galaxy-commits January 2016

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[galaxyproject/galaxy] 33ba1f: Link from the 16.01 announcement to the Admin whee...
by GitHub 28 Jan '16

28 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 33ba1face9e1f1bf025f37dc4e508143972845dc https://github.com/galaxyproject/galaxy/commit/33ba1face9e1f1bf025f37dc4e50… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/releases/16.01_announce.rst Log Message: ----------- Link from the 16.01 announcement to the Admin wheels documentation, document the process of adding new wheels. Commit: 27685377f629c536e56189e795bc91bb8caf0736 https://github.com/galaxyproject/galaxy/commit/27685377f629c536e56189e795bc… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/releases/16.01_announce.rst Log Message: ----------- Merge pull request #1612 from natefoo/admin-docs [16.01] Additional documentation regarding wheels Compare: https://github.com/galaxyproject/galaxy/compare/f499ec0cabef...27685377f629

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[galaxyproject/galaxy] bc9f9b: Adapt release notes boot strap to new issues.
by GitHub 28 Jan '16

28 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bc9f9b9bf1de555db3a56b50a6655862f3cb4c73 https://github.com/galaxyproject/galaxy/commit/bc9f9b9bf1de555db3a56b50a665… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Adapt release notes boot strap to new issues. Commit: 528f80e40b7f7d729ce0761a25315b2a140f758a https://github.com/galaxyproject/galaxy/commit/528f80e40b7f7d729ce0761a2531… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: A doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst A doc/source/releases/16.04_announce.rst Log Message: ----------- Auto-generate 16.01 release notes. Commit: 4064bbf94f6d167d62e65b5fed988fb4232fd6ca https://github.com/galaxyproject/galaxy/commit/4064bbf94f6d167d62e65b5fed98… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst M doc/source/releases/index.rst Log Message: ----------- 16.01 release notes. Commit: f0b5f7757e4df3226db30271e64646c828306aad https://github.com/galaxyproject/galaxy/commit/f0b5f7757e4df3226db30271e646… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M doc/source/releases/16.01_announce.rst Log Message: ----------- add link to Main tour; add sentence to WF nesting Commit: 79dfff4d65a6e8a2e102aae5d9af129c445fe9a5 https://github.com/galaxyproject/galaxy/commit/79dfff4d65a6e8a2e102aae5d9af… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M doc/source/releases/16.01.rst Log Message: ----------- Typo discovered by @nsoranzo Commit: 281a53d97567dbc5458b47e283f891e91b680bc9 https://github.com/galaxyproject/galaxy/commit/281a53d97567dbc5458b47e283f8… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M doc/source/releases/16.01.rst Log Message: ----------- Small RST fixes. Commit: 08fbd8923af0ba5012e23a774adea7e878ea2047 https://github.com/galaxyproject/galaxy/commit/08fbd8923af0ba5012e23a774ade… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M doc/source/releases/16.01.rst Log Message: ----------- Merge some entries. Add some missing PRs. Commit: b1ae5d8c67f1565084eb811a8e84632718ac5543 https://github.com/galaxyproject/galaxy/commit/b1ae5d8c67f1565084eb811a8e84… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- UI, users: allow '/user' and '/user/' to default controller and correctly return the user/index.mako template (preventing an internal error) Commit: 55f67e59d654588ff0fca9e168e8f5e1411af50a https://github.com/galaxyproject/galaxy/commit/55f67e59d654588ff0fca9e168e8… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Core, HDCAs: fix 'copy_item_annotation' error when copying a history with an hdca by adding UsesAnnotations mixin to HDCA model Commit: d3277072cc49d9a7e50a9619e899c0796c2a808e https://github.com/galaxyproject/galaxy/commit/d3277072cc49d9a7e50a9619e899… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #1594 from carlfeberhard/release_16.01 [16.01] UI, users: allow '/user' and '/user/' to default controller and corre… Commit: c60ddc241b9bb92ea0c67fea16b2ec5fa415bceb https://github.com/galaxyproject/galaxy/commit/c60ddc241b9bb92ea0c67fea16b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #1599 from carlfeberhard/fix.hdca-copy [16.01] Core, HDCAs: fix 'copy_item_annotation' error when copying a history … Commit: f499ec0cabefb62b87d43af223d0473e2528dcc7 https://github.com/galaxyproject/galaxy/commit/f499ec0cabefb62b87d43af223d0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: A doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst A doc/source/releases/16.04_announce.rst M doc/source/releases/index.rst M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #1585 from jmchilton/16.01_release_notes [16.01] Release notes for 16.01 Commit: a2887dfe189dae64f08a0e7d12d65bbc2492c7ba https://github.com/galaxyproject/galaxy/commit/a2887dfe189dae64f08a0e7d12d6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: A doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst A doc/source/releases/16.04_announce.rst M doc/source/releases/index.rst M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/user.py M scripts/bootstrap_history.py Log Message: ----------- Merge 16.01 into dev. Commit: db221325dac10d84ed56691cc08d1b666491e26c https://github.com/galaxyproject/galaxy/commit/db221325dac10d84ed56691cc08d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: A doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst A doc/source/releases/16.04_announce.rst M doc/source/releases/index.rst M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/user.py M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #1607 from jmchilton/dev_merge_4 Merge 16.01 into dev. Compare: https://github.com/galaxyproject/galaxy/compare/51188233cee3...db221325dac1

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[galaxyproject/galaxy] bc9f9b: Adapt release notes boot strap to new issues.
by GitHub 28 Jan '16

28 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: bc9f9b9bf1de555db3a56b50a6655862f3cb4c73 https://github.com/galaxyproject/galaxy/commit/bc9f9b9bf1de555db3a56b50a665… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M scripts/bootstrap_history.py Log Message: ----------- Adapt release notes boot strap to new issues. Commit: 528f80e40b7f7d729ce0761a25315b2a140f758a https://github.com/galaxyproject/galaxy/commit/528f80e40b7f7d729ce0761a2531… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: A doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst A doc/source/releases/16.04_announce.rst Log Message: ----------- Auto-generate 16.01 release notes. Commit: 4064bbf94f6d167d62e65b5fed988fb4232fd6ca https://github.com/galaxyproject/galaxy/commit/4064bbf94f6d167d62e65b5fed98… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst M doc/source/releases/index.rst Log Message: ----------- 16.01 release notes. Commit: f0b5f7757e4df3226db30271e64646c828306aad https://github.com/galaxyproject/galaxy/commit/f0b5f7757e4df3226db30271e646… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M doc/source/releases/16.01_announce.rst Log Message: ----------- add link to Main tour; add sentence to WF nesting Commit: 79dfff4d65a6e8a2e102aae5d9af129c445fe9a5 https://github.com/galaxyproject/galaxy/commit/79dfff4d65a6e8a2e102aae5d9af… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M doc/source/releases/16.01.rst Log Message: ----------- Typo discovered by @nsoranzo Commit: 281a53d97567dbc5458b47e283f891e91b680bc9 https://github.com/galaxyproject/galaxy/commit/281a53d97567dbc5458b47e283f8… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M doc/source/releases/16.01.rst Log Message: ----------- Small RST fixes. Commit: 08fbd8923af0ba5012e23a774adea7e878ea2047 https://github.com/galaxyproject/galaxy/commit/08fbd8923af0ba5012e23a774ade… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M doc/source/releases/16.01.rst Log Message: ----------- Merge some entries. Add some missing PRs. Commit: f499ec0cabefb62b87d43af223d0473e2528dcc7 https://github.com/galaxyproject/galaxy/commit/f499ec0cabefb62b87d43af223d0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: A doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst A doc/source/releases/16.04_announce.rst M doc/source/releases/index.rst M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #1585 from jmchilton/16.01_release_notes [16.01] Release notes for 16.01 Compare: https://github.com/galaxyproject/galaxy/compare/c60ddc241b9b...f499ec0cabef

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[galaxyproject/galaxy] 55f67e: Core, HDCAs: fix 'copy_item_annotation' error when...
by GitHub 28 Jan '16

28 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 55f67e59d654588ff0fca9e168e8f5e1411af50a https://github.com/galaxyproject/galaxy/commit/55f67e59d654588ff0fca9e168e8… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Core, HDCAs: fix 'copy_item_annotation' error when copying a history with an hdca by adding UsesAnnotations mixin to HDCA model Commit: c60ddc241b9bb92ea0c67fea16b2ec5fa415bceb https://github.com/galaxyproject/galaxy/commit/c60ddc241b9bb92ea0c67fea16b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #1599 from carlfeberhard/fix.hdca-copy [16.01] Core, HDCAs: fix 'copy_item_annotation' error when copying a history … Compare: https://github.com/galaxyproject/galaxy/compare/d3277072cc49...c60ddc241b9b

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[galaxyproject/galaxy]
by GitHub 28 Jan '16

28 Jan '16

Branch: refs/heads/upgrade_ts_db Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] c80a21: disable email notifications from travis
by GitHub 28 Jan '16

28 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c80a212732246923fe8dff9961a172e82bb8d48e https://github.com/galaxyproject/galaxy/commit/c80a212732246923fe8dff9961a1… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M .travis.yml Log Message: ----------- disable email notifications from travis travis would send email to every committer on every failed build for every galaxy instance running travis (ie this one and jmchilton one) we have enough visibility of runs on PR statuses so I think we do not need this Commit: 51188233cee3cd3f7385f18bd475cddeffcec5f6 https://github.com/galaxyproject/galaxy/commit/51188233cee3cd3f7385f18bd475… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #1592 from martenson/remove-travis-notifications disable email notifications from travis Compare: https://github.com/galaxyproject/galaxy/compare/30dcd0e39f0a...51188233cee3

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[galaxyproject/galaxy] b1ae5d: UI, users: allow '/user' and '/user/' to default c...
by GitHub 28 Jan '16

28 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: b1ae5d8c67f1565084eb811a8e84632718ac5543 https://github.com/galaxyproject/galaxy/commit/b1ae5d8c67f1565084eb811a8e84… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- UI, users: allow '/user' and '/user/' to default controller and correctly return the user/index.mako template (preventing an internal error) Commit: d3277072cc49d9a7e50a9619e899c0796c2a808e https://github.com/galaxyproject/galaxy/commit/d3277072cc49d9a7e50a9619e899… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-01-28 (Thu, 28 Jan 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #1594 from carlfeberhard/release_16.01 [16.01] UI, users: allow '/user' and '/user/' to default controller and corre… Compare: https://github.com/galaxyproject/galaxy/compare/954aff7fa806...d3277072cc49

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[galaxyproject/usegalaxy-playbook] 1d1a4d: Enable harakiri mode in uWSGI to see if this helps...
by GitHub 27 Jan '16

27 Jan '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1d1a4ddcb15fccf17c28c87bc37afddb66e8e870 https://github.com/galaxyproject/usegalaxy-playbook/commit/1d1a4ddcb15fccf1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/uwsgi.ini.j2 M templates/galaxy/usegalaxy.org/config/uwsgi.ini.j2 Log Message: ----------- Enable harakiri mode in uWSGI to see if this helps to bring workers to life. Also enable py-tracebacker, although I'm not sure it will reveal any useful information.

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[galaxyproject/galaxy] c8b005: Add a requirements file suitable for use with `con...
by GitHub 27 Jan '16

27 Jan '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c8b0057349be9a683e295c073f66163f47c257e7 https://github.com/galaxyproject/galaxy/commit/c8b0057349be9a683e295c073f66… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-21 (Thu, 21 Jan 2016) Changed paths: A lib/galaxy/dependencies/conda-requirements.txt Log Message: ----------- Add a requirements file suitable for use with `conda {create,install} --file`. Commit: dc801dc1f6097b283e01c784d09261b3c4ee21e5 https://github.com/galaxyproject/galaxy/commit/dc801dc1f6097b283e01c784d092… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: A doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst Log Message: ----------- Add admin documentation for framework dependencies (wheels) for the 16.01 release. Commit: 1486af0ef90a186b5648f737af32e84640263857 https://github.com/galaxyproject/galaxy/commit/1486af0ef90a186b5648f737af32… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: A lib/galaxy/dependencies/conda-environment.txt R lib/galaxy/dependencies/conda-requirements.txt Log Message: ----------- Rename conda-requirements.txt to conda-environment.txt since it is not a requirements file, include instructions on how to install remaining dependencies from pip. Commit: 9827f32775b34a566c887963103a1f921e2b7a95 https://github.com/galaxyproject/galaxy/commit/9827f32775b34a566c887963103a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- conda-requirements.txt renamed to conda-environment.txt Commit: c2d94c43bbd5929d4773e859dc1f5d8e436b0ee8 https://github.com/galaxyproject/galaxy/commit/c2d94c43bbd5929d4773e859dc1f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: A lib/galaxy/dependencies/conda-environment.txt Log Message: ----------- Merge pull request #1560 from natefoo/conda-interop [16.01] Add a requirements file suitable for use with `conda {create,install} --file` Commit: 168f453094d546cd1552a1a179decc4914c1d93a https://github.com/galaxyproject/galaxy/commit/168f453094d546cd1552a1a179de… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Suggest installing virtualenv from brew Commit: 954aff7fa806ee77682476ac56ec95027482bb0c https://github.com/galaxyproject/galaxy/commit/954aff7fa806ee77682476ac56ec… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: A doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst Log Message: ----------- Merge pull request #1589 from natefoo/admin-docs [16.01] Add admin documentation for framework dependencies (wheels) Commit: 30dcd0e39f0ae5d2eb7671bbfaf212c0c5a77eff https://github.com/galaxyproject/galaxy/commit/30dcd0e39f0ae5d2eb7671bbfaf2… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-01-27 (Wed, 27 Jan 2016) Changed paths: A doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst A lib/galaxy/dependencies/conda-environment.txt Log Message: ----------- Merge branch 'release_16.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/f725e964333d...30dcd0e39f0a

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[galaxyproject/galaxy] dc801d: Add admin documentation for framework dependencies...
by GitHub 26 Jan '16

26 Jan '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: dc801dc1f6097b283e01c784d09261b3c4ee21e5 https://github.com/galaxyproject/galaxy/commit/dc801dc1f6097b283e01c784d092… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: A doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst Log Message: ----------- Add admin documentation for framework dependencies (wheels) for the 16.01 release. Commit: 9827f32775b34a566c887963103a1f921e2b7a95 https://github.com/galaxyproject/galaxy/commit/9827f32775b34a566c887963103a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- conda-requirements.txt renamed to conda-environment.txt Commit: 168f453094d546cd1552a1a179decc4914c1d93a https://github.com/galaxyproject/galaxy/commit/168f453094d546cd1552a1a179de… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Suggest installing virtualenv from brew Commit: 954aff7fa806ee77682476ac56ec95027482bb0c https://github.com/galaxyproject/galaxy/commit/954aff7fa806ee77682476ac56ec… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-01-26 (Tue, 26 Jan 2016) Changed paths: A doc/source/admin/framework_dependencies.rst M doc/source/admin/index.rst Log Message: ----------- Merge pull request #1589 from natefoo/admin-docs [16.01] Add admin documentation for framework dependencies (wheels) Compare: https://github.com/galaxyproject/galaxy/compare/c2d94c43bbd5...954aff7fa806

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galaxy-commits January 2016