.rst M lib/galaxy/app.py M lib/galaxy/config.py R lib/galaxy/container/__init__.py R lib/galaxy/container/docker_swarm.py A lib/galaxy/containers/__init__.py A lib/galaxy/containers/docker.py A lib/galaxy/containers/docker_decorators.py A lib/galaxy/containers/docker_model.py A lib/galaxy/containers/docker_swarm.py A lib/galaxy/containers/docker_swarm_manager.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/datatypes/text.py M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/exceptions/__init__.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/dynamic_tool_destination.py M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/metrics/__init__.py 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templates/webapps/galaxy/galaxy.masthead.mako M templates/webapps/galaxy/workflow/display.mako M templates/webapps/tool_shed/base_panels.mako A test-data/filter_labels_1.txt A test-data/new_labels_1.txt A test-data/new_labels_2.txt A test-data/new_labels_bad_1.txt A test-data/new_labels_bad_2.txt M test/api/test_libraries.py M test/api/test_tools.py M test/api/test_workflows.py A test/functional/tools/identifier_multiple_in_conditional.xml A test/functional/tools/identifier_multiple_in_repeat.xml M test/functional/tools/samples_tool_conf.xml M test/galaxy_selenium/navigates_galaxy.py M test/integration/test_workflow_handler_configuration.py A test/integration/workflow_handler_configuration_workflow_scheduler_conf.xml M test/qunit/tests/form_tests.js M test/qunit/tests/ui_tests.js M test/unit/tools/test_toolbox.py M test/unit/tools/test_wrappers.py M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/filters/trimmer.py M tools/filters/trimmer.xml M tox.ini Log Message: ----------- Merging with dev Commit: 35adfeaea613a2d0eb56145e0111036fbdbafb47 https://github.com/galaxyproject/galaxy/commit/35adfeaea613a2d0eb56145e0111… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-04-30 (Sun, 30 Apr 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/workflow/workflow.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/workflow/workflow.js M static/style/blue/base.css Log Message: ----------- Adding table for showing all workflows Commit: 70ce1541a5282300ec8e926d0946a76b4da8af69 https://github.com/galaxyproject/galaxy/commit/70ce1541a5282300ec8e926d0946… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M static/maps/mvc/workflow/workflow.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/workflow/workflow.js M static/style/blue/base.css Log Message: ----------- Adding client side search for workflows Commit: 490b11bfc5f4337315c16da8c3b5602d13986441 https://github.com/galaxyproject/galaxy/commit/490b11bfc5f4337315c16da8c3b5… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-01 (Mon, 01 May 2017) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/layout/menu.js.map M static/maps/mvc/workflow/workflow.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/layout/menu.js M static/scripts/mvc/workflow/workflow.js Log Message: ----------- Converting run mako to plain javascript and modifying menu for url Commit: 0abf1a18c07cba79de2e0fb4f7efb80994b4986e https://github.com/galaxyproject/galaxy/commit/0abf1a18c07cba79de2e0fb4f7ef… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/selenium/run_tests.sh M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/tag.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M config/job_conf.xml.sample_advanced M config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample M config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample M 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static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/tag.js.map M static/maps/mvc/workflow/workflow-terminals.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/collection/collection-model.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/tag.js M static/scripts/mvc/workflow/workflow-terminals.js M test/api/test_jobs.py M test/base/driver_util.py M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/framework.py M test/selenium_tests/test_workflow_run.py M test/unit/tools/test_toolbox.py M tools/data_source/upload.py M tox.ini Log Message: ----------- Merging with dev Commit: 63aeaa5e0300b0680633d7e78ab5f3859cb1a55c https://github.com/galaxyproject/galaxy/commit/63aeaa5e0300b0680633d7e78ab5… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-05 (Fri, 05 May 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow.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/workflow/workflow.js Log Message: ----------- Moving the action buttons text to their tooltips Commit: a99605d04a46797a2b55746096b050d0514a4c39 https://github.com/galaxyproject/galaxy/commit/a99605d04a46797a2b55746096b0… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-09 (Tue, 09 May 2017) Changed paths: M lib/galaxy/jobs/runners/condor.py M lib/galaxy/web/framework/middleware/graphite.py M test/api/test_workflows.py M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_history_sharing.py M test/selenium_tests/test_login.py M test/selenium_tests/test_registration.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Merge branch 'dev' of https://github.com/bgruening/galaxy into workflowexport_mako Commit: 29ac63ac5675b0c514bbed392ac2ae1c804a8c58 https://github.com/galaxyproject/galaxy/commit/29ac63ac5675b0c514bbed392ac2… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-09 (Tue, 09 May 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/mvc/workflow/workflow.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/workflow/workflow.js R templates/webapps/galaxy/workflow/list.mako Log Message: ----------- Deleting list.mako file and updating code for workflow run Commit: c0decb71db316d6345af0cfcfa80b2902316bbf4 https://github.com/galaxyproject/galaxy/commit/c0decb71db316d6345af0cfcfa80… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-09 (Tue, 09 May 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fixing pylint comments for build failure Commit: 822abebd9e09457c544617c0eca583a8ff5f9821 https://github.com/galaxyproject/galaxy/commit/822abebd9e09457c544617c0eca5… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-09 (Tue, 09 May 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/workflow/workflow.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/workflow/workflow.js Log Message: ----------- Fixing PR review comments Commit: c825f45590739b2eca816106782238643fc4e3bd https://github.com/galaxyproject/galaxy/commit/c825f45590739b2eca8161067822… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-10 (Wed, 10 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: ----------- Merging the static files Commit: d5d10f0ef0994906a434f48bbdf86437547ce526 https://github.com/galaxyproject/galaxy/commit/d5d10f0ef0994906a434f48bbdf8… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-10 (Wed, 10 May 2017) Changed paths: M client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/nls/de/locale.js A client/galaxy/scripts/nls/es/locale.js M client/galaxy/scripts/nls/fr/locale.js M client/galaxy/scripts/nls/locale.js M static/maps/layout/menu.js.map A static/maps/nls/de/locale.js.map A static/maps/nls/es/locale.js.map M static/maps/nls/fr/locale.js.map 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/layout/menu.js A static/scripts/nls/de/locale.js A static/scripts/nls/es/locale.js M static/scripts/nls/fr/locale.js M static/scripts/nls/locale.js Log Message: ----------- Merging with dev and resolving conflicts Commit: e1d197b27e9a43c8b00a37160f7db54e44566d9c https://github.com/galaxyproject/galaxy/commit/e1d197b27e9a43c8b00a37160f7d… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-10 (Wed, 10 May 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/workflow/workflow.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/workflow/workflow.js Log Message: ----------- Fixing PR review comments Commit: b91729eaf637ff2741913f5ec3de1679fb65ee09 https://github.com/galaxyproject/galaxy/commit/b91729eaf637ff2741913f5ec3de… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow.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/workflow/workflow.js Log Message: ----------- Fixing review comments for proxy_prefix and 'All workflows' link in the tool panel Commit: b6bf961cd7793c3efdbd3cb5252cda198d684d6d https://github.com/galaxyproject/galaxy/commit/b6bf961cd7793c3efdbd3cb5252c… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fixing for prefix url for actions in workflow controller Commit: 004f843ba428c7b73f8ec035d1f930a5819b3069 https://github.com/galaxyproject/galaxy/commit/004f843ba428c7b73f8ec035d1f9… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py R templates/webapps/galaxy/workflow/list_for_run.mako Log Message: ----------- Removing list_for_run.mako and its corresponding method in workflow controller Commit: c76c588ed1c2e336f65b9b930a08cae7fb8f2957 https://github.com/galaxyproject/galaxy/commit/c76c588ed1c2e336f65b9b930a08… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_management.py Log Message: ----------- Fix Selenium test cases for JavaScript-izing workflow management. Commit: 7374558ca576f50b9225e97c058d983479df57f2 https://github.com/galaxyproject/galaxy/commit/7374558ca576f50b9225e97c058d… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_management.py Log Message: ----------- Merge pull request #34 from jmchilton/workflowexport_mako_test_fixes Fix Selenium test cases for JavaScript-izing workflow management. Commit: 2e34b6c3e38e84f507297d45bcbb9a50e3748755 https://github.com/galaxyproject/galaxy/commit/2e34b6c3e38e84f507297d45bcbb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fix require inclusion scoping in analysis.js Commit: 6f89baba42ba629ad29b144706fb8475197c3b8b https://github.com/galaxyproject/galaxy/commit/6f89baba42ba629ad29b144706fb… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Merge pull request #35 from dannon/workflowexport_mako Fix require inclusion scoping in analysis.js Commit: a72035b4972f20637290a0cf94088e0199accd6b https://github.com/galaxyproject/galaxy/commit/a72035b4972f20637290a0cf9408… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow.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/workflow/workflow.js Log Message: ----------- Removing unused imports in workflow main view Commit: e74653feace21206686905413943c86cae68eb8a https://github.com/galaxyproject/galaxy/commit/e74653feace21206686905413943… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M static/maps/nls/fr/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js M test/selenium_tests/framework.py Log Message: ----------- Merging with dev Commit: 2f6d9590feecf3a58e5d47f4eccbfa4f3aa209c7 https://github.com/galaxyproject/galaxy/commit/2f6d9590feecf3a58e5d47f4eccb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/tool-panel.js M client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/layout/menu.js.map A static/maps/mvc/workflow/workflow.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/layout/menu.js A static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css R templates/webapps/galaxy/workflow/list.mako R templates/webapps/galaxy/workflow/list_for_run.mako M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_workflow_management.py Log Message: ----------- Merge pull request #4047 from bgruening/workflowexport_mako New Workflow Management Screen UI using JavaScript Compare: https://github.com/galaxyproject/galaxy/compare/163de025a20a...2f6d9590feec

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[galaxyproject/galaxy] a8ddd7: Reset Selenium test connection between test retrie...
by GitHub 11 May '17

11 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a8ddd73ab4d72c91d53a641d867240663eb85737 https://github.com/galaxyproject/galaxy/commit/a8ddd73ab4d72c91d53a641d8672… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M test/selenium_tests/framework.py Log Message: ----------- Reset Selenium test connection between test retries. Otherwise the state of one test can affect the next attempt. Commit: 163de025a20ac1187389c876bebc04a40064458a https://github.com/galaxyproject/galaxy/commit/163de025a20ac1187389c876bebc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M test/selenium_tests/framework.py Log Message: ----------- Merge pull request #4053 from jmchilton/selenium_fixes_13 Reset Selenium test connection between test retries. Compare: https://github.com/galaxyproject/galaxy/compare/09e018d3e6be...163de025a20a

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[galaxyproject/galaxy] e1c388: French error
by GitHub 11 May '17

11 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e1c3886651661c872ab01b20d104254205573aba https://github.com/galaxyproject/galaxy/commit/e1c3886651661c872ab01b20d104… Author: Yvan Le Bras <yvan.le_bras(a)irisa.fr> Date: 2017-05-10 (Wed, 10 May 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- French error Commit: 09e018d3e6be0d40b52ac520f40db4b1ef97e558 https://github.com/galaxyproject/galaxy/commit/09e018d3e6be0d40b52ac520f40d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M static/maps/nls/fr/locale.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/nls/fr/locale.js Log Message: ----------- Merge #4051 and rebuild client Compare: https://github.com/galaxyproject/galaxy/compare/70cc3ebb0882...09e018d3e6be

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[galaxyproject/galaxy] ced568: Fix destructive tag rerender to be a simple replac...
by GitHub 11 May '17

11 May '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: ced568a9e5974d0a4944abce99a64f1b8eb6e6f6 https://github.com/galaxyproject/galaxy/commit/ced568a9e5974d0a4944abce99a6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-10 (Wed, 10 May 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M static/maps/mvc/dataset/dataset-li.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/dataset/dataset-li.js Log Message: ----------- Fix destructive tag rerender to be a simple replacement. Left the original template/render in place, we could refactor as this becomes more standardized. Commit: 650691c943c096ee15233c61e4459982b2c6928d https://github.com/galaxyproject/galaxy/commit/650691c943c096ee15233c61e445… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-11 (Thu, 11 May 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M static/maps/mvc/dataset/dataset-li.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/dataset/dataset-li.js Log Message: ----------- Merge pull request #4052 from dannon/1705_fix_tag_drag [17.05] Fix destructive tag rerender to be a simpler, more precise html replacement. Compare: https://github.com/galaxyproject/galaxy/compare/9e6c15299291...650691c943c0

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