- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 72d07e: remove mention of 18.09, that is only for dev
by GitHub 23 May '18

23 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 72d07e07d5164519e31bfe5811ce9dbd980ecf1e https://github.com/galaxyproject/galaxy/commit/72d07e07d5164519e31bfe5811ce… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: R doc/source/releases/18.09_announce.rst M doc/source/releases/index.rst Log Message: ----------- remove mention of 18.09, that is only for dev Commit: bd049665d1201a3c35d3bd1e3ff48891cd54fbcd https://github.com/galaxyproject/galaxy/commit/bd049665d1201a3c35d3bd1e3ff4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: R doc/source/releases/18.09_announce.rst M doc/source/releases/index.rst Log Message: ----------- Merge pull request #6203 from martenson/remove-1809 [18.05] remove mention of 18.09, that is only for dev Compare: https://github.com/galaxyproject/galaxy/compare/a8e0eda44db8...bd049665d120 **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] 980595: Update Test
by GitHub 23 May '18

23 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 980595026090b885992705a0a5531b009de47054 https://github.com/galaxyproject/usegalaxy-playbook/commit/980595026090b885… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/group_vars/all.yml Log Message: ----------- Update Test **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] 84c599: Allow non-ascii chars in passwords.
by GitHub 23 May '18

23 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 84c59917e6e0c4b90d4f29720d547de816302230 https://github.com/galaxyproject/galaxy/commit/84c59917e6e0c4b90d4f29720d54… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M lib/galaxy/security/passwords.py Log Message: ----------- Allow non-ascii chars in passwords. Commit: a8e0eda44db84f756004e266865d16d0fb13eb3e https://github.com/galaxyproject/galaxy/commit/a8e0eda44db84f756004e266865d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M lib/galaxy/security/passwords.py Log Message: ----------- Merge pull request #6175 from dannon/password_fixes [18.05] Allow non-ascii chars in pbkdf2 passwords Compare: https://github.com/galaxyproject/galaxy/compare/44e57ba8b45d...a8e0eda44db8 **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] 7bf55f: Fix history list bottom border
by GitHub 23 May '18

23 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7bf55fc301cb6819b371e25030014cde830c05c9 https://github.com/galaxyproject/galaxy/commit/7bf55fc301cb6819b371e2503001… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Fix history list bottom border Commit: 029975a9f8abe57b6f4ef9d9a9cc50a07f401113 https://github.com/galaxyproject/galaxy/commit/029975a9f8abe57b6f4ef9d9a9cc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/style/scss/history.scss Log Message: ----------- A more accurate version of what was set before, with the same outcome (though, it could change if we toggle the grey) Commit: 8d1cff2bba25c70baeebf8fde0878b4e5caa8b2f https://github.com/galaxyproject/galaxy/commit/8d1cff2bba25c70baeebf8fde087… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/style/scss/list-item.scss M static/style/blue/base.css Log Message: ----------- Fix dataset messagesmall display, was a TODO left from migration Commit: e06639e9456ba022ce6a12e4eba15a696fb37e51 https://github.com/galaxyproject/galaxy/commit/e06639e9456ba022ce6a12e4eba1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Fix one more busted fade Commit: eadfd406d238b5ef7ad97c964a44e39d6a9d46e9 https://github.com/galaxyproject/galaxy/commit/eadfd406d238b5ef7ad97c964a44… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix (ancient, should replace this, but might as well make it work until we do) tool-shed-only grid search button Commit: 74377074ac12fcadb771f5ea212fa1bd7a048df8 https://github.com/galaxyproject/galaxy/commit/74377074ac12fcadb771f5ea212f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css M templates/webapps/tool_shed/common/grid_common.mako Log Message: ----------- Drop submit-image custom styling, use standard fa; left it as inline style to keep it clean and remove all at once when this grid goes. Commit: 162fa3a5bbd52ea75db5ec22c32a7a3d86560029 https://github.com/galaxyproject/galaxy/commit/162fa3a5bbd52ea75db5ec22c32a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M client/galaxy/style/scss/list-item.scss M static/style/blue/base.css Log Message: ----------- Fix list panel control message margins. Commit: 51b93ebc48b96278342b06583642af14fe48ce3a https://github.com/galaxyproject/galaxy/commit/51b93ebc48b96278342b06583642… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M client/galaxy/style/scss/upload.scss Log Message: ----------- This is correct now Commit: a57600cadfe4b3f383ce69afaf3dc09c237456f8 https://github.com/galaxyproject/galaxy/commit/a57600cadfe4b3f383ce69afaf3d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/list-item.scss M client/galaxy/style/scss/upload.scss M static/style/blue/base.css M templates/webapps/tool_shed/common/grid_common.mako Log Message: ----------- Merge pull request #6197 from dannon/1805stylefixes [18.05] Minor style fixes Compare: https://github.com/galaxyproject/galaxy/compare/2cf1c0013786...a57600cadfe4 **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] 72d228: Put limits on reserved jobs
by GitHub 23 May '18

23 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 72d228f3b217aff385bc408d6eac47aa141181c7 https://github.com/galaxyproject/usegalaxy-playbook/commit/72d228f3b217aff3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Put limits on reserved 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] 65c1cd: Fix data_source.py for upload changes in 18.05 rel...
by GitHub 23 May '18

23 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 65c1cd761c48ba121a847d4d501eb8a97a911e70 https://github.com/galaxyproject/galaxy/commit/65c1cd761c48ba121a847d4d501e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/upload_util.py M lib/galaxy/jobs/__init__.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Fix data_source.py for upload changes in 18.05 release cycle. handle_uploaded_dataset_file was used by tools external to ``lib/`` include data_source.py and potentially tools in the tool shed. This restores the interface as a wrapper around a new method handle_uploaded_dataset_file_internal. Broken in https://github.com/galaxyproject/galaxy/commit/ef6f7f62ab679928045c816a3cb7… I believe. Commit: 44e57ba8b45d2ddd624333547ec1adeb62d70b9c https://github.com/galaxyproject/galaxy/commit/44e57ba8b45d2ddd624333547ec1… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-05-23 (Wed, 23 May 2018) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/datatypes/upload_util.py M lib/galaxy/jobs/__init__.py M lib/galaxy_ext/metadata/set_metadata.py Log Message: ----------- Merge pull request #6196 from jmchilton/fix_metadata [18.05] Fix data_source.py for upload changes in 18.05 release cycle. Compare: https://github.com/galaxyproject/galaxy/compare/ebc6734ed787...44e57ba8b45d **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] cfaf71: Support building and publishing pre-release docs
by GitHub 23 May '18

23 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cfaf7186bda346445e0c1e0bd706eefe826b9323 https://github.com/galaxyproject/galaxy/commit/cfaf7186bda346445e0c1e0bd706… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/source/conf.versioning.py Log Message: ----------- Support building and publishing pre-release docs Commit: ebc6734ed787fd4b10858d622e3c7e49d33309ac https://github.com/galaxyproject/galaxy/commit/ebc6734ed787fd4b10858d622e3c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/source/conf.versioning.py Log Message: ----------- Merge pull request #6199 from natefoo/docs-pre-release [18.05] Support building and publishing pre-release docs Commit: 2cf1c00137862fd90ce8ccc2fa34751e65e7f960 https://github.com/galaxyproject/galaxy/commit/2cf1c00137862fd90ce8ccc2fa34… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/source/conf.versioning.py Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/bffeacad0816...2cf1c0013786 **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] cfaf71: Support building and publishing pre-release docs
by GitHub 22 May '18

22 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: cfaf7186bda346445e0c1e0bd706eefe826b9323 https://github.com/galaxyproject/galaxy/commit/cfaf7186bda346445e0c1e0bd706… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/source/conf.versioning.py Log Message: ----------- Support building and publishing pre-release docs Commit: ebc6734ed787fd4b10858d622e3c7e49d33309ac https://github.com/galaxyproject/galaxy/commit/ebc6734ed787fd4b10858d622e3c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M doc/source/conf.versioning.py Log Message: ----------- Merge pull request #6199 from natefoo/docs-pre-release [18.05] Support building and publishing pre-release docs Compare: https://github.com/galaxyproject/galaxy/compare/a5297af19017...ebc6734ed787 **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] 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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[galaxyproject/galaxy] fcde0d: Avoid overlapping change handlers
by GitHub 22 May '18

22 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fcde0d669f3e65bf92f05dc517fe550d017c86c4 https://github.com/galaxyproject/galaxy/commit/fcde0d669f3e65bf92f05dc517fe… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js Log Message: ----------- Avoid overlapping change handlers Commit: 49c824cf01d3b03d7041dc9a2ebe438471dd27e0 https://github.com/galaxyproject/galaxy/commit/49c824cf01d3b03d7041dc9a2ebe… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js Log Message: ----------- Merge pull request #6185 from guerler/fix_repeat_inputs [18.05] Fix repeated inputs Commit: 4d38c25c9f746370d9070dfc3d00a488a3b9e27f https://github.com/galaxyproject/galaxy/commit/4d38c25c9f746370d9070dfc3d00… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Right align button menu popup Commit: 2fe24e470d9e555674685006475c9f5cbe00f0c3 https://github.com/galaxyproject/galaxy/commit/2fe24e470d9e555674685006475c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Merge pull request #6188 from guerler/fix_popup_right [18.05] Right align button menu popup Commit: b931356ef3ea6a2b99add6ed180fa81c64b59632 https://github.com/galaxyproject/galaxy/commit/b931356ef3ea6a2b99add6ed180f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- Fix sphinx. Commit: 440f17875f6b5ce36147ee1e830162e40c0c0d48 https://github.com/galaxyproject/galaxy/commit/440f17875f6b5ce36147ee1e8301… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- Merge pull request #6191 from jmchilton/fix_sphinx [18.05] Lock dependency on Sphinx to <1.7. Commit: d47e5f25e44405c8bbf5a5fa7a5d62ef709c5e8b https://github.com/galaxyproject/galaxy/commit/d47e5f25e44405c8bbf5a5fa7a5d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/a992637de17d...d47e5f25e444 **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] b93135: Fix sphinx.
by GitHub 22 May '18

22 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: b931356ef3ea6a2b99add6ed180fa81c64b59632 https://github.com/galaxyproject/galaxy/commit/b931356ef3ea6a2b99add6ed180f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- Fix sphinx. Commit: 440f17875f6b5ce36147ee1e830162e40c0c0d48 https://github.com/galaxyproject/galaxy/commit/440f17875f6b5ce36147ee1e8301… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-22 (Tue, 22 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/develop/Pipfile M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt Log Message: ----------- Merge pull request #6191 from jmchilton/fix_sphinx [18.05] Lock dependency on Sphinx to <1.7. Compare: https://github.com/galaxyproject/galaxy/compare/2fe24e470d9e...440f17875f6b **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] aa34f8: Increase memory for GIEs to 2GB
by GitHub 21 May '18

21 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: aa34f8162afa0fc1089bb5d478c5b7801f100ce4 https://github.com/galaxyproject/usegalaxy-playbook/commit/aa34f8162afa0fc1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M env/main/group_vars/galaxywebservers.yml Log Message: ----------- Increase memory for GIEs to 2GB **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] 691bbf: Restart docker nightly on swarm managers because I...
by GitHub 21 May '18

21 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 691bbfbf5db0cee5d7c5c25cbb15029d5c504ee0 https://github.com/galaxyproject/infrastructure-playbook/commit/691bbfbf5db… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M env/galaxy/group_vars/dockerswarmmanagers/vars.yml M env/galaxy/playbook.yml Log Message: ----------- Restart docker nightly on swarm managers because I hate swarm **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] 4d38c2: Right align button menu popup
by GitHub 21 May '18

21 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 4d38c25c9f746370d9070dfc3d00a488a3b9e27f https://github.com/galaxyproject/galaxy/commit/4d38c25c9f746370d9070dfc3d00… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Right align button menu popup Commit: 2fe24e470d9e555674685006475c9f5cbe00f0c3 https://github.com/galaxyproject/galaxy/commit/2fe24e470d9e555674685006475c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Merge pull request #6188 from guerler/fix_popup_right [18.05] Right align button menu popup Compare: https://github.com/galaxyproject/galaxy/compare/49c824cf01d3...2fe24e470d9e **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] fcde0d: Avoid overlapping change handlers
by GitHub 21 May '18

21 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: fcde0d669f3e65bf92f05dc517fe550d017c86c4 https://github.com/galaxyproject/galaxy/commit/fcde0d669f3e65bf92f05dc517fe… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js Log Message: ----------- Avoid overlapping change handlers Commit: 49c824cf01d3b03d7041dc9a2ebe438471dd27e0 https://github.com/galaxyproject/galaxy/commit/49c824cf01d3b03d7041dc9a2ebe… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-section.js Log Message: ----------- Merge pull request #6185 from guerler/fix_repeat_inputs [18.05] Fix repeated inputs Compare: https://github.com/galaxyproject/galaxy/compare/805854aa6b16...49c824cf01d3 **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] c25343: Fix append() for ANY_COLLECTION_TYPE type descript...
by GitHub 21 May '18

21 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c253436b4a7c646910bdc1f8ce9c2f01fe43f1ff https://github.com/galaxyproject/galaxy/commit/c253436b4a7c646910bdc1f8ce9c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-18 (Fri, 18 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Fix append() for ANY_COLLECTION_TYPE type description in WF editor. Append means take a collection type and extend it by the current type - so appending to list to paired -> list:paired for instance. ANY_COLLECTION_TYPE is a representation of incomplete information - it means this type description might be any kind of collection type (the way we use "input" to mean any kind of datatype in the editor). This is really a second order approximation of what a correct solution would be - a first order approximation would somehow represent the result of append being at least of "depth" specified (list:* or *:list instead of * for instance). A not approximation would be to do that but use ANY_COLLECTION_TYPE much less frequently by capturing type_source information and propagating it throughout the workflow properly. But these are harder things to do, this incorrect fix will allow many valid workflows to be editted that currently cannot be so I think it is good. "Fixes" #5205. Commit: f8fc8232a68dd1b0693ff9b007734cfa087cccdf https://github.com/galaxyproject/galaxy/commit/f8fc8232a68dd1b0693ff9b00773… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-19 (Sat, 19 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js Log Message: ----------- Merge pull request #6178 from jmchilton/fix_append_for_any_collection_Type [18.05] Fix append() for ANY_COLLECTION_TYPE type description in WF editor. Commit: 872dbfb3c42ec36ffe3c452e164e0dcc2545c3cb https://github.com/galaxyproject/galaxy/commit/872dbfb3c42ec36ffe3c452e164e… Author: Ubuntu <ubuntu(a)ip-172-31-23-81.ec2.internal> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- adding idat Commit: 258c4a4d8fddacba64a5cc7ac634910a4839b371 https://github.com/galaxyproject/galaxy/commit/258c4a4d8fddacba64a5cc7ac634… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #6179 from kpbioteam/idat [18.05] add idat datatype Commit: f56150468984cc96e37fe52cefd33499e5f422b4 https://github.com/galaxyproject/galaxy/commit/f56150468984cc96e37fe52cefd3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Rev subprocess32 dependency - that older version is not compatible with manylinux. https://github.com/google/python-subprocess32/issues/12 Commit: f07ba172418bdea209481b56b60980d2c9906823 https://github.com/galaxyproject/galaxy/commit/f07ba172418bdea209481b56b609… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- extraneous self Commit: 92ebf285088c744cef588a05b941ca6adf7848ee https://github.com/galaxyproject/galaxy/commit/92ebf285088c744cef588a05b941… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/tools/errors.py Log Message: ----------- Merge pull request #6184 from erasche/gdpr [18.05] extraneous self causing bug reporter to fail Commit: 805854aa6b16eb2b68b6ab5f94b92e84342c2f9e https://github.com/galaxyproject/galaxy/commit/805854aa6b16eb2b68b6ab5f94b9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #6183 from jmchilton/subprocess32_rev [18.05] Rev subprocess32 dependency - that older version is not compatible with manylinux. Commit: a992637de17d36b9b821dabc5342f636c530e4bc https://github.com/galaxyproject/galaxy/commit/a992637de17d36b9b821dabc5342… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-21 (Mon, 21 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M config/datatypes_conf.xml.sample M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt M lib/galaxy/tools/errors.py Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/d0cb1d6f3c1c...a992637de17d **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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