galaxy-commits February 2019

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[galaxyproject/usegalaxy-playbook] 0e7966: 1. Fix a bug in the Bridges dynamic rule that woul...
by Nate Coraor 13 Feb '19

13 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0e7966e82ed6eed5b35e8fb5207e9b0f7165df18 https://github.com/galaxyproject/usegalaxy-playbook/commit/0e7966e82ed6eed5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M env/common/files/galaxy/dynamic_rules/bridges_select.py Log Message: ----------- 1. Fix a bug in the Bridges dynamic rule that would've prevented Trinity jobs for receiving more than the default 480GB of memory. 2. Set `RLIMIT_STACK` for Unicycler (SPAdes) jobs to 24MB (the value from br005), fixes #185. 3. Decrease Unicycler jobs to 288GB of memory.

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[galaxyproject/usegalaxy-playbook] fc30c9: Updated featurecounts to 1.6.3+galaxy2
by Dave B. 13 Feb '19

13 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: fc30c998ead3245e883d7093c6bae15cbd9e927b https://github.com/galaxyproject/usegalaxy-playbook/commit/fc30c998ead3245e… Author: Dave B <dave(a)bx.psu.edu> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Updated featurecounts to 1.6.3+galaxy2

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[galaxyproject/usegalaxy-playbook] f3e558: Updated VCFFilter to 1.0.0_rc1+galaxy2
by Dave B. 13 Feb '19

13 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f3e55863f8b900fffb03d00fbac4774b126185f8 https://github.com/galaxyproject/usegalaxy-playbook/commit/f3e55863f8b900ff… Author: Dave B <dave(a)bx.psu.edu> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Updated VCFFilter to 1.0.0_rc1+galaxy2

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[galaxyproject/usegalaxy-playbook] ba5f58: Add Qiang Gu to admin users on usegalaxy.org
by Dave B. 13 Feb '19

13 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ba5f588c3eba443db2d3cdb8b5f8e4e54d0f5bee https://github.com/galaxyproject/usegalaxy-playbook/commit/ba5f588c3eba443d… Author: Dave B <dave(a)bx.psu.edu> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M env/main/group_vars/galaxyservers/vault.yml Log Message: ----------- Add Qiang Gu to admin users on usegalaxy.org

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[galaxyproject/galaxy] a10d2c: Add/pin configurable node version to 18.09. Backp...
by Nicola Soranzo 12 Feb '19

12 Feb '19

Branch: refs/heads/release_19.01 Home: https://github.com/galaxyproject/galaxy Commit: a10d2c51d3e29ceef17b056992f04f98b0f8472c https://github.com/galaxyproject/galaxy/commit/a10d2c51d3e29ceef17b056992f0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M scripts/common_startup.sh Log Message: ----------- Add/pin configurable node version to 18.09. Backport/tweak of https://github.com/galaxyproject/galaxy/pull/7220) Commit: 9c9c8a5d50d7c8ae68f34712d0e9b053aed33ea2 https://github.com/galaxyproject/galaxy/commit/9c9c8a5d50d7c8ae68f34712d0e9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #7239 from dannon/node_ver_pin_18.09 [18.09] Add/pin configurable node version Commit: b33b06440ffdd7e58b6172315df1e015e4ac0e52 https://github.com/galaxyproject/galaxy/commit/b33b06440ffdd7e58b6172315df1… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2019-02-12 (Tue, 12 Feb 2019) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge branch 'release_18.09' into release_19.01 Compare: https://github.com/galaxyproject/galaxy/compare/f7322d85a317...b33b06440ffd

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[galaxyproject/galaxy] a10d2c: Add/pin configurable node version to 18.09. Backp...
by Martin Cech 12 Feb '19

12 Feb '19

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: a10d2c51d3e29ceef17b056992f04f98b0f8472c https://github.com/galaxyproject/galaxy/commit/a10d2c51d3e29ceef17b056992f0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2019-01-18 (Fri, 18 Jan 2019) Changed paths: M scripts/common_startup.sh Log Message: ----------- Add/pin configurable node version to 18.09. Backport/tweak of https://github.com/galaxyproject/galaxy/pull/7220) Commit: 9c9c8a5d50d7c8ae68f34712d0e9b053aed33ea2 https://github.com/galaxyproject/galaxy/commit/9c9c8a5d50d7c8ae68f34712d0e9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M scripts/common_startup.sh Log Message: ----------- Merge pull request #7239 from dannon/node_ver_pin_18.09 [18.09] Add/pin configurable node version Compare: https://github.com/galaxyproject/galaxy/compare/c8b3d5e4c415...9c9c8a5d50d7

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[galaxyproject/usegalaxy-playbook] 5ea19c: Remove Jeremy from reserved
by Nate Coraor 12 Feb '19

12 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5ea19c5707412976c194e7823a115fed4ee91bbc https://github.com/galaxyproject/usegalaxy-playbook/commit/5ea19c5707412976… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py M env/common/files/galaxy/dynamic_rules/reserved.py Log Message: ----------- Remove Jeremy from reserved

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[galaxyproject/usegalaxy-playbook] 76555e: Finish Test tool panel
by Nate Coraor 12 Feb '19

12 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 76555e1154a818df862ce652c48836ad435b1d66 https://github.com/galaxyproject/usegalaxy-playbook/commit/76555e1154a818df… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/migrated_tools_conf.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Finish Test tool panel Commit: 0d9b413d8a9cc5df562034cd98a4ca12bfbfba60 https://github.com/galaxyproject/usegalaxy-playbook/commit/0d9b413d8a9cc5df… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/migrated_tools_conf.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Final Main tool panel fixes Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/9075cd028b90...…

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[galaxyproject/usegalaxy-playbook]
by Martin Cech 11 Feb '19

11 Feb '19

Branch: refs/heads/martenson-patch-2 Home: https://github.com/galaxyproject/usegalaxy-playbook

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[galaxyproject/usegalaxy-playbook] 38a244: limit nginx upload size for toolsheds server
by Nate Coraor 11 Feb '19

11 Feb '19

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 38a244ffeb8d61277113e89a69ae3636a21a4090 https://github.com/galaxyproject/usegalaxy-playbook/commit/38a244ffeb8d6127… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M env/common/group_vars/toolshedwebservers.yml Log Message: ----------- limit nginx upload size for toolsheds server should resolve galaxyproject/galaxy#2517, suggested by @natefoo Commit: 9075cd028b9069b64f852f9b6ac5c2875103ea87 https://github.com/galaxyproject/usegalaxy-playbook/commit/9075cd028b9069b6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2019-02-11 (Mon, 11 Feb 2019) Changed paths: M env/common/group_vars/toolshedwebservers.yml Log Message: ----------- Merge pull request #189 from galaxyproject/martenson-patch-2 limit nginx upload size for toolsheds server Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/c089d23463b3...…

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galaxy-commits February 2019