- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 8edb74: Keep xlsx files compressed
by GitHub 15 Oct '18

15 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 8edb7499c8d336d727fa751a2097d0356cf5bcbe https://github.com/galaxyproject/galaxy/commit/8edb7499c8d336d727fa751a2097… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-13 (Sat, 13 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Keep xlsx files compressed Fixes https://github.com/galaxyproject/galaxy/issues/6849 Commit: 0c7cc50e73827ac65eabf10400c90a644a15f10b https://github.com/galaxyproject/galaxy/commit/0c7cc50e73827ac65eabf10400c9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-13 (Sat, 13 Oct 2018) Changed paths: M lib/galaxy/datatypes/upload_util.py Log Message: ----------- Only warn about multi-file zips if we don't keep the compressed archive Commit: 03073ed1249d2403994013d9f4486f85d7a23e80 https://github.com/galaxyproject/galaxy/commit/03073ed1249d2403994013d9f448… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/upload_util.py Log Message: ----------- Merge pull request #6867 from mvdbeek/fix_xlsx_unpacking [18.09] Keep xlsx files compressed Compare: https://github.com/galaxyproject/galaxy/compare/01f1f1b95fba...03073ed1249d **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 20526c: Share ssh key generation across tests
by GitHub 15 Oct '18

15 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 20526ceb50b4406618de9cfbff771c86f6ea4af8 https://github.com/galaxyproject/galaxy/commit/20526ceb50b4406618de9cfbff77… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-14 (Sun, 14 Oct 2018) Changed paths: A test/base/ssh_util.py M test/integration/test_cli_runners.py M test/unit/test_remote_shell.py Log Message: ----------- Share ssh key generation across tests Closes https://github.com/galaxyproject/galaxy/issues/6860 Commit: 2a422fa61f946f7ca37d96dc18cbf765601e2924 https://github.com/galaxyproject/galaxy/commit/2a422fa61f946f7ca37d96dc18cb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-14 (Sun, 14 Oct 2018) Changed paths: A test/base/ssh_util.py M test/integration/test_cli_runners.py M test/unit/test_remote_shell.py Log Message: ----------- Merge pull request #6865 from mvdbeek/share_key_function Share ssh key generation across tests Compare: https://github.com/galaxyproject/galaxy/compare/504cecfebb03...2a422fa61f94 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] dd97c5: Stop reimplementing priority queueing for Slurm......
by GitHub 14 Oct '18

14 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: dd97c5e1a55da1013517e16d9a7b2d1e8f6f3695 https://github.com/galaxyproject/infrastructure-playbook/commit/dd97c5e1a55… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-14 (Sun, 14 Oct 2018) Changed paths: M env/tacc/group_vars/slurmservers.yml M env/tacc/templates/slurm/slurm.conf.j2 Log Message: ----------- Stop reimplementing priority queueing for Slurm... =/ **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 1b1fef: Create container_resolvers_conf.xml.sample
by GitHub 13 Oct '18

13 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1b1fefca4598210b1045ceb6a6f2610a70517454 https://github.com/galaxyproject/galaxy/commit/1b1fefca4598210b1045ceb6a6f2… Author: Pablo Moreno <pcm32(a)users.noreply.github.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: A config/container_resolvers_conf.xml.sample Log Message: ----------- Create container_resolvers_conf.xml.sample Commit: 35b030486335ce802eb88510fd52d82a25ac0fb0 https://github.com/galaxyproject/galaxy/commit/35b030486335ce802eb88510fd52… Author: Pablo Moreno <pcm32(a)users.noreply.github.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M config/container_resolvers_conf.xml.sample Log Message: ----------- Minor changes as requested Commit: b17665c9131878fb93225e613c863e1dc0411027 https://github.com/galaxyproject/galaxy/commit/b17665c9131878fb93225e613c86… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M config/container_resolvers_conf.xml.sample Log Message: ----------- Minor wording changes Commit: 02d5caae6915b1292b44870ca60361aff67816c4 https://github.com/galaxyproject/galaxy/commit/02d5caae6915b1292b44870ca603… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M config/container_resolvers_conf.xml.sample Log Message: ----------- Reword container to image where appropriate Commit: 504cecfebb0357e8a842a8b2bd11dfa7ffa6a4e1 https://github.com/galaxyproject/galaxy/commit/504cecfebb0357e8a842a8b2bd11… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-13 (Sat, 13 Oct 2018) Changed paths: A config/container_resolvers_conf.xml.sample Log Message: ----------- Merge pull request #6700 from pcm32/patch-1 Create container_resolvers_conf.xml.sample Compare: https://github.com/galaxyproject/galaxy/compare/ca95d7a26e70...504cecfebb03 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 4153f0: Add a special destination increasing the concurren...
by GitHub 12 Oct '18

12 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4153f00dec4071d657448f35ff780b6e2fbea18a https://github.com/galaxyproject/usegalaxy-playbook/commit/4153f00dec4071d6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Add a special destination increasing the concurrency limit for du novo align families **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 1dd2f3: include one column of cards and one of twitter
by GitHub 12 Oct '18

12 Oct '18

Branch: refs/heads/new-welcome Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1dd2f3d65e621a15c111be0166f2ca559f2fa488 https://github.com/galaxyproject/usegalaxy-playbook/commit/1dd2f3d65e621a15… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- include one column of cards and one of twitter **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 7246d5: Update Test
by GitHub 12 Oct '18

12 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7246d5f669b9cf58d6f71a5d4ebd11993daf05b3 https://github.com/galaxyproject/usegalaxy-playbook/commit/7246d5f669b9cf58… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test Commit: 3223a978e35a2140713d147c10d95d8f65d61021 https://github.com/galaxyproject/usegalaxy-playbook/commit/3223a978e35a2140… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main Commit: 0257084d6910b8d01759ea7f91a09c1a00093d1e https://github.com/galaxyproject/usegalaxy-playbook/commit/0257084d6910b8d0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M env/main/group_vars/galaxyservers/vault.yml Log Message: ----------- Update admin users Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/1f66079a08f4...… **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] d791a2: Revert selective metadata flushing - seems to brea...
by GitHub 12 Oct '18

12 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d791a2c80f3290d66c2252f29981a16a4459661b https://github.com/galaxyproject/galaxy/commit/d791a2c80f3290d66c2252f29981… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Revert selective metadata flushing - seems to break upload changes. Commit: f3da0864b45a3aa307c7fe9eeb8c5d26dd9c8527 https://github.com/galaxyproject/galaxy/commit/f3da0864b45a3aa307c7fe9eeb8c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M test/api/test_tools.py A test/functional/tools/for_workflows/mapper_two.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test case for regression #6856. Commit: 01f1f1b95fba671a2d92d7111676229a7ed5d58a https://github.com/galaxyproject/galaxy/commit/01f1f1b95fba671a2d92d7111676… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/model/metadata.py M test/api/test_tools.py A test/functional/tools/for_workflows/mapper_two.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6858 from jmchilton/fix_metadata_revert [18.09] Revert selective metadata flushing - breaks multiple uploads/outputs. Commit: ca95d7a26e70ca02159febd971fa8b63c2667ab5 https://github.com/galaxyproject/galaxy/commit/ca95d7a26e70ca02159febd971fa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/model/metadata.py M test/api/test_tools.py A test/functional/tools/for_workflows/mapper_two.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/ff32e5434145...ca95d7a26e70 **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 1f6607: Test mutable configs
by GitHub 12 Oct '18

12 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1f66079a08f4dbd7b62aa74cfd10800312ef4912 https://github.com/galaxyproject/usegalaxy-playbook/commit/1f66079a08f4dbd7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Test mutable configs **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] d791a2: Revert selective metadata flushing - seems to brea...
by GitHub 12 Oct '18

12 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: d791a2c80f3290d66c2252f29981a16a4459661b https://github.com/galaxyproject/galaxy/commit/d791a2c80f3290d66c2252f29981… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Revert selective metadata flushing - seems to break upload changes. Commit: f3da0864b45a3aa307c7fe9eeb8c5d26dd9c8527 https://github.com/galaxyproject/galaxy/commit/f3da0864b45a3aa307c7fe9eeb8c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M test/api/test_tools.py A test/functional/tools/for_workflows/mapper_two.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test case for regression #6856. Commit: 01f1f1b95fba671a2d92d7111676229a7ed5d58a https://github.com/galaxyproject/galaxy/commit/01f1f1b95fba671a2d92d7111676… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/model/metadata.py M test/api/test_tools.py A test/functional/tools/for_workflows/mapper_two.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6858 from jmchilton/fix_metadata_revert [18.09] Revert selective metadata flushing - breaks multiple uploads/outputs. Compare: https://github.com/galaxyproject/galaxy/compare/4805304e0bf3...01f1f1b95fba **NOTE:** This service has been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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