Nicola Soranzo
e34590b687
Update deprecated Python import
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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.
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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
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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
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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 Cuccuru and Marius van den Beek
f402de57f1
Update tools/interactive/interactivetool_climate_notebook.xml
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Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2022-04-26 14:48:51 +02:00
Gianmauro Cuccuru and Marius van den Beek
58d48caa44
Update tools/interactive/interactivetool_jupyter_notebook.xml
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Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2022-04-26 14:48:22 +02:00
Gianmauro Cuccuru and Marius van den Beek
3a8fda196f
Update tools/interactive/interactivetool_metashark.xml
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Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2022-04-26 14:48:09 +02:00
Gianmauro Cuccuru and Marius van den Beek
4eb305c70d
Update tools/interactive/interactivetool_pangeo_notebook.xml
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Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2022-04-26 14:47:54 +02:00
Gianmauro Cuccuru and Marius van den Beek
41adb59151
Update tools/interactive/interactivetool_pangeo_notebook.xml
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Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2022-04-26 14:47:18 +02:00
Gianmauro Cuccuru and Marius van den Beek
9bdbb381dd
Update tools/interactive/interactivetool_rstudio.xml
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Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2022-04-26 14:47:05 +02:00
Gianmauro Cuccuru and Marius van den Beek
513c873e0c
Update tools/interactive/interactivetool_vrm_editor.xml
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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
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co-authored by @bgruening and @mvdbeek
2022-04-26 12:19:47 +02:00
Gianmauro Cuccuru
86a27dead3
update IT jupyter notebook
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authored by @bgruening
2022-04-26 12:17:49 +02:00
Gianmauro Cuccuru
04820a6306
add IT vrm editor
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authored by @annefou
2022-04-26 12:16:28 +02:00
Gianmauro Cuccuru
1955bf3e0b
add IT pangeo notebook
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authored by @annefou
2022-04-26 12:15:53 +02:00
Gianmauro Cuccuru
3767c7ee87
update IT cliamte notebook
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authored by @annefou
2022-04-26 12:15:03 +02:00
Gianmauro Cuccuru
2a050e7796
add IT metashark
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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
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
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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
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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.
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Apply isort.
2022-02-03 07:42:20 -05:00
Alex Ostrovsky
f884f9b149
Allow any format in export tool
2022-01-11 13:10:03 -08:00
Nicola Soranzo
bd0cefa020
Don't use triple-quoted strings as comments
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They are expressions that get uselessly evaluated.
These were reported as B018 errors by flake8-bugbear 21.11.28 , but B018 for
strings has then been disabled in 21.11.29 since these strings can also be
used as inline attribute doc strings or module variable docstrings (not our
case though).
2021-11-29 23:02:34 +00:00
mvdbeek
6e01abe4b2
Bump version and add profile
2021-11-26 16:18:31 +01:00
Gianmauro Cuccuru
0cf0b82959
Update interactivetool_pyiron.xml
2021-11-26 15:57:34 +01:00
Nicola Soranzo
1f8ac6c7bb
Merge pull request #12965 from common-workflow-lab/type_ignore_narrow
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tighten type ignores
2021-11-23 16:32:28 +00:00
Nicola Soranzo
30337fbd94
Merge branch 'release_21.09' into dev
2021-11-23 13:30:36 +00:00
Michael R. Crusoe
7819fdc7a6
tighten type ignores
2021-11-23 13:12:07 +01:00
Marius van den Beek
90c2f31cb4
Don't add ca-ceritificates to tool requirements
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ca-certificates is now part of the ncbi-datasets-cli conda package
2021-11-18 17:17:19 +01:00
Marius van den Beek and Helena
f1986a481f
Export just once
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Thanks!
Co-authored-by: Helena <hxr@hx42.org >
2021-11-17 15:28:07 +01:00
mvdbeek
47120ca48f
Fix containerized NCBI Datasets Genomes data source tool
2021-11-12 20:17:34 +01:00
John Chilton
4fe7109ab1
Track transformations applied during uploads.
2021-11-12 10:21:55 -05:00
John Chilton
8643daf1dd
Attempt to type more upload related things.
2021-11-05 11:58:53 -04:00
mvdbeek
58b2837c7c
Merge branch 'release_21.09' into dev
2021-11-01 18:17:54 +01:00
mvdbeek
63e25b20f4
Set profile version of ncbi_datasets so it can run containerized
2021-10-31 16:28:38 +01:00
Dannon Baker
c3605c7112
Merge remote-tracking branch 'upstream/release_21.09' into dev
2021-10-19 09:59:21 -04:00
mvdbeek
4dbf235f23
Ignore type in unused function
2021-10-12 15:25:30 +02:00
David López
2ed29639bb
Merge pull request #12691 from jmchilton/more_type_fixes
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Check types of modules without type annotations in the their signatures on new modules.
2021-10-12 13:33:17 +02:00
Nicola Soranzo