October 2017 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 1b7b4d: GIEs: Grandfather automatic uppercasing of some en...
by GitHub 05 Oct '17

05 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: 1b7b4da9a266fac29486aef3b3a290e1c9749199 https://github.com/galaxyproject/galaxy/commit/1b7b4da9a266fac29486aef3b3a2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- GIEs: Grandfather automatic uppercasing of some env_override variables. Commit: f9eae90944790530274a9079d7eb76fc10ce68eb https://github.com/galaxyproject/galaxy/commit/f9eae90944790530274a9079d7eb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #4760 from natefoo/gie-upper-grandfather [17.09] GIEs: Grandfather automatic uppercasing of some env_override variables Compare: https://github.com/galaxyproject/galaxy/compare/8c769b2e29d0...f9eae9094479

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[galaxyproject/usegalaxy-playbook] c937b1: Update Test, set a 5 minute container timeout for ...
by GitHub 05 Oct '17

05 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c937b14b0beea9d29f9a684a8cb58dab491009d1 https://github.com/galaxyproject/usegalaxy-playbook/commit/c937b14b0beea9d2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M env/test/files/galaxy/galaxy_version.yml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Update Test, set a 5 minute container timeout for GIEs, return to using the swarm, and upgrade to the 17.09 Jupyter image

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[galaxyproject/infrastructure-playbook] 8e287a: Switch back to the swarm keys.
by GitHub 05 Oct '17

05 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 8e287a916ce58e876d76f249f41314c71823deb6 https://github.com/galaxyproject/infrastructure-playbook/commit/8e287a916ce… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M taccenv/group_vars/dockerclients.yml Log Message: ----------- Switch back to the swarm keys.

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[galaxyproject/infrastructure-playbook] 296f4a: Switch the docker role to use the common ssl role, ...
by GitHub 05 Oct '17

05 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 296f4adeeec6962e94d9c4014b39773fcf743e88 https://github.com/galaxyproject/infrastructure-playbook/commit/296f4adeeec… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: A common_env/files/ssl/docker/ca-key.pem A common_env/files/ssl/docker/ca.pem A common_env/files/ssl/docker/ca.srl A common_env/files/ssl/docker/client.pem A common_env/files/ssl/docker/client_privatekey.yml A common_env/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server.pem A common_env/files/ssl/docker/cvmfs1-psu0.galaxyproject.org/server_privatekey… A common_env/files/ssl/docker/jetstream-iu0.galaxyproject.org/server.pem A common_env/files/ssl/docker/jetstream-iu0.galaxyproject.org/server_privatek… A common_env/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server-cert.p… A common_env/files/ssl/docker/jetstream-tacc0.galaxyproject.org/server_privat… A common_env/files/ssl/docker_test/ca-key.pem A common_env/files/ssl/docker_test/ca.pem A common_env/files/ssl/docker_test/ca.srl A common_env/files/ssl/docker_test/client.pem A common_env/files/ssl/docker_test/client_privatekey.yml A common_env/files/ssl/docker_test/gie-standalone/server.pem A common_env/files/ssl/docker_test/gie-standalone/server_privatekey.yml R common_env/group_vars/dockersslclients.yml M common_env/group_vars/sslservers/vars.yml R common_env/secret_group_vars/dockersslclients.yml M common_roles M galaxyenv/playbook.yml A jetstreamdockerenv/files/ssl R jetstreamdockerenv/group_vars/all.yml A jetstreamdockerenv/group_vars/all/vars.yml A jetstreamdockerenv/group_vars/all/vault.yml M jetstreamdockerenv/group_vars/baseinstances.yml M jetstreamdockerenv/group_vars/imageinstances.yml A jetstreamdockerenv/group_vars/sslservers A jetstreamdockerenv/host_vars/gie-standalone/vars.yml A jetstreamdockerenv/host_vars/gie-standalone/vault.yml M jetstreamdockerenv/inc_clouds_yaml.yml M jetstreamdockerenv/inc_spawn.yml M jetstreamdockerenv/inventory A jetstreamdockerenv/inventory.standalone M jetstreamdockerenv/snapshot_docker_base.yml M jetstreamdockerenv/snapshot_docker_image.yml M jetstreamdockerenv/ssh_config.jetstream_iu A jetstreamdockerenv/standalone.yml R roles/docker/README.md M roles/docker/tasks/main.yml R roles/docker/tasks/ssl-ca-passphrase.yml R roles/docker/tasks/ssl-ca.yml R roles/docker/tasks/ssl-client.yml R roles/docker/tasks/ssl-gen-ca.yml R roles/docker/tasks/ssl-gen-client-cert.yml R roles/docker/tasks/ssl-gen-server-cert.yml R roles/docker/tasks/ssl-server.yml A taccenv/group_vars/dockerclients.yml R taccenv/group_vars/dockersslclients.yml M taccenv/host_vars/galaxy07.tacc.utexas.edu.yml M taccenv/inventory M taccenv/playbook.yml Log Message: ----------- Switch the docker role to use the common ssl role, and create a docker_test CA for testing new GIE docker images on Test. Commit: 163886f8096e50f4dca55724f0f16d70402e30a9 https://github.com/galaxyproject/infrastructure-playbook/commit/163886f8096… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M jetstreamdockerenv/group_vars/all/vars.yml M jetstreamdockerenv/group_vars/all/vault.yml M jetstreamdockerenv/group_vars/imageinstances.yml A jetstreamdockerenv/group_vars/testinstances/vars.yml A jetstreamdockerenv/group_vars/testinstances/vault.yml R jetstreamdockerenv/host_vars/gie-standalone/vars.yml R jetstreamdockerenv/host_vars/gie-standalone/vault.yml M jetstreamdockerenv/inc_clouds_yaml.yml M jetstreamdockerenv/inventory A jetstreamdockerenv/launch_test_instance.yml R jetstreamdockerenv/secret_group_vars/instances.yml R jetstreamdockerenv/standalone.yml Log Message: ----------- Simplify js docker env a bit Commit: be3e978556b0d97550a645d25c2e5cad90b45d59 https://github.com/galaxyproject/infrastructure-playbook/commit/be3e978556b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: A env/common A env/jsdocker/README.md A env/jsdocker/_inc_clouds_yaml.yml A env/jsdocker/_inc_delete.yml A env/jsdocker/_inc_spawn.yml A env/jsdocker/files/ssl A env/jsdocker/group_vars/all/vars.yml A env/jsdocker/group_vars/all/vault.yml A env/jsdocker/group_vars/baseinstances.yml A env/jsdocker/group_vars/imageinstances.yml A env/jsdocker/group_vars/sslservers A env/jsdocker/group_vars/testinstances/vars.yml A env/jsdocker/group_vars/testinstances/vault.yml A env/jsdocker/inventory A env/jsdocker/inventory.standalone A env/jsdocker/launch_test_instance.yml A env/jsdocker/snapshot_docker_base.yml A env/jsdocker/snapshot_docker_image.yml A env/jsdocker/ssh_config.jetstream_iu A env/jsdocker/ssh_config.jetstream_tacc R jetstreamdockerenv/README.md R jetstreamdockerenv/files/ssl R jetstreamdockerenv/group_vars/all/vars.yml R jetstreamdockerenv/group_vars/all/vault.yml R jetstreamdockerenv/group_vars/baseinstances.yml R jetstreamdockerenv/group_vars/imageinstances.yml R jetstreamdockerenv/group_vars/sslservers R jetstreamdockerenv/group_vars/testinstances/vars.yml R jetstreamdockerenv/group_vars/testinstances/vault.yml R jetstreamdockerenv/inc_clouds_yaml.yml R jetstreamdockerenv/inc_delete.yml R jetstreamdockerenv/inc_spawn.yml R jetstreamdockerenv/inventory R jetstreamdockerenv/inventory.standalone R jetstreamdockerenv/launch_test_instance.yml R jetstreamdockerenv/snapshot_docker_base.yml R jetstreamdockerenv/snapshot_docker_image.yml R jetstreamdockerenv/ssh_config.jetstream_iu R jetstreamdockerenv/ssh_config.jetstream_tacc Log Message: ----------- Move to an env folder like usegalaxy-playbook Commit: 638eeda2f43bda35ebc5f720eb11ab53bd0d7061 https://github.com/galaxyproject/infrastructure-playbook/commit/638eeda2f43… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M ansible.cfg Log Message: ----------- Don't create *.retry files Commit: 580a32b87183e1358b49b0f3ec943201a59ccd0e https://github.com/galaxyproject/infrastructure-playbook/commit/580a32b8718… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M .gitignore M common_env/files/ssl/docker_test/ca.srl R common_env/files/ssl/docker_test/gie-standalone/server.pem R common_env/files/ssl/docker_test/gie-standalone/server_privatekey.yml A common_env/files/ssl/docker_test/iu-gie-test/server.pem A common_env/files/ssl/docker_test/iu-gie-test/server_privatekey.yml A env/jsdocker/_inc_clean.yml M env/jsdocker/_inc_clouds_yaml.yml M env/jsdocker/_inc_delete.yml M env/jsdocker/_inc_spawn.yml M env/jsdocker/group_vars/all/vars.yml M env/jsdocker/inventory R env/jsdocker/inventory.standalone M env/jsdocker/launch_test_instance.yml A env/jsdocker/snapshot_base.yml R env/jsdocker/snapshot_docker_base.yml R env/jsdocker/snapshot_docker_image.yml A env/jsdocker/snapshot_gie_images.yml R env/jsdocker/ssh_config.jetstream_iu R env/jsdocker/ssh_config.jetstream_tacc A env/jsdocker/templates/ssh_config.jetstream.j2 M roles/docker/tasks/main.yml Log Message: ----------- Additional fixes that should make it possible for anyone to run the image updates (previously you had to have a valid key in your ssh-agent). Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/80aaa80b96…

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[galaxyproject/infrastructure-playbook] be3e97: Move to an env folder like usegalaxy-playbook
by GitHub 05 Oct '17

05 Oct '17

Branch: refs/heads/docker-test Home: https://github.com/galaxyproject/infrastructure-playbook Commit: be3e978556b0d97550a645d25c2e5cad90b45d59 https://github.com/galaxyproject/infrastructure-playbook/commit/be3e978556b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: A env/common A env/jsdocker/README.md A env/jsdocker/_inc_clouds_yaml.yml A env/jsdocker/_inc_delete.yml A env/jsdocker/_inc_spawn.yml A env/jsdocker/files/ssl A env/jsdocker/group_vars/all/vars.yml A env/jsdocker/group_vars/all/vault.yml A env/jsdocker/group_vars/baseinstances.yml A env/jsdocker/group_vars/imageinstances.yml A env/jsdocker/group_vars/sslservers A env/jsdocker/group_vars/testinstances/vars.yml A env/jsdocker/group_vars/testinstances/vault.yml A env/jsdocker/inventory A env/jsdocker/inventory.standalone A env/jsdocker/launch_test_instance.yml A env/jsdocker/snapshot_docker_base.yml A env/jsdocker/snapshot_docker_image.yml A env/jsdocker/ssh_config.jetstream_iu A env/jsdocker/ssh_config.jetstream_tacc R jetstreamdockerenv/README.md R jetstreamdockerenv/files/ssl R jetstreamdockerenv/group_vars/all/vars.yml R jetstreamdockerenv/group_vars/all/vault.yml R jetstreamdockerenv/group_vars/baseinstances.yml R jetstreamdockerenv/group_vars/imageinstances.yml R jetstreamdockerenv/group_vars/sslservers R jetstreamdockerenv/group_vars/testinstances/vars.yml R jetstreamdockerenv/group_vars/testinstances/vault.yml R jetstreamdockerenv/inc_clouds_yaml.yml R jetstreamdockerenv/inc_delete.yml R jetstreamdockerenv/inc_spawn.yml R jetstreamdockerenv/inventory R jetstreamdockerenv/inventory.standalone R jetstreamdockerenv/launch_test_instance.yml R jetstreamdockerenv/snapshot_docker_base.yml R jetstreamdockerenv/snapshot_docker_image.yml R jetstreamdockerenv/ssh_config.jetstream_iu R jetstreamdockerenv/ssh_config.jetstream_tacc Log Message: ----------- Move to an env folder like usegalaxy-playbook Commit: 638eeda2f43bda35ebc5f720eb11ab53bd0d7061 https://github.com/galaxyproject/infrastructure-playbook/commit/638eeda2f43… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M ansible.cfg Log Message: ----------- Don't create *.retry files Commit: 580a32b87183e1358b49b0f3ec943201a59ccd0e https://github.com/galaxyproject/infrastructure-playbook/commit/580a32b8718… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M .gitignore M common_env/files/ssl/docker_test/ca.srl R common_env/files/ssl/docker_test/gie-standalone/server.pem R common_env/files/ssl/docker_test/gie-standalone/server_privatekey.yml A common_env/files/ssl/docker_test/iu-gie-test/server.pem A common_env/files/ssl/docker_test/iu-gie-test/server_privatekey.yml A env/jsdocker/_inc_clean.yml M env/jsdocker/_inc_clouds_yaml.yml M env/jsdocker/_inc_delete.yml M env/jsdocker/_inc_spawn.yml M env/jsdocker/group_vars/all/vars.yml M env/jsdocker/inventory R env/jsdocker/inventory.standalone M env/jsdocker/launch_test_instance.yml A env/jsdocker/snapshot_base.yml R env/jsdocker/snapshot_docker_base.yml R env/jsdocker/snapshot_docker_image.yml A env/jsdocker/snapshot_gie_images.yml R env/jsdocker/ssh_config.jetstream_iu R env/jsdocker/ssh_config.jetstream_tacc A env/jsdocker/templates/ssh_config.jetstream.j2 M roles/docker/tasks/main.yml Log Message: ----------- Additional fixes that should make it possible for anyone to run the image updates (previously you had to have a valid key in your ssh-agent). Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/163886f809…

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[galaxyproject/galaxy] a8aea1: Fix missing support for command_inject when using ...
by GitHub 05 Oct '17

05 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a8aea10dfb609fbd0790b6df22b49a60192966e3 https://github.com/galaxyproject/galaxy/commit/a8aea10dfb609fbd0790b6df22b4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Fix missing support for command_inject when using containers lib in GIEs Commit: f118fc32c0d7222b2ef2aad3146ef66b4247825f https://github.com/galaxyproject/galaxy/commit/f118fc32c0d7222b2ef2aad3146e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Fix linting error Commit: 8c769b2e29d0503d76b6cc35c734871a3216ef4a https://github.com/galaxyproject/galaxy/commit/8c769b2e29d0503d76b6cc35c734… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #4740 from natefoo/containers-env [17.09] Fix missing support for command_inject when using containers lib in GIEs Commit: 9de98a6a9fd91eeaf83e920e5482bda0f4e16bc6 https://github.com/galaxyproject/galaxy/commit/9de98a6a9fd91eeaf83e920e5482… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M lib/galaxy/visualization/plugins/interactive_environments.py Log Message: ----------- Merge branch 'release_17.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/d195ef88de9b...9de98a6a9fd9

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[galaxyproject/galaxy] e459b5: Stop running common_startup.sh twice when starting...
by GitHub 05 Oct '17

05 Oct '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e459b51f40cf0ce501ea95a8b861bdf3db02c7fb https://github.com/galaxyproject/galaxy/commit/e459b51f40cf0ce501ea95a8b861… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M run.sh Log Message: ----------- Stop running common_startup.sh twice when starting from run.sh Commit: d195ef88de9b078cda5b037fc3aa21e7d12f1d63 https://github.com/galaxyproject/galaxy/commit/d195ef88de9b078cda5b037fc3aa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M run.sh Log Message: ----------- Merge pull request #4759 from natefoo/common-startup-dedup Stop running common_startup.sh twice when starting from run.sh Compare: https://github.com/galaxyproject/galaxy/compare/562465ffe9c6...d195ef88de9b

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[galaxyproject/galaxy] a8aea1: Fix missing support for command_inject when using ...
by GitHub 05 Oct '17

05 Oct '17

Branch: refs/heads/release_17.09 Home: https://github.com/galaxyproject/galaxy Commit: a8aea10dfb609fbd0790b6df22b49a60192966e3 https://github.com/galaxyproject/galaxy/commit/a8aea10dfb609fbd0790b6df22b4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-03 (Tue, 03 Oct 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Fix missing support for command_inject when using containers lib in GIEs Commit: f118fc32c0d7222b2ef2aad3146ef66b4247825f https://github.com/galaxyproject/galaxy/commit/f118fc32c0d7222b2ef2aad3146e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Fix linting error Commit: 8c769b2e29d0503d76b6cc35c734871a3216ef4a https://github.com/galaxyproject/galaxy/commit/8c769b2e29d0503d76b6cc35c734… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #4740 from natefoo/containers-env [17.09] Fix missing support for command_inject when using containers lib in GIEs Compare: https://github.com/galaxyproject/galaxy/compare/9a954ca3432e...8c769b2e29d0

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[galaxyproject/infrastructure-playbook] 163886: Simplify js docker env a bit
by GitHub 05 Oct '17

05 Oct '17

Branch: refs/heads/docker-test Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 163886f8096e50f4dca55724f0f16d70402e30a9 https://github.com/galaxyproject/infrastructure-playbook/commit/163886f8096… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-05 (Thu, 05 Oct 2017) Changed paths: M jetstreamdockerenv/group_vars/all/vars.yml M jetstreamdockerenv/group_vars/all/vault.yml M jetstreamdockerenv/group_vars/imageinstances.yml A jetstreamdockerenv/group_vars/testinstances/vars.yml A jetstreamdockerenv/group_vars/testinstances/vault.yml R jetstreamdockerenv/host_vars/gie-standalone/vars.yml R jetstreamdockerenv/host_vars/gie-standalone/vault.yml M jetstreamdockerenv/inc_clouds_yaml.yml M jetstreamdockerenv/inventory A jetstreamdockerenv/launch_test_instance.yml R jetstreamdockerenv/secret_group_vars/instances.yml R jetstreamdockerenv/standalone.yml Log Message: ----------- Simplify js docker env a bit

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[galaxyproject/usegalaxy-playbook] 8e2c21: Fix typo in RNA STAR explicit destination rule
by GitHub 04 Oct '17

04 Oct '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8e2c21c36668d3b5633009801b54863980e16f63 https://github.com/galaxyproject/usegalaxy-playbook/commit/8e2c21c36668d3b5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-10-04 (Wed, 04 Oct 2017) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py Log Message: ----------- Fix typo in RNA STAR explicit destination rule

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