John Davis
874cd961b2
Merge pull request #17328 from bernt-matthias/topic/hide-wig_to_bigWig
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Hide wig_to_bigWig tool
2024-02-26 14:15:27 -05:00
Martin Cech
3690af66eb
Merge pull request #17515 from wm75/data_source_fixes2
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Fixing bugs with data_source tools - part 2
2024-02-26 19:14:19 +01:00
Nate Coraor
5bbfa85ab3
Update RStudio GxIT to use the reworked 23.1 image
2024-02-22 15:08:08 -05:00
Wolfgang Maier
76968a68c7
Adjust UCSC Table browser tools to code changes
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Since the code now drops undeclared incoming parameters it enforces
cleaner wrapper style.
2024-02-22 17:29:33 +01:00
Marius van den Beek
9415df899e
Merge pull request #17422 from wm75/data_source_tools_fixes
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Fix data_source and data_source_async bugs
2024-02-15 12:36:25 +01:00
Matthias Bernt
e1457c8c3b
hide wig_to_bigWig tool
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now present at IUC https://github.com/galaxyproject/tools-iuc/pull/5704
2024-02-15 11:38:05 +01:00
Wolfgang Maier
fd3a19afd2
Fix linting
2024-02-09 09:19:33 +01:00
Wolfgang Maier
eef015d4e2
Preserve original request params as nested dict
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and use them in final POST request
2024-02-09 09:14:20 +01:00
Wolfgang Maier
561bf92a1b
Format import section with isort
2024-02-08 21:41:19 +01:00
Wolfgang Maier
3c178b559e
Fix linting
2024-02-08 16:58:28 +01:00
Wolfgang Maier
bd0f257452
Switch data_source.py to modern tool-provided metadata
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Allows moving all data source tools using the script to profile 20.09.
For more recent profiles data_source.py would have to work outside of
Galaxy's Python environment.
2024-02-08 16:43:39 +01:00
Wolfgang Maier
c554023c5e
Simply exit on errors
2024-02-08 15:33:33 +01:00
Wolfgang Maier
387c9f0c87
Start modernizing data_source.py script
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- Drop support for very old format of specifying execution params in a
tabular file instead of a json one
- Use O_TRUNC to discard previous file contents instead of opening for
writing, then closing
- Do not silently ignore non-integer values for max_file_size
2024-02-08 15:23:03 +01:00
mvdbeek
5e16978e12
Fix or ignore additional unreachable code
2024-02-01 10:32:04 +01:00
mvdbeek
f9e3380a48
Drop unreachable compression extension stripping
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Not going to do further work on upload1, so not fixing this.
2024-02-01 10:32:03 +01:00
Nicola Soranzo
e975ca3754
Update to black 2024 stable style
2024-01-30 18:09:51 +00:00
mvdbeek
03f01da108
Merge branch 'release_23.2' into dev
2024-01-15 12:09:43 +01:00
mvdbeek
a2cb91487a
Merge branch 'release_23.1' into release_23.2
2024-01-15 12:05:09 +01:00
John Davis
5597d9f718
Merge pull request #16883 from mvdbeek/copy_nonsense_tool_version
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[23.1] Add back 1.1.0 version of Filtering1 tool
2024-01-10 14:07:14 -05:00
Björn Grüning
26ffc86b93
Merge pull request #17170 from thepineapplepirate/qiskit_in_galaxy
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Qiskit in galaxy
2023-12-12 21:26:59 +01:00
thepineapplepirate and Nicola Soranzo
48417b0409
Update tools/interactive/interactivetool_qiskit_jupyter_notebook.xml
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2023-12-12 14:09:27 -05:00
Raubenolt
46d53d14c8
made suggested changes
2023-12-11 20:47:25 -05:00
mvdbeek
33ccacf77a
Fix upload1 tool
2023-12-01 19:57:38 +01:00
Sveinung Gundersen
b0e13e5149
Added "requires_path_in_url" and "requires_path_in_header" attributes to entry points for tools. Sendoff to gx-it-proxy. Cleanup
2023-11-15 12:54:14 +01:00
Sveinung Gundersen
51db30370c
Using label instead of name to identify entrypoint
2023-11-15 12:54:14 +01:00
Sveinung Gundersen
05f8de5d98
Updated JupyTool, Open Refine, Guacamole Desktop, and RStudio tools to potentially support path-based proxy
2023-11-15 12:48:39 +01:00
John Davis
f91693dc6e
Merge pull request #16783 from SergeyYakubov/get-rid-of-filename-property
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Replace file_name property with get_file_name function
2023-11-08 17:19:40 -05:00
Yakubov, Sergey
c30a4c06c2
Replace file_name property with get_file_name function
2023-11-08 17:17:14 -05:00
Lucille Delisle
4e15e6929e
Fix maf_thread_for_species.py
2023-11-08 10:45:11 +01:00
Lucille Delisle
1072f07de9
Fix maf_thread_for_species.py
2023-11-03 08:35:06 +01:00
Martin Cech
c7bd694462
Merge branch 'release_23.1' into merge231in
2023-10-26 11:09:05 -07:00
Matthias Bernt
856930eef6
Fix missing grep input in sort1 tool
2023-10-24 15:14:50 +02:00
Marius van den Beek
eecaeb7fad
Merge pull request #15313 from pcm32/patch-14
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Update cellxgene interactive tool to 1.1.1
2023-10-20 15:48:14 +02:00
mvdbeek
85f20770c1
Add back 1.1.0 version of Filtering1 tool
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Which is the same as 1.1.1 but hard to explain to users why the run form
shows a different version than what is shown in the user interface.
2023-10-19 10:06:17 +02:00
Heinz-Alexander Fuetterer and Nicola Soranzo
347e7b8301
chore: fix typos
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2023-10-13 16:29:27 +02:00
mvdbeek
50fe6a9cfb
Add missing requirements to perl tools
2023-10-06 13:43:55 -04:00
thepineapplepirate
566f3973ad
new interactive tool for Qiskit in Galaxy
2023-10-04 15:57:32 -04:00
mvdbeek
626c86e7e9
Add missing requirements to perl tools
2023-09-29 15:22:09 +02:00
Nicola Soranzo
d258e5791e
Fix new E721 errors from ruff 0.0.290
2023-09-20 01:43:40 +01:00
mvdbeek
c631c629dd
Merge branch 'release_23.1' into dev
2023-09-18 10:06:27 +02:00
Marius van den Beek
3e991f1cb4
Merge pull request #16704 from bgruening/universial_newline
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[23.1] FileInput no longer accept 'U' in the file mode
2023-09-17 09:17:36 +02:00
Björn Grüning
a9f5400eae
FileInput no longer accept 'U' in the file mode
2023-09-16 18:33:07 +02:00
mvdbeek
913182fac9
Merge branch 'release_23.1' into dev
2023-08-31 13:04:47 +02:00
Cameron Hyde
517ca97c03
Remove render.py script from iSEE
2023-08-30 09:50:48 +10:00
Sandy Rogers
330310e69f
Update interactivetool_mgnify_notebook to v1.2.2
2023-08-04 11:28:39 +01:00
mvdbeek
0bac18d0bb
Drop old run_as_real_user check
2023-06-06 18:52:32 +02:00
Sandy Rogers
8a1b58caf0
Update MGnify interactive tool to v1.1.0
2023-06-02 17:34:00 +01:00
Marius van den Beek
9855a51cd7
Merge pull request #15656 from bernt-matthias/tools/deprecate-evolution
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Deprecate tools/evolution
2023-05-09 10:52:21 +02:00
Nicola Soranzo
64af46c4ae
Fix new B018 errors raised by ruff 0.0.260
2023-04-13 16:53:01 +01:00
Pablo Moreno
1741fa45ee
Some tabs to spaces
2023-03-28 10:19:54 +01:00
John Davis