May 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook] c65014: Run slurm stats every minute
by GitHub 22 May '18

22 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c650144c4491729aaaba019ab180802f2109ecb8 https://github.com/galaxyproject/infrastructure-playbook/commit/c650144c449… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M env/tacc/group_vars/statsservers/vars.yml Log Message: ----------- Run slurm stats every minute **NOTE:** This service 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] c9ef61: Record 0s for 0 pending/running jobs
by GitHub 22 May '18

22 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: c9ef615b7a8a95f8b3099afbdf31bcf1e78fc720 https://github.com/galaxyproject/infrastructure-playbook/commit/c9ef615b7a8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M roles/stats/templates/galaxy_services_slurp.py.j2 Log Message: ----------- Record 0s for 0 pending/running jobs **NOTE:** This service 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] a00bd8: escape pipe in details
by GitHub 22 May '18

22 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a00bd8bf8eb22bfb38be9146c244fd22f60d3a8f https://github.com/galaxyproject/galaxy/commit/a00bd8bf8eb22bfb38be9146c244… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M doc/parse_gx_xsd.py Log Message: ----------- escape pipe in details so we can have pipes inside markdown tables Commit: 01d2a5c2ae7e5a1f3b5fcfdd2b1eca766a69d5ec https://github.com/galaxyproject/galaxy/commit/01d2a5c2ae7e5a1f3b5fcfdd2b1e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Fix parsing of `scontrol show job` Fix the following traceback: ``` galaxy.jobs.runners.slurm ERROR 2018-05-22 13:01:07,050 (1024816/14094939) Failure in SLURM _complete_terminal_job(), job final state will be: failed Traceback (most recent call last): File "/tgac/services/galaxy/prod/galaxy/lib/galaxy/jobs/runners/slurm.py", line 86, in _complete_terminal_job slurm_state = _get_slurm_state() File "/tgac/services/galaxy/prod/galaxy/lib/galaxy/jobs/runners/slurm.py", line 81, in _get_slurm_state job_info_dict = dict([out_param.split('=', 1) for out_param in stdout.split()]) ValueError: dictionary update sequence element #52 has length 1; 2 is required ``` Commit: 939c3be132b9cd606cd5f1189293f15000a486d8 https://github.com/galaxyproject/galaxy/commit/939c3be132b9cd606cd5f1189293… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #6194 from nsoranzo/fix__get_slurm_state [18.01] Fix parsing of `scontrol show job` Commit: 9a840537cb5037e280a8db14125a46fbb422d305 https://github.com/galaxyproject/galaxy/commit/9a840537cb5037e280a8db14125a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/parse_gx_xsd.py Log Message: ----------- pass the check for pipe presence in details the docs build fine and the table renders fine too Commit: 6f79f28f1793c135b1e0f332987fd62e9dea93b6 https://github.com/galaxyproject/galaxy/commit/6f79f28f1793c135b1e0f332987f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/parse_gx_xsd.py Log Message: ----------- Merge pull request #6187 from martenson/fix-doc-markdown-table [18.01] escape pipe while parsing xsd details Commit: a5297af19017a009fe887a5c04dae281ab234cae https://github.com/galaxyproject/galaxy/commit/a5297af19017a009fe887a5c04da… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/parse_gx_xsd.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: bffeacad081678dc56eeb0af54c8e4eb8443e5ce https://github.com/galaxyproject/galaxy/commit/bffeacad081678dc56eeb0af54c8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/parse_gx_xsd.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/d47e5f25e444...bffeacad0816 **NOTE:** This service 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] a00bd8: escape pipe in details
by GitHub 22 May '18

22 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: a00bd8bf8eb22bfb38be9146c244fd22f60d3a8f https://github.com/galaxyproject/galaxy/commit/a00bd8bf8eb22bfb38be9146c244… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M doc/parse_gx_xsd.py Log Message: ----------- escape pipe in details so we can have pipes inside markdown tables Commit: 01d2a5c2ae7e5a1f3b5fcfdd2b1eca766a69d5ec https://github.com/galaxyproject/galaxy/commit/01d2a5c2ae7e5a1f3b5fcfdd2b1e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Fix parsing of `scontrol show job` Fix the following traceback: ``` galaxy.jobs.runners.slurm ERROR 2018-05-22 13:01:07,050 (1024816/14094939) Failure in SLURM _complete_terminal_job(), job final state will be: failed Traceback (most recent call last): File "/tgac/services/galaxy/prod/galaxy/lib/galaxy/jobs/runners/slurm.py", line 86, in _complete_terminal_job slurm_state = _get_slurm_state() File "/tgac/services/galaxy/prod/galaxy/lib/galaxy/jobs/runners/slurm.py", line 81, in _get_slurm_state job_info_dict = dict([out_param.split('=', 1) for out_param in stdout.split()]) ValueError: dictionary update sequence element #52 has length 1; 2 is required ``` Commit: 939c3be132b9cd606cd5f1189293f15000a486d8 https://github.com/galaxyproject/galaxy/commit/939c3be132b9cd606cd5f1189293… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #6194 from nsoranzo/fix__get_slurm_state [18.01] Fix parsing of `scontrol show job` Commit: 9a840537cb5037e280a8db14125a46fbb422d305 https://github.com/galaxyproject/galaxy/commit/9a840537cb5037e280a8db14125a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/parse_gx_xsd.py Log Message: ----------- pass the check for pipe presence in details the docs build fine and the table renders fine too Commit: 6f79f28f1793c135b1e0f332987fd62e9dea93b6 https://github.com/galaxyproject/galaxy/commit/6f79f28f1793c135b1e0f332987f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/parse_gx_xsd.py Log Message: ----------- Merge pull request #6187 from martenson/fix-doc-markdown-table [18.01] escape pipe while parsing xsd details Commit: a5297af19017a009fe887a5c04dae281ab234cae https://github.com/galaxyproject/galaxy/commit/a5297af19017a009fe887a5c04da… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/parse_gx_xsd.py M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/440f17875f6b...a5297af19017 **NOTE:** This service 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] a00bd8: escape pipe in details
by GitHub 22 May '18

22 May '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: a00bd8bf8eb22bfb38be9146c244fd22f60d3a8f https://github.com/galaxyproject/galaxy/commit/a00bd8bf8eb22bfb38be9146c244… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M doc/parse_gx_xsd.py Log Message: ----------- escape pipe in details so we can have pipes inside markdown tables Commit: 9a840537cb5037e280a8db14125a46fbb422d305 https://github.com/galaxyproject/galaxy/commit/9a840537cb5037e280a8db14125a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/parse_gx_xsd.py Log Message: ----------- pass the check for pipe presence in details the docs build fine and the table renders fine too Commit: 6f79f28f1793c135b1e0f332987fd62e9dea93b6 https://github.com/galaxyproject/galaxy/commit/6f79f28f1793c135b1e0f332987f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/parse_gx_xsd.py Log Message: ----------- Merge pull request #6187 from martenson/fix-doc-markdown-table [18.01] escape pipe while parsing xsd details Compare: https://github.com/galaxyproject/galaxy/compare/939c3be132b9...6f79f28f1793 **NOTE:** This service 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] 0930bf: Collect slurm stuff in influxdb
by GitHub 22 May '18

22 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 0930bff77ce0b532bf551cefad95fc94ee3ec372 https://github.com/galaxyproject/infrastructure-playbook/commit/0930bff77ce… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M env/tacc/group_vars/statsservers/vars.yml M roles/stats/tasks/main.yml A roles/stats/templates/galaxy_services_slurp.py.j2 Log Message: ----------- Collect slurm stuff in influxdb **NOTE:** This service 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] 4c8055: Don't create a useless volume when launching Swarm...
by GitHub 22 May '18

22 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4c805531cc017dd931ecb454d3aa87c2c3ceb201 https://github.com/galaxyproject/usegalaxy-playbook/commit/4c805531cc017dd9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: R roles/usegalaxy_swarmscale/files/inc_spawn.yml M roles/usegalaxy_swarmscale/files/inventory.spawn M roles/usegalaxy_swarmscale/files/spawn.yml M roles/usegalaxy_swarmscale/tasks/main.yml Log Message: ----------- Don't create a useless volume when launching Swarm workers that don't use volumes **NOTE:** This service 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] 01d2a5: Fix parsing of `scontrol show job`
by GitHub 22 May '18

22 May '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 01d2a5c2ae7e5a1f3b5fcfdd2b1eca766a69d5ec https://github.com/galaxyproject/galaxy/commit/01d2a5c2ae7e5a1f3b5fcfdd2b1e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Fix parsing of `scontrol show job` Fix the following traceback: ``` galaxy.jobs.runners.slurm ERROR 2018-05-22 13:01:07,050 (1024816/14094939) Failure in SLURM _complete_terminal_job(), job final state will be: failed Traceback (most recent call last): File "/tgac/services/galaxy/prod/galaxy/lib/galaxy/jobs/runners/slurm.py", line 86, in _complete_terminal_job slurm_state = _get_slurm_state() File "/tgac/services/galaxy/prod/galaxy/lib/galaxy/jobs/runners/slurm.py", line 81, in _get_slurm_state job_info_dict = dict([out_param.split('=', 1) for out_param in stdout.split()]) ValueError: dictionary update sequence element #52 has length 1; 2 is required ``` Commit: 939c3be132b9cd606cd5f1189293f15000a486d8 https://github.com/galaxyproject/galaxy/commit/939c3be132b9cd606cd5f1189293… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #6194 from nsoranzo/fix__get_slurm_state [18.01] Fix parsing of `scontrol show job` Compare: https://github.com/galaxyproject/galaxy/compare/bd4f562005e2...939c3be132b9 **NOTE:** This service 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] 1fbb46: Make it possible to run Jetstream Swarm nodes w/o ...
by GitHub 22 May '18

22 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1fbb465b650947c950e9cdc55afffb7523eb7b90 https://github.com/galaxyproject/infrastructure-playbook/commit/1fbb465b650… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: R env/jsdocker/.snapshot_base.yml.swp M env/jsdocker/_inc_spawn.yml M env/jsdocker/group_vars/all/vars.yml M env/jsdocker/group_vars/baseinstances.yml M env/jsdocker/group_vars/imageinstances.yml M env/jsdocker/launch_test_instance.yml M env/jsdocker/snapshot_base.yml M roles/docker/tasks/install_debian.yml M roles/docker/tasks/install_redhat.yml Log Message: ----------- Make it possible to run Jetstream Swarm nodes w/o a separate volume. Update the image and run in an m1.medium. **NOTE:** This service 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] b2e3c7: Update to new Jetstream Openstack/Docker image, ru...
by GitHub 22 May '18

22 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b2e3c75783cca9e66f55e612ec6aa57109431f36 https://github.com/galaxyproject/usegalaxy-playbook/commit/b2e3c75783cca9e6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M env/main/group_vars/galaxywebservers.yml M env/test/group_vars/galaxyservers/vars.yml M roles/usegalaxy_swarmscale/files/inventory.spawn Log Message: ----------- Update to new Jetstream Openstack/Docker image, run on an m1.medium **NOTE:** This service 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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