mvdbeek
f0da15fbae
Document job handler pool
2022-02-16 19:56:58 +01:00
mvdbeek
2a6491c9bc
Fix typo
2022-02-16 19:56:58 +01:00
Marius van den Beek and Nicola Soranzo
5b65486444
Use backticks around run.sh
...
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2022-02-16 19:53:29 +01:00
Marius van den Beek and Nicola Soranzo
3af4671ffc
Improve structure, add links
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2022-02-16 19:33:52 +01:00
mvdbeek
131af43957
Describe job handling
2022-02-16 19:31:27 +01:00
mvdbeek
7079008772
Recommend a proxy
...
No, really, it's the better option.
2022-02-16 19:00:27 +01:00
mvdbeek
5dc3a6f037
More progress, describe some basic gunicorn options
2022-02-16 18:41:43 +01:00
Marius van den Beek and Nicola Soranzo
a11e29b6f7
More details on adding or updating framework dependencies
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2022-02-16 15:38:20 +01:00
mvdbeek
62362d541c
Clarify that we only need wheels if upstream doesn't provide
2022-02-16 12:02:08 +01:00
mvdbeek
2a84df94ad
Drop unpinned dependencies section
2022-02-16 11:58:56 +01:00
mvdbeek
e7c37e60d5
Don't reference uwsgi only option in introductory statement
2022-02-15 17:26:58 +01:00
mvdbeek
f4dd77b382
Downgrade pre-assignment to the fallback method it is
2022-02-15 17:25:35 +01:00
mvdbeek
2d1b341fcd
WIP: Drop uWSGI from scaling documentation
2022-02-15 17:22:58 +01:00
mvdbeek
9c7c5429ee
Touch up wheel building instructions
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This is far from complete, but better than sending people to the wrong
place.
2022-02-15 16:19:20 +01:00
mvdbeek
04f6cd7f84
Drop irrelvant uWSGI virtualenv tips in framework dependencies docs
2022-02-15 16:19:14 +01:00
Assunta DeSanto and John Chilton
2c92eac235
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into feature/convert-collections-to-vue
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Co-authored-by: John Chilton <jmchilton@gmail.com >
2022-02-07 18:50:32 -05:00
Assunta DeSanto
4e23a6a8ca
redirecting how to cite to NAR paper
2022-02-07 18:34:25 -05:00
Assunta DeSanto
5bed44f612
changing Wiki to Community Hub
2022-02-07 17:03:16 -05:00
Assunta DeSanto
1ae0933f9d
redirecting Videos option from vimeo to youtube channel
2022-02-07 16:39:58 -05:00
Assunta DeSanto
15c8e9d9dc
removing mailing lists from help menu
2022-02-07 16:36:05 -05:00
Assunta DeSanto
4d6c1838c1
added support link back to menu, removed search link from help dropdown
2022-02-07 16:32:31 -05:00
mvdbeek
2895dd36e1
Add config variable for setting tus upload directory
2022-02-06 10:41:35 +01:00
mvdbeek
d0fb11c015
Drop OpenID post authentication protocols
2022-02-01 11:04:48 +01:00
John Chilton
0faf54d06c
Add option for disabling tool shed datatypes...
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...and start the process of disabling them. These have been broken since they were introduced. They have no clear upgrade path and loading Python code from the tool shed is fundamentally not something we should be doing.
Workaround for #11915
2022-01-26 10:54:11 -05:00
Dannon Baker
30cf0af05c
Drop old galaxy_qa url, which is replaced by the 'galaxy help' option and site we have now.
2022-01-25 15:31:38 -05:00
Dannon Baker
96e1c4c3d7
Drop 'support url' from Galaxy config, preferring the 'help' option that goes to discourse
2022-01-25 15:29:57 -05:00
Dannon Baker
b7d033aec1
Update default helpsite_url, enabled by default. Rebuild config.
2022-01-25 08:11:16 -05:00
mvdbeek
26a98ae8f4
Implement max_discovered_files
2022-01-18 11:49:00 +01:00
Matthias Bernt
2d91a858ab
make maximum number of retries for username validation configurable
...
with each retry the username gets username+"-{retry_number}"
rationale: on systems where jobs are submitted as real_user the username
must not be modified in this way. this can now be achieved by
setting max-retries to 0
2022-01-17 13:32:48 +01:00
mvdbeek
c9aa48ea25
Fix (per-domain) favicon url
2022-01-05 14:06:12 +01:00
mvdbeek
8ce2690ea9
Implement fastAPI prefix handling
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Admins just need to set `galaxy_url_prefix`, the rest should just work.
2022-01-05 13:31:54 +01:00
Nuwan Goonasekera
01ca66fa98
Merge branch 'dev' into vault_impl
2021-12-22 23:55:37 +05:30
Sergey Golitsynskiy
bc6f766d5a
Update migrated_tools_config schema description, run config-rebuild
2021-12-21 10:54:28 -05:00
Sergey Golitsynskiy
91af9c51ed
Run make config-rebuild
2021-12-21 10:54:28 -05:00
Nuwan Goonasekera and Enis Afgan
d4fe61a424
Update vault docs
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Co-authored-by: Enis Afgan <afgane@gmail.com >
2021-12-20 18:40:20 +05:30
Nuwan Goonasekera and Marius van den Beek
592603eb41
Add file upload test to vault
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Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2021-12-20 18:00:53 +05:30
Darren Cullerne
65f7259b29
Adding /doc/source/admin/reports_options.rst from make config-rebuild and additional change to file_path value in /lib/galaxy/webapps/reports/config.py
2021-12-17 09:23:03 +11:00
Nuwan Goonasekera and Marius van den Beek
3e993667e3
Typo in doc/source/admin/special_topics/vault.md
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Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2021-12-15 20:08:45 +05:30
Simon Bray
d6b0ee1900
add docs for mulled-hash, few other small fixes to existing docs
2021-12-15 10:22:23 +01:00
Nuwan Goonasekera
d9f2c0bf91
Added admin docs on configuring and using the vault
2021-12-01 21:44:44 +05:30
mvdbeek
1a08eb57b3
Make tool_evaluation_strategy configurable on app and destination level
2021-11-30 12:27:14 +01:00
mvdbeek
9aec355752
Rename allow_tool_source_display to enable_tool_source_display
2021-11-23 12:05:46 +01:00
Nuwan Goonasekera
e1535db412
Add vault conditional dependencies
2021-11-18 01:12:23 +05:30
mvdbeek
d7c34bfdb4
Return tool source language in header,
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disable view unless admin or allow_tool_source_display is set
2021-11-15 11:33:13 +01:00
mvdbeek
9f463b6f82
Adapt scripts/resumable_upload.py to fetch API
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Finding out that the `files` parameter is required took way more time
than I want to admit ... .
2021-10-13 18:05:42 +02:00
mvdbeek
e088b04b3e
Fix documented nginx location for tus
2021-10-12 18:06:09 +02:00
mvdbeek
03698ee4ac
Update docs with correct headers to forward
2021-10-12 16:43:14 +02:00
mvdbeek
600f59b0ee
Use client-logic to run upload tool
...
It is pretty cool to use hooks and an alternative tool submission
endpoint, but this is less invasive. We'd have to do this anyway for
cases where the upload is already on the server and the pre-finish hook
doesn't fire.
2021-10-12 13:43:45 +02:00
mvdbeek
82abf51069
Implement chunked upload using tus-js-client
2021-10-12 13:34:56 +02:00
mvdbeek
c13e3f49c5
Add admin documentation for running tusd + nginx
2021-10-12 13:34:55 +02:00
mvdbeek