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
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
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
Pablo Moreno
0b20473129
Layer and optionally make var field unique.
2023-03-27 15:06:15 +01:00
Pablo Moreno
703751b65c
Avoid errors automatically detected by galaxy due to stderr output
2023-03-08 13:17:11 +00:00
Pablo Moreno
999322b354
Adds previous version as separate file
2023-03-07 12:05:10 +00:00
Pablo Moreno
e9e8f9be27
Change name and tutorial link
2023-03-07 12:03:34 +00:00
Pablo Moreno
acc34f6d21
Adds help
2023-03-07 08:59:43 +00:00
Matthias Bernt
c9c3966128
deprecate tools/evolution
2023-02-27 19:22:37 +01:00
Nicola Soranzo
30f60493c3
Format Python code with black 23.1.0
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with manual fixes to 3 files to make them compatible with black 22.12.0 .
We need to keep black pinned at `<23` until we vendorise `packaging`, since
the new version of black depends on `packaging >=22.0` which is the version
where `LegacyVersion` (which we use for tool lineages) was removed.
2023-02-01 23:51:03 +00:00
Anup Kumar
56a2ace72d
Update interactivetool_ml_jupyter_notebook.xml
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Add changes to GPU Jupyterlab tool based on Jupytool
2023-01-24 16:02:15 +01:00
Pablo Moreno
acd862c632
Clean up
2023-01-16 17:29:22 +00:00
Pablo Moreno
b860465f9c
Handling of files not indexed by gene symbols and output recovery
2023-01-16 17:28:43 +00:00
Pablo Moreno
998cd562c1
Update cellxgene interactive tool to 1.1.1
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Call is the same on 1.1.1, at least as it is used here. Will try to add some options here as well (to specify gene symbols field and others).
2023-01-16 15:05:43 +00:00
Nicola Soranzo
7fee81607c
Add linting with ruff
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ruff (https://github.com/charliermarsh/ruff ) is a new and extremely fast
Python linter, written in Rust.
Ruff can be used to replace Flake8 (plus a variety of plugins), isort,
pydocstyle, yesqa, eradicate, pyupgrade, and autoflake.
Here ruff is added to our current linters (flake8, flake8-bugbear and isort)
while we assess its reliability.
I've not enabled the isort rules because many of the options we use are not
implemented yet. I have instead enabled the pyupgrade rules (a tool which I
run manually every few months).
Also:
- Fix new linting errors reported by ruff.
2023-01-16 14:34:56 +00:00
mvdbeek
73dc126e67
Use format_source="input" instead of format="input"
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Fixes https://github.com/galaxyproject/galaxy/issues/15302
2023-01-13 10:58:57 +01:00
Björn Grüning
5f2b31b088
Merge pull request #15068 from bebatut/pavian-gxit
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Add interactive tool for Pavian
2022-12-10 15:06:19 +01:00
Björn Grüning
7eea95e7d6
use versioned image instead
2022-12-10 13:03:36 +01:00
Dannon
8095fb7460
Merge pull request #14950 from bebatut/interactivetool_mgnify_notebook
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Add interactive tool for Mgnify Jupyter lab
2022-12-09 11:53:59 -05:00
Björn Grüning
128c2c53ac
Update interactivetool_mgnify_notebook.xml
2022-12-09 16:17:17 +01:00
bebatut
012c448227
Make the tool parsing input data
2022-11-28 14:44:28 +01:00
Bérénice Batut
c390c7256a
Add interactive tool for Pavian
2022-11-25 14:03:48 +01:00
Björn Grüning
0f9a364396
used tag container version
2022-11-15 23:06:20 +01:00
mvdbeek
350508909d
Fix more tests
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Include a perl dependency and profile version for the `addValue` tool.
It otherwise fails on OSX with
```
INFO galaxy.tool_util.output_checker:output_checker.py:155 Job failed because of contents in the standard error stream: [perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LC_ALL = (unset),
LC_CTYPE = "C.UTF-8",
LANG = (unset)
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
]
```
Also fix CollectionTypeDescription when collection_type is already CollectionTypeDescription
and fix some wrong type annotations in lib/galaxy/tools/actions/__init__.py
Into more fixes
2022-11-09 15:35:31 +01:00
Björn Grüning