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330310e69f24d7b4ef28fcade7d6ba3383d0f787
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3010 Commits
Author SHA1 Message Date
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 
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
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 
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 
Add changes to GPU Jupyterlab tool based on Jupytool
 2023-01-24 16:02:15 +01:00
Nicola Soranzo 7fee81607c Add linting with ruff 
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" 
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 
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 
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 
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 d6a2feb270 remove not used inputs 2022-11-09 15:00:42 +01:00
Bérénice Batut 67608c274e Add interactive tool for Mgnify Jupyter lab 2022-11-08 17:12:03 +01:00
Anup Kumar 4052551b7d Update interactivetool_ml_jupyter_notebook.xml 2022-11-03 10:03:40 +01:00
Wolfgang Maier ddebbd97b2 Bump wrapper version and declare updates to it WF-safe 2022-10-31 23:03:32 +01:00
Wolfgang Maier 74b7ed8b10 Simplify head wrapper - same functionality, no pipe 2022-10-31 15:27:40 +01:00
Matthias Bernt 13b7fb1bc2 partially revert d674f2ba6e 
and add comment to interval2maf tool stating that it's deprecated
 2022-09-26 11:24:56 +02:00
Matthias Bernt d674f2ba6e remove interval2maf 
its listed as broken anyway and we have it working (https://github.com/galaxyproject/tools-iuc/pull/4769) at IUC
 2022-09-16 13:06:49 +02:00
Nicola Soranzo ac6ffb28d1 Fix typos 2022-09-09 17:20:23 +01:00
mvdbeek 2e22b9e1f8 Merge branch 'release_22.05' into dev 2022-08-22 19:17:35 +02:00
jancrichter 912dc47c8a bump version 2022-08-18 17:49:06 +02:00
jancrichter f9f7e97043 adjust tests to correctly test for retainment of header 2022-08-18 17:49:05 +02:00
jancrichter 7b10be9cb8 Append grep results to avoid overwriting header 
Currently, if "keep_header" is true, the header is copied to the output file, but is then overwritten by the grep results.
 2022-08-18 17:49:04 +02:00
Nicola Soranzo d6b771c242 Merge branch 'release_22.05' into dev 2022-07-12 22:16:48 +01:00
Daniel Blankenberg 689a91d83b superfluous 2022-07-12 12:20:46 -04:00
Daniel Blankenberg 4a83e6f04d Fixes for JupyTool, and overlapping versions with jupyter. 2022-07-11 18:06:35 -04:00
mvdbeek 4b20d96866 Remove legacy root controller methods 
And removes viewer applets that are hgighly unlikely to work and be
relevant. The tools are not installed on usegalaxy.org.
 2022-07-11 10:35:51 +03:00
Marius van den Beek 3a18da8523 Merge pull request #14040 from nsoranzo/modernise_package_build 
Modernise build of packages
 2022-06-15 10:48:23 +02:00
Marius van den Beek 00333722fd Merge pull request #13606 from blankenberg/jupytool 
Add JupyTool, user-configurable interactive Jupyter-based tool.
 2022-06-15 10:41:47 +02:00
mvdbeek 3ce6a1687c Keep version lineage 2022-06-14 18:46:15 +02:00
Nicola Soranzo 3bca59b8e9 Remove uses of six library 
Remove unused file `tools/data_source/hbvar_filter.py` .
 2022-06-10 10:32:00 +01:00
Nicola Soranzo e34590b687 Update deprecated Python import 
which doesn't work any more on Python 3.10 .
 2022-06-02 17:58:42 +01:00
John Chilton 37892dcabc Refactor sniff.stream_url_to_file to galaxy.files.uris. 
The value of this can be seen for instance in unpack_tar_gz_archive - which should have nothing to do with datatypes and now doesn't need to load the whole datatypes module.

Use this in workflows API to allow downloading workflow files from configured URIs.
 2022-05-21 17:22:41 -04:00
Marius van den Beek ddbd8bd8c5 Merge pull request #13811 from gmauro/IT_updates 
IT updates from EU
 2022-05-05 17:02:55 +02:00
mvdbeek 4ca0d63c3b Merge branch 'release_22.01' into dev 2022-05-04 17:10:29 +02:00
mvdbeek da1dd283f3 Add @TOOL_VERSION@ token for NCBI Datasets Genomes 2022-05-04 16:34:09 +02:00
mvdbeek 5c014d2048 Bump ncb-datasets-cli dependency to 13.14.0 
Fixes

```
panic: runtime error: invalid memory address or nil pointer dereference
[signal SIGSEGV: segmentation violation code=0x1 addr=0x10 pc=0x8a3fea]

goroutine 1 [running]:
main/datasets/datasets.downloadData(0xc000010380, 0x0, 0x0, 0x0, 0x7ffe36956316, 0x62, 0xffffffffffffffff, 0x0, 0x0)
	src/datasets/datasets/Download.go:41 +0xea
main/datasets/datasets.downloadAssembly(0xc000069100, 0x7ffe36956316, 0x62, 0x8ef4a0, 0xc000010298)
	src/datasets/datasets/DownloadGenome.go:63 +0x294
main/datasets/datasets.glob..func1(0xd9d080, 0xc000074730, 0x0, 0x5, 0x0, 0x0)
	src/datasets/datasets/Download.go:106 +0x2a7
github.com/spf13/cobra.(*Command).execute(0xd9d080, 0xc0000746e0, 0x5, 0x5, 0xd9d080, 0xc0000746e0)
	external/com_github_spf13_cobra/command.go:842 +0x472
github.com/spf13/cobra.(*Command).ExecuteC(0xd9cde0, 0x4686c5, 0xc000000180, 0x200000003)
	external/com_github_spf13_cobra/command.go:950 +0x375
github.com/spf13/cobra.(*Command).Execute(...)
	external/com_github_spf13_cobra/command.go:887
main/datasets/datasets.Execute()
	src/datasets/datasets/root.go:444 +0x31
main.main()
	src/cmd/datasets/main.go:10 +0x25
```
 2022-05-03 17:13:16 +02:00
Gianmauro Cuccuru 92a10ebe9d drop detect_errors 2022-04-26 14:52:30 +02:00
Gianmauro CuccuruandMarius van den Beek f402de57f1 Update tools/interactive/interactivetool_climate_notebook.xml 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-04-26 14:48:51 +02:00
Gianmauro CuccuruandMarius van den Beek 58d48caa44 Update tools/interactive/interactivetool_jupyter_notebook.xml 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-04-26 14:48:22 +02:00
Gianmauro CuccuruandMarius van den Beek 3a8fda196f Update tools/interactive/interactivetool_metashark.xml 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-04-26 14:48:09 +02:00
Gianmauro CuccuruandMarius van den Beek 4eb305c70d Update tools/interactive/interactivetool_pangeo_notebook.xml 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-04-26 14:47:54 +02:00
Gianmauro CuccuruandMarius van den Beek 41adb59151 Update tools/interactive/interactivetool_pangeo_notebook.xml 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-04-26 14:47:18 +02:00