- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] e14ec1: Update fastx-toolkit to version 0.0.14
by GitHub 08 May '18

08 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e14ec11f0429ebccc527740ef9469333a8aec730 https://github.com/galaxyproject/usegalaxy-playbook/commit/e14ec11f0429ebcc… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Update fastx-toolkit to version 0.0.14 **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] 1083fa: [18.05] Fix sniff validation for dynamic compresse...
by GitHub 08 May '18

08 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 1083fa4ddb611300892516d1947dfd975e60978e https://github.com/galaxyproject/galaxy/commit/1083fa4ddb611300892516d1947d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- [18.05] Fix sniff validation for dynamic compressed types. This was broken in a bad PR merge/rebase process since the validation mode didn't exist when the initial dynamic compressed types PR was opened. Commit: fba70530abf4470e98fc6f1d56d770f33092530b https://github.com/galaxyproject/galaxy/commit/fba70530abf4470e98fc6f1d56d7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Merge pull request #6091 from jmchilton/sniff_prefix_fixes [18.05] Fix sniff validation for dynamic compressed types. Compare: https://github.com/galaxyproject/galaxy/compare/de5ed28120fd...fba70530abf4 **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] fb291e: check memory later
by GitHub 08 May '18

08 May '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: fb291eb530858c79c83be10502d4b78b585d77cb https://github.com/galaxyproject/galaxy/commit/fb291eb530858c79c83be10502d4… Author: E Rasche <hxr(a)hx42.org> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- check memory later Commit: 765a834497ebfc555ac0de98cbbae9ad395f1c49 https://github.com/galaxyproject/galaxy/commit/765a834497ebfc555ac0de98cbba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Memory statement and cd both before instrument_pre_commands Commit: 098f638d26355abe54c83bd43b8daf1078e1ccd3 https://github.com/galaxyproject/galaxy/commit/098f638d26355abe54c83bd43b8d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Merge pull request #5925 from erasche/cd-before-metrics [18.01] jobscript - check memory later Compare: https://github.com/galaxyproject/galaxy/compare/8255d1ccc819...098f638d2635 **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] e55cf0: reword text feedback on viz job submission
by GitHub 08 May '18

08 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: e55cf0114f6f230a1b7935a73336546efd9b57b2 https://github.com/galaxyproject/galaxy/commit/e55cf0114f6f230a1b7935a73336… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js Log Message: ----------- reword text feedback on viz job submission Commit: de5ed28120fdd35495c837148c48526aec7a45d8 https://github.com/galaxyproject/galaxy/commit/de5ed28120fdd35495c837148c48… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js Log Message: ----------- Merge pull request #6090 from martenson/text-adjustment reword text feedback on viz job submission Compare: https://github.com/galaxyproject/galaxy/compare/7b558ddc5965...de5ed28120fd **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] 664a67: update TTS
by GitHub 08 May '18

08 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 664a6765d19ac372d4cbe22cab808a29b3f77732 https://github.com/galaxyproject/usegalaxy-playbook/commit/664a6765d19ac372… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- update TTS **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] 483e87: Fix dropdown zindex handling for history panels
by GitHub 08 May '18

08 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 483e879ca6fee1e58b6f9c99bf07291064ad5065 https://github.com/galaxyproject/galaxy/commit/483e879ca6fee1e58b6f9c99bf07… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Fix dropdown zindex handling for history panels Commit: 7cc01380afd017c5cac2af2b2d735b2265774a68 https://github.com/galaxyproject/galaxy/commit/7cc01380afd017c5cac2af2b2d73… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- Update bs4 style dropdowns, minor cleanup Commit: 7b558ddc5965f6223c862680341e81b345c73d82 https://github.com/galaxyproject/galaxy/commit/7b558ddc5965f6223c862680341e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Merge pull request #6079 from dannon/dropdown-zindex-fix [18.05] Dropdown zindex fix Compare: https://github.com/galaxyproject/galaxy/compare/7d4109bac158...7b558ddc5965 **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] 880fa1: Add sandbox user to docker group on stratum0
by GitHub 08 May '18

08 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 880fa1080588dc830f10973dcaa0ab3a70de18ac https://github.com/galaxyproject/infrastructure-playbook/commit/880fa108058… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M env/galaxy/host_vars/cvmfs0-psu0.galaxyproject.org/vars.yml Log Message: ----------- Add sandbox user to docker group on stratum0 **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] d3901e: Update text processing tools on Test
by GitHub 08 May '18

08 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d3901e9762ed456fdb3ab22ab89a7e5f434491a0 https://github.com/galaxyproject/usegalaxy-playbook/commit/d3901e9762ed456f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 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: ----------- Update text processing tools on Test Commit: 6b5301798e5a50ccef030cbda0b5489f0ed8736b https://github.com/galaxyproject/usegalaxy-playbook/commit/6b5301798e5a50cc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml M env/test/group_vars/all.yml Log Message: ----------- Run a branch of my repo on Test for testing job destination config params Commit: 21dbcefb57df0edd6af5a6c8e2e02018cb061fd0 https://github.com/galaxyproject/usegalaxy-playbook/commit/21dbcefb57df0edd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M env/test/group_vars/galaxyservers/vars.yml M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Test running tools w/ Singularity on Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/55bc28e603e6...… **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] 9da558: Install singularity-runtime on roundup*
by GitHub 08 May '18

08 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 9da558293a25e015543873545a43fdfc6f2fbe6e https://github.com/galaxyproject/infrastructure-playbook/commit/9da558293a2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M env/tacc/group_vars/galaxynodes.yml Log Message: ----------- Install singularity-runtime on roundup* Commit: 5fcca9fece9b040426d4c9686eaddbc9ca5a10e7 https://github.com/galaxyproject/infrastructure-playbook/commit/5fcca9fece9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M env/common/files/ssl/docker/ca.srl A env/common/files/ssl/docker/client.pem A env/common/files/ssl/docker/client_privatekey.yml Log Message: ----------- Generate client cert for docker CA Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/cc99547bbe… **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] 2466bb: Increase UnkillableStepTimeout to try to stop node...
by GitHub 08 May '18

08 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 2466bbc9bc2264b399afe51e4eb1fcd13b13dae5 https://github.com/galaxyproject/infrastructure-playbook/commit/2466bbc9bc2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-03 (Thu, 03 May 2018) Changed paths: M env/tacc/templates/slurm/slurm.conf.j2 Log Message: ----------- Increase UnkillableStepTimeout to try to stop node drain Commit: cc99547bbeeb76c4c1616ad46e373946b1ac0001 https://github.com/galaxyproject/infrastructure-playbook/commit/cc99547bbee… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: R env/galaxy/group_vars/cvmfsstratum1servers.yml A env/galaxy/group_vars/cvmfsstratum1servers/vars.yml A env/galaxy/group_vars/cvmfsstratum1servers/vault.yml M env/galaxy/group_vars/sshservers/vault.yml M env/galaxy/host_vars/cvmfs0-psu0.galaxyproject.org/vars.yml M env/galaxy/host_vars/cvmfs0-psu0.galaxyproject.org/vault.yml M env/galaxy/host_vars/orval.galaxyproject.org/vars.yml M env/galaxy/host_vars/orval.galaxyproject.org/vault.yml M roles/cvmfs/defaults/main.yml Log Message: ----------- Merge branch 'master' of github.com:galaxyproject/infrastructure-playbook Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/8e49e012ce… **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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