galaxy-commits May 2017

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[galaxyproject/galaxy] c40957: Handle potential regex expression in workflow para...
by GitHub 01 Jun '17

01 Jun '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: c409572ef8510e0c4322d835c5ba90f32bc9c653 https://github.com/galaxyproject/galaxy/commit/c409572ef8510e0c4322d835c5ba… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-05-31 (Wed, 31 May 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map 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/tool/tool-form-composite.js Log Message: ----------- Handle potential regex expression in workflow parameter names Commit: 75028ac1eec7de53a197217921ebd5b7dac4daac https://github.com/galaxyproject/galaxy/commit/75028ac1eec7de53a197217921eb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-31 (Wed, 31 May 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M static/maps/mvc/tool/tool-form-composite.js.map 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/tool/tool-form-composite.js Log Message: ----------- Merge pull request #4133 from guerler/escape_regex [17.05] Properly escape potential regex expression in workflow parameters Compare: https://github.com/galaxyproject/galaxy/compare/f6ced00ef0de...75028ac1eec7

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[galaxyproject/galaxy] a9d0d3: Fix for returning a fileobject in compression_util...
by GitHub 01 Jun '17

01 Jun '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: a9d0d3671afc2be90509517b53b96af694ff22e5 https://github.com/galaxyproject/galaxy/commit/a9d0d3671afc2be90509517b53b9… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2017-05-31 (Wed, 31 May 2017) Changed paths: M lib/galaxy/util/compression_utils.py Log Message: ----------- Fix for returning a fileobject in compression_utils.py when handling a zipfile. Will return the first named object in the archive. zipfile.os_zipfile does not exist... Commit: f6ced00ef0de0fa67e2ecd06fa2db204e73f25ad https://github.com/galaxyproject/galaxy/commit/f6ced00ef0de0fa67e2ecd06fa2d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-31 (Wed, 31 May 2017) Changed paths: M lib/galaxy/util/compression_utils.py Log Message: ----------- Merge pull request #4135 from blankenberg/17.05_zipfile [17.05] Fix for returning a fileobject in compression_utils.py when handling a zipfile. Compare: https://github.com/galaxyproject/galaxy/compare/42e274d33427...f6ced00ef0de

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[galaxyproject/galaxy] 68433b: Force uniqueness of preserved tags (so, don't allo...
by GitHub 31 May '17

31 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 68433b1eff0a93704544a49f3d8f3a912d97c285 https://github.com/galaxyproject/galaxy/commit/68433b1eff0a93704544a49f3d8f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-25 (Thu, 25 May 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Force uniqueness of preserved tags (so, don't allow many inputs with a 'name:foo' tag to add a ton of 'name:foo' tags to a dataset; just use one) Commit: b6e8d3e8acd00c1a595f15f2654c1b7809ecc831 https://github.com/galaxyproject/galaxy/commit/b6e8d3e8acd00c1a595f15f2654c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-26 (Fri, 26 May 2017) Changed paths: M lib/galaxy/managers/collections.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Slight refactoring to use a dict for unique'ing preserved tags. TODO: enhance object builtins to compare correctly so we can use a set, maybe. Not a big deal unless/until we have a second type of preserved tag though. Commit: dd06a01746f2ace048b9e1e604756e648a6ef1fd https://github.com/galaxyproject/galaxy/commit/dd06a01746f2ace048b9e1e60475… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-26 (Fri, 26 May 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Handle *both* paths for tag appending using the now-dict correctly. Commit: 2ac04bbf095573f2621ffeea0e2fdeb59b21da53 https://github.com/galaxyproject/galaxy/commit/2ac04bbf095573f2621ffeea0e2f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-26 (Fri, 26 May 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hdca-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 M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Uniqueify hashtag display Commit: 3d16319a15b7ac2f947eca24c36957894ae00afe https://github.com/galaxyproject/galaxy/commit/3d16319a15b7ac2f947eca24c369… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-05-27 (Sat, 27 May 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M lib/galaxy/managers/collections.py M lib/galaxy/tools/actions/__init__.py M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hdca-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 M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Merge pull request #4114 from dannon/force_uniqueness_preserved_tags [17.05] Force uniqueness of preserved tags Commit: 55336d2c3142051f605231e6db1cb6a45639417c https://github.com/galaxyproject/galaxy/commit/55336d2c3142051f605231e6db1c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-28 (Sun, 28 May 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix legacy Python path for genome diversity tools from miller lab. Fixes #4108. Commit: 96e1cf58f480549cf5b39647c8772863405f582f https://github.com/galaxyproject/galaxy/commit/96e1cf58f480549cf5b39647c877… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-05-29 (Mon, 29 May 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #4117 from jmchilton/genome_diversity_fixes [17.01] Fix legacy Python path for genome diversity tools from miller lab. Commit: 42e274d3342720037d441222b9fb1bbcbce2d7c1 https://github.com/galaxyproject/galaxy/commit/42e274d3342720037d441222b9fb… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-30 (Tue, 30 May 2017) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #4122 from galaxyproject/release_17.01 [17.05] merge Release 17.01 Commit: b6597d43f39b621ada9e0aaffc47134f7daf47b3 https://github.com/galaxyproject/galaxy/commit/b6597d43f39b621ada9e0aaffc47… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-31 (Wed, 31 May 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/hdca-li.js M lib/galaxy/managers/collections.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/history/hdca-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 M static/scripts/mvc/history/hdca-li.js Log Message: ----------- Merge remote-tracking branch 'upstream/release_17.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/5845af256239...b6597d43f39b

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[galaxyproject/infrastructure-playbook] 8b8037: Add role for RabbitMQ and make galaxy08 a RabbitMQ...
by GitHub 31 May '17

31 May '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 8b80375a65e0df09a255a21caf702dfcc3ff7e37 https://github.com/galaxyproject/infrastructure-playbook/commit/8b80375a65e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-31 (Wed, 31 May 2017) Changed paths: A common_env/files/ssl/rabbitmq/ca-key.pem A common_env/files/ssl/rabbitmq/ca.pem A common_env/files/ssl/rabbitmq/ca.srl A common_env/files/ssl/rabbitmq/galaxy08.tacc.utexas.edu/server.pem A common_env/files/ssl/rabbitmq/galaxy08.tacc.utexas.edu/server_privatekey.yml A common_env/group_vars/sslservers/vars.yml A common_env/group_vars/sslservers/vault.yml M common_roles A roles/rabbitmq/handlers/main.yml A roles/rabbitmq/tasks/main.yml A roles/rabbitmq/templates/rabbitmq.config.j2 A taccenv/files/ssl R taccenv/files/ssl/wildcard_cert.pem A taccenv/group_vars/rabbitmqservers/vars.yml A taccenv/group_vars/rabbitmqservers/vault.yml A taccenv/group_vars/sslservers M taccenv/inventory M taccenv/playbook.yml Log Message: ----------- Add role for RabbitMQ and make galaxy08 a RabbitMQ server. Upgrade common roles to use the new SSL role

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[galaxyproject/infrastructure-playbook] 6611e0: Add role for RabbitMQ and make galaxy08 a RabbitMQ...
by GitHub 31 May '17

31 May '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6611e02953441e66abed045cfcf61885d291f380 https://github.com/galaxyproject/infrastructure-playbook/commit/6611e029534… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-31 (Wed, 31 May 2017) Changed paths: A common_env/files/ssl/rabbitmq/ca-key.pem A common_env/files/ssl/rabbitmq/ca.pem A common_env/files/ssl/rabbitmq/ca.srl A common_env/files/ssl/rabbitmq/galaxy08.tacc.utexas.edu/server.pem A common_env/files/ssl/rabbitmq/galaxy08.tacc.utexas.edu/server_privatekey.yml A common_env/group_vars/sslservers/vars.yml A common_env/group_vars/sslservers/vault.yml M common_roles A taccenv/files/ssl R taccenv/files/ssl/wildcard_cert.pem A taccenv/group_vars/rabbitmqservers/vars.yml A taccenv/group_vars/rabbitmqservers/vault.yml A taccenv/group_vars/sslservers M taccenv/inventory M taccenv/playbook.yml Log Message: ----------- Add role for RabbitMQ and make galaxy08 a RabbitMQ server. Upgrade common roles to use the new SSL role

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[galaxyproject/galaxy] 7037a5: Fix typo
by GitHub 31 May '17

31 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7037a57a420c0db16ef89434d0c5d8f11103ba43 https://github.com/galaxyproject/galaxy/commit/7037a57a420c0db16ef89434d0c5… Author: Manabu ISHII <manabu.ishii.rb(a)gmail.com> Date: 2017-05-31 (Wed, 31 May 2017) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Fix typo Commit: 5845af256239a85a58c4e8679dadf3d2a5f59615 https://github.com/galaxyproject/galaxy/commit/5845af256239a85a58c4e8679dad… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-05-31 (Wed, 31 May 2017) Changed paths: M config/job_conf.xml.sample_advanced Log Message: ----------- Merge pull request #4126 from manabuishii/patch-5 Fix typo Compare: https://github.com/galaxyproject/galaxy/compare/d61ab1644bfe...5845af256239

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[galaxyproject/infrastructure-playbook] e276c4: Use vars/vault for authorized keys
by GitHub 30 May '17

30 May '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: e276c43f00fc7ad82e78c187d25e2fc7e6044935 https://github.com/galaxyproject/infrastructure-playbook/commit/e276c43f00f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-30 (Tue, 30 May 2017) Changed paths: R taccenv/group_vars/maingalaxyservers.yml A taccenv/group_vars/maingalaxyservers/vars.yml A taccenv/group_vars/maingalaxyservers/vault.yml R taccenv/group_vars/testgalaxyservers.yml A taccenv/group_vars/testgalaxyservers/vars.yml A taccenv/group_vars/testgalaxyservers/vault.yml R taccenv/secret_group_vars/maingalaxyservers.yml R taccenv/secret_group_vars/testgalaxyservers.yml Log Message: ----------- Use vars/vault for authorized keys

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[galaxyproject/galaxy] 8080c0: Fix escaping of status/message passed by querystri...
by GitHub 30 May '17

30 May '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8080c08ae646e4a2ea56b0b9a657c05413128a2e https://github.com/galaxyproject/galaxy/commit/8080c08ae646e4a2ea56b0b9a657… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-30 (Tue, 30 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: ----------- Fix escaping of status/message passed by querystring in the new workflow menu. Commit: 5c954139fa7cb1fee56c0438024d88a9a7a542a8 https://github.com/galaxyproject/galaxy/commit/5c954139fa7cb1fee56c0438024d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-05-30 (Tue, 30 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: ----------- Since we're using addClass to inject status type, it's not necessary to escape this one. Commit: d61ab1644bfedd9e6e4db8ba7c7762dcf3363c40 https://github.com/galaxyproject/galaxy/commit/d61ab1644bfedd9e6e4db8ba7c77… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-05-30 (Tue, 30 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: ----------- Merge pull request #4124 from dannon/fix_workflow_menu_escaping New workflow menu message fix Compare: https://github.com/galaxyproject/galaxy/compare/9896fc0e9f47...d61ab1644bfe

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[galaxyproject/infrastructure-playbook] 46979f: Increase max walltime to 96 hours
by GitHub 30 May '17

30 May '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 46979f02615fca10e60f211f32da6ee8aca35482 https://github.com/galaxyproject/infrastructure-playbook/commit/46979f02615… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-30 (Tue, 30 May 2017) Changed paths: M taccenv/templates/slurm/slurm.conf.j2 Log Message: ----------- Increase max walltime to 96 hours

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[galaxyproject/usegalaxy-playbook] 19846e: give salmon 16gb and rna_Star 64
by GitHub 30 May '17

30 May '17

Branch: refs/heads/reorg Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 19846e3ebdd8597e9e21d9e6a4f3ec0c13b8491c https://github.com/galaxyproject/usegalaxy-playbook/commit/19846e3ebdd8597e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-30 (Tue, 30 May 2017) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- give salmon 16gb and rna_Star 64 Commit: 9c6af8b03364613a7873fb91407893b55ce6fcb0 https://github.com/galaxyproject/usegalaxy-playbook/commit/9c6af8b03364613a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-05-30 (Tue, 30 May 2017) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py M env/main/files/galaxy/galaxy_version.yml M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_data_manager_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Fix walltime exception for align families running on local cluster and update Main Conflicts: production/galaxy_version.yml Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/376b8c62fac4...…

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galaxy-commits May 2017