Nicola Soranzo
961472cfff
Merge branch 'release_22.01' into release_22.05
2022-08-16 23:25:42 +01:00
Nicola Soranzo
69defb7a20
Doc fixes
2022-08-15 19:15:02 +01:00
mvdbeek
3818f50af5
Drop interactive environments
2022-03-23 15:43:24 +01:00
mvdbeek
7a72fe5756
Drop "starting galaxy" docs
...
They're outdated and changing rapidly. Without context I don't think
they're all that helpful.
2022-03-15 21:59:21 +01:00
mvdbeek
4c4f10e24f
Drop interactive environment build instructions form docs
2022-02-24 19:34:48 +01:00
Nicola Soranzo
98ecc39b1b
Remove PhantomJS support, dropped in Selenium 4.0
2021-12-08 08:14:10 +00:00
Marius van den Beek and Nicola Soranzo
5a9b95179c
Clarify position of pytest arguments
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2021-10-14 11:40:15 +02:00
mvdbeek
0b461c7bd7
Extend debugging test instructions for GHA
2021-10-14 11:29:18 +02:00
Dannon
0b3c7aa834
Merge pull request #12427 from hexylena/es-ui
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Spanish Translations for remaining untranslated UI components
2021-09-15 09:19:58 -04:00
Helena and Nicola Soranzo
291c39aac8
Review and improvements of the documentation/short-tut
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2021-09-15 13:55:21 +02:00
Helena Rasche
c7a7c83fb1
Add translating rst file
2021-09-15 10:21:21 +02:00
Helena Rasche
9decfc2ba2
Document what I did
2021-09-14 19:05:55 +02:00
John Chilton
cd2e6527fc
Merge pull request #12255 from bernt-matthias/topic/deprecate_datamanager_version
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Deprecate data manager version
2021-09-08 14:36:01 -04:00
Kaivan Kamali
952d947087
Removed resources section per John's comment
2021-09-03 12:49:36 -04:00
Kaivan Kamali
99880294c6
Minor revision
2021-09-03 09:27:29 -04:00
Kaivan Kamali
b47374aef7
Added instructions for debuuging Galaxy using a Slurm cluster
2021-09-02 17:10:15 -04:00
Kaivan Kamali
96ef23a79b
Added instructions on how to debug Galaxy backed by a Slurm cluster
2021-09-02 16:10:41 -04:00
Matthias Bernt
ee4c5d0817
deprecate data manager version
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Data managers (DM) could define a version for the data manager
(`<data_manager version="0.0.1">`) and for the data manager tool (DMT).
The version attribute of the data manager was undocumented and only
used seldomly (for IUC in 24 out of 88). If no version was set for
the DM it defaults to 0.0.1. Hence in `shed_data_manager_conf.xml`
multiple versions of the (DM) with version 0.0.1 are listed.
This leads to loading only one DM (I guess the oldest) and a
warning like the following on startup:
`A data manager has been defined twice: toolshed.g2.bx.psu.edu/repos/galaxyp/data_manager_eggnog_mapper/data_manager/data_manager_eggnog/0.0.1 `
which is easily overlooked.
2021-07-14 15:24:38 +02:00
Dannon
38f89e18b5
Merge pull request #12234 from eancelet/debug-doc-update
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Add a note to get Python extension and set interpreter
2021-07-06 14:28:29 -04:00
Sergey Golitsynskiy
59ee7b55e7
Update doc/source/dev/debugging_tests.md
2021-07-06 14:21:21 -04:00
Estelle Ancelet
beaabd1817
Add a note to get Python extension and set interpreter
2021-07-06 14:07:05 +02:00
Dannon Baker
a57202da59
Consistency in referring to assumed galaxy root
2021-07-01 12:09:30 -04:00
Dannon Baker
44b7d165c6
Add a note about needing galaxy.yml (and not sample) here.
2021-07-01 12:05:55 -04:00
Dannon Baker
9058c02026
Update debug target name in example .vscode launchconfig
2021-07-01 11:58:22 -04:00
mvdbeek
5cb1b8176c
Update instructions for debugging using vscode
2021-01-29 17:15:42 +01:00
John Chilton
422d48bce1
Link to some recently filled out pydocs from sphinx testing docs.
2021-01-18 17:24:28 -05:00
John Chilton and Nicola Soranzo
400da5d677
Apply suggestions from code review
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2021-01-13 18:19:29 -05:00
John Chilton
21f06bafef
API design guidelines.
2021-01-13 18:18:39 -05:00
Sergey Golitsynskiy and Nicola Soranzo
64139e9bb3
Update doc/source/dev/writing_tests.md
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2021-01-12 10:04:27 -05:00
Sergey Golitsynskiy and Nicola Soranzo
f9b38719fd
Update doc/source/dev/writing_tests.md
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2021-01-12 10:03:41 -05:00
Sergey Golitsynskiy and Nicola Soranzo
0b0ec0cada
Update doc/source/dev/writing_tests.md
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2021-01-12 00:37:06 -05:00
Sergey Golitsynskiy
204538c387
Add more edits
2021-01-12 00:35:45 -05:00
Sergey Golitsynskiy
dad51dee87
Make minor improvements, add ToC
2021-01-11 23:28:15 -05:00
Nicola Soranzo
ed084a77c3
Add framework tests to Overview
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Also fix some typos.
2021-01-11 19:07:39 +00:00
John Chilton
1a7215b040
Documentation on writing Galaxy tests.
2021-01-10 18:52:26 -05:00
John Chilton
1d63a3abd5
Link to high-quality developer documentation.
2021-01-10 18:52:26 -05:00
Nolan Woods
4ee6a1e6a0
Correct data table config documentation
2020-10-28 09:27:16 -07:00
Nolan Woods
ccf2eadd38
Document data manager repository layout
2020-10-28 08:41:42 -07:00
Kaivan Kamali
3904b68a42
Move Galaxy configuration file for VS Code debugging into Galaxy repo
2020-10-21 12:14:55 -04:00
Kaivan Kamali
04ef92829f
Update link for Galaxy configuration file in Galaxy debug document
2020-10-21 11:57:12 -04:00
Nicola Soranzo
db904f2056
Don't allow datatype change by default if it's composite
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Also re-use the HDA deserializer in the dataset controller.
2020-09-24 09:39:58 +01:00
Kaivan Kamali
9de2112448
Updated documentation to show how a job is de-qued and processed.
2020-09-03 11:33:20 -04:00
John Chilton
3cab834085
Merge pull request #9963 from kxk302/documentation
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Added doc explaining what happens when you upload a file to Galaxy.
2020-08-13 16:59:43 -04:00
Matthias Bernt
92bbb82577
add missing $ in docs
2020-08-04 11:51:00 +02:00
Kaivan Kamali
e80c6f25ac
Fixed a typo
2020-07-06 13:52:24 -04:00
Kaivan Kamali
402fed9fed
Added doc explaining what happens when you upload a file to Galaxy.
2020-07-06 11:32:21 -04:00
Kaivan Kamali
072be091e2
Removed trailing whitespace
2020-06-25 15:31:39 -04:00
Kaivan Kamali
2f6063c1f8
Revised documentation per code review feedback.
2020-06-25 15:04:16 -04:00
Kaivan Kamali
b2ad77340a
Revised doc based on PR feedback.
2020-06-25 15:02:23 -04:00
Kaivan Kamali
ed30e7b051
More small revision
2020-06-25 15:02:23 -04:00
Nicola Soranzo