dannon
8fe7eb116a
Change auth_debug behavior -- simply use an appropriate loglevel
2015-03-02 17:26:11 -05:00
John Chilton
9787ce8c63
Default auth provider should allow password change.
2015-03-01 22:23:55 -05:00
Nicola Soranzo
bfcdff0f8b
Rename CustomAuth to Auth.
2015-03-01 22:23:54 -05:00
Nicola Soranzo
832514bf6e
Make customauth always active.
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Added a config/customauth_conf.xml.sample file containing only the normal
Galaxy database authentication method.
Removed enable_customauth config option.
2015-03-01 22:23:54 -05:00
Nicola Soranzo
7951d0ced5
Rename enable_customauth_echo config option to customauth_debug.
2015-03-01 22:23:54 -05:00
Andrew Robinson
357a23b290
Added Custom Authentication module support (CustomAuth)
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Initial modules:
- ActiveDirectory (ldap)
- LocalDB (fall back to galaxy users)
- AlwaysAccept (whitelist)
- AlwaysReject (blacklist)
Sysadmin documentation at: https://docs.google.com/document/d/1CJp_m3vW7QKtAyBTMbE1MLgV6FAMuG3VO4HR-wHPkGk
Testing documentation at: https://docs.google.com/document/d/1Cocx6Rt3eqPdm8IjOKYAR4RaY-9P2iFNXCt3AYg3PlA
2015-03-01 22:23:53 -05:00
guerler
5c38a22063
Merge branch 'release_15.03' into dev
2015-02-28 12:26:54 -05:00
guerler
5bee11df4c
Charts: Add data point labels to all nvd3 charts (without this gene expression analysis using scatter plots is not very useful)
2015-02-28 12:12:10 -05:00
Daniel Blankenberg
86f66bc1c4
Allow External display applications to use Tool Data Tables.
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Have IGV external display application load a set of links for available genomes via a tool data table that reads a URL (http://igv.broadinstitute.org/genomes/genomes.txt ). The manually specified builds links should now be used to add additional builds, or for alias mapping (e.g. hg_g1k_v37-->b37).
Merge branch 'release_15.03' into dev
2015-02-27 15:53:58 -05:00
Daniel Blankenberg
1260d07a28
Have IGV external display application load a set of links for available genomes via a tool data table that reads a URL ( http://igv.broadinstitute.org/genomes/genomes.txt ). The manually specified builds links should now be used to add additional builds, or for alias mapping (e.g. hg_g1k_v37-->b37).
2015-02-27 15:50:28 -05:00
Dannon Baker
fa78855616
Merge branch 'release_15.03' into dev
2015-02-27 15:19:40 -05:00
Nate Coraor
002fef995a
Fix a typo in datatypes_conf.xml.sample
2015-02-27 14:21:22 -05:00
guerler
ced2acbfad
Merge branch 'release_15.03' into dev
2015-02-24 19:42:26 -05:00
guerler
e6399874e8
Charts: Fix missing data message
2015-02-24 19:41:30 -05:00
guerler
b71e864d78
Merge branch 'release_15.03' into dev
2015-02-24 19:10:46 -05:00
guerler
e2f5e9e326
Charts: Rebuild and update charts
2015-02-24 19:08:36 -05:00
Daniel Blankenberg
ca41396d2a
Fix for installing .loc files from the toolshed to respect shed_tool_data_path. Mention shed_tool_data_path in galaxy.ini.sample.
2015-02-24 12:02:42 -05:00
Daniel Blankenberg
fef8273448
Fix for installing .loc files from the toolshed to respect shed_tool_data_path. Mention shed_tool_data_path in galaxy.ini.sample.
2015-02-24 11:55:11 -05:00
John Chilton
1bbea26e55
Docfixes - grammar and spelling problems caught by Nicola.
2015-02-24 11:03:42 -05:00
John Chilton
dde2fc9572
Allow setting job_conf params via environment variables & galaxy.ini.
2015-02-23 20:33:05 -05:00
John Chilton
86bed7586f
Merge branch 'release_15.03' into dev
2015-02-23 19:59:04 -05:00
John Chilton
2bcc9e202e
Fix for watching tools on some more interesting file systems.
2015-02-23 19:58:12 -05:00
Dannon Baker
3af3bf5742
Per IRC discussion, remove demo_sequencer webapp.
2015-02-21 13:29:58 -05:00
Dannon Baker
d91ce3f6cd
Merged in erasche2/galaxy-central (pull request #570 )
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Enable user/email list for sharing of datasets
2015-02-17 09:46:09 -05:00
Carl Eberhard
8a79dfe99e
UI, multi-history: minor fixes, tabindeces, cleanup; Scatterplot: refactor mako and fix missing figure tag; Client build, styles: add jstree to cleaned files
2015-02-16 11:43:22 -05:00
Nate Coraor
e64ab4c85c
There's no reliable way to use the Galaxy config file to control egg use/fetching since so many things use galaxy.eggs from outside of Galaxy, so drop the support for the config file options and rely on the environment variables only. Reverse the defaults so that eggs and fetching are enabled by default. I'll make sure that they properly get passed to the tool execution environments in the next commit.
2015-02-12 15:10:19 -05:00
Nate Coraor
0c8cb50c1d
Use GALAXY_CONFIG_ environment variables instead of GALAXY_ to fall in line with convention.
2015-02-12 12:31:58 -05:00
Nate Coraor
49cc443b81
Make it possible to disable egg fetching or the use of eggs entirely and provide a requirements.txt.
2015-02-12 12:13:24 -05:00
Aysam Guerler
3ffcc2448c
Charts: Fix error message
2015-02-11 20:56:10 -05:00
Aysam Guerler
7eec63204d
Charts: Repack scripts
2015-02-11 20:26:46 -05:00
Dannon Baker
59d73090fe
Add more accurate sample for specifying a swift object store in object_store_conf.sample
2015-02-10 09:55:03 -05:00
Dannon Baker
61360355dd
Update objectstore sample to supply better defaults (and not host/port, which are unnecessary for s3).
2015-02-09 17:37:16 -05:00
Carl Eberhard
2b8fca4a03
Visualizations, scatterplot: update handlebars since server runtime was updated
2015-02-09 11:02:31 -05:00
Aysam Guerler
68d9ea0fad
Ui: Fix class name
2015-02-06 11:23:19 -05:00
Aysam Guerler
836b3bb913
Ui: Revise portlet margins
2015-02-06 11:05:23 -05:00
Aysam Guerler
c8aece99eb
Workflow: Add style for workflow tool form
2015-02-05 22:25:22 -05:00
Eric Rasche
96d2be2a67
Merged galaxy/galaxy-central into default
2015-02-05 14:43:26 -06:00
Dannon Baker
05ba490f7c
Initial version of session_timeout. Still needs client side work to handle API/web.json requests better but that turned out to be a large project -- see TODOs for more details.
2015-02-04 10:33:07 -05:00
Dannon Baker
04bd3c77c1
Merged in dan/galaxy-central-prs (pull request #643 )
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Add ZebrafishMine Data Source Tool.
2015-02-02 12:04:23 -05:00
John Chilton
4f223913e8
Temporary config option to isolate tool commands in their own shell.
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Like done for Docker to isolate metadata commands from the environment modifications required to resolve tool dependencies. Should allow for Python 3 dependencies (originally also allowed samtools - but Nate other commit resolved that problem also).
Just meant as a config option for now - it will become the default once tested more thoroughly. For now enable it by setting enable_beta_tool_command_isolation to True in galaxy.ini.
2015-02-02 09:27:19 -05:00
John Chilton
e39581e6fa
Another round of reports config improvements.
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- Respect GALAXY_CONFIG_* when configuring reports web app.
- Leave new_file_path and file_path unset in reports config (all defaults should be unspecified and environment variables are more useful).
2015-01-30 17:40:25 -05:00
John Chilton
a8b5923026
Reduce config duplication related to setting up webapps.
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And apply some fixes/improvements for galaxy back into tool shed and reports.
2015-01-30 15:54:02 -05:00
Dannon Baker
77360660e6
Add sentry_dsn to toolshed sample.
2015-01-30 11:23:36 -05:00
Nicola Soranzo
8d669857d5
Whitespace fixes. 80 character limit. Small rewordings.
2015-01-29 14:47:47 +00:00
Nicola Soranzo
c4fb70d945
Enhancements for galaxy.ini documentation
2015-01-29 14:43:59 +00:00
Aysam Guerler
d38ca6c5eb
Workflow: Add tool form switch to config, fix late validation check
2015-01-29 00:38:02 -05:00
Aysam Guerler
a97c07c87f
ToolForm: Activate by default
2015-01-28 23:59:43 -05:00
Nate Coraor
23f3e479be
Remove memdump, which probably has not worked for many years.
2015-01-28 16:20:30 -05:00
Aysam Guerler
b05ffd2d52
ToolForm: Fix configuration flag
2015-01-27 18:31:20 -05:00
John Chilton
2d978973a6
Add comments to config/galaxy.ini.sample about recent workflow changes.
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Thanks for Philip Mabon for letting me know there were not included along with the original changes.
2015-01-27 13:48:01 -05:00
dannon