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2985 Commits
Author SHA1 Message Date
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
Gianmauro CuccuruandMarius van den Beek 9bdbb381dd Update tools/interactive/interactivetool_rstudio.xml 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-04-26 14:47:05 +02:00
Gianmauro CuccuruandMarius van den Beek 513c873e0c Update tools/interactive/interactivetool_vrm_editor.xml 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-04-26 14:44:35 +02:00
Gianmauro Cuccuru 73be453f38 update IT rstudio 
co-authored by @bgruening and @mvdbeek
 2022-04-26 12:19:47 +02:00
Gianmauro Cuccuru 86a27dead3 update IT jupyter notebook 
authored by @bgruening
 2022-04-26 12:17:49 +02:00
Gianmauro Cuccuru 04820a6306 add IT vrm editor 
authored by @annefou
 2022-04-26 12:16:28 +02:00
Gianmauro Cuccuru 1955bf3e0b add IT pangeo notebook 
authored by @annefou
 2022-04-26 12:15:53 +02:00
Gianmauro Cuccuru 3767c7ee87 update IT cliamte notebook 
authored by @annefou
 2022-04-26 12:15:03 +02:00
Gianmauro Cuccuru 2a050e7796 add IT metashark 
authored by @yvanlebras
 2022-04-26 12:12:11 +02:00
Nicola Soranzo 2438d24667 Merge pull request #13666 from hexylena/fix-david 2022-04-04 16:45:57 +01:00
Helena Rasche 20c3c43543 Fix david url 2022-04-04 15:11:22 +02:00
Nicola Soranzo aa22088d2b Rename variables to fix B020 (false positive) errors 2022-03-26 23:43:08 +00:00
Daniel Blankenberg 2216a532b0 Update JupyTool 2022-03-23 16:42:31 -04:00
Daniel Blankenberg 62ca0c3424 Update JupyTool. 2022-03-23 16:01:36 -04:00
Daniel Blankenberg f998b1997f Update JupyTool 2022-03-22 12:01:30 -04:00
Daniel Blankenberg c07deb8fa8 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into jupytool 2022-03-22 08:12:53 -04:00
Nicola Soranzo 00f7522e7e Merge branch 'release_22.01' into dev 2022-03-19 01:57:33 +00:00
Nicola Soranzo 5114b67902 Merge branch 'release_21.09' into release_22.01 2022-03-18 18:28:15 +00:00
Nicola Soranzo 8e4bdb58e4 Merge branch 'release_21.05' into release_21.09 2022-03-18 18:08:10 +00:00
mvdbeek e2d43806dc Fix `sff_extract` tool, drop type annotation 
I don't think this tool is really used much, but it is loaded in
`tool_conf.xml`.
https://github.com/galaxyproject/galaxy/pull/11877 added type
annotations, and that's a syntax error on 2.7

The alternative would be to fix the rest of the tool for 3.x,
but I think we're just wasting our time there and we shouldn't
touch this again.
 2022-03-16 15:24:55 +01:00
Nicola Soranzo 7f04b5d698 Merge branch 'release_22.01' into dev 2022-03-02 20:08:55 +00:00
Nicola Soranzo 856269b248 Merge branch 'release_21.09' into release_22.01 2022-03-02 19:18:43 +00:00
mvdbeek a9eb669158 Add profile version to ethercalc 
It writes to stderr, so that fails on most job runners (why not all???).
 2022-03-02 14:10:52 +01:00
Dannon Baker 03351d2a9f Apply black to tools as well 2022-02-03 09:12:13 -05:00
Nicola Soranzo dc87e8f38a Help black with placement of noqa comments 2022-02-03 14:07:14 +00:00
Dannon Baker 623a5e165a Apply black formatting. 
Apply isort.
 2022-02-03 07:42:20 -05:00