mvdbeek
657b9f7f6c
Add separate out file for MAF_Limit_To_Species1 test
...
The test file is shared with MAF_filter, so if you use the same file
only one of the tests can pass.
2025-09-26 12:47:24 +02:00
Nate Coraor
7a88000aff
Update maf tools with profiles, required_files, and requirements.
2025-09-25 18:13:26 +02:00
Nicola Soranzo
857948c033
Update requirements of sort1 tool
...
Otherwise the conda environment for it fails to solve with the following
error:
```
Solving environment: failed
LibMambaUnsatisfiableError: Encountered problems while solving:
- package grep-2.14-h470a237_2 is excluded by strict repo priority
```
This is due to the fact that grep 2.14 is only available on the bioconda
channel, while newer versions are on conda-forge, which has a higher
priority.
Reported by @mvdbeek in https://github.com/galaxyproject/galaxy/pull/20876/files#r2336209775 .
2025-09-11 01:44:30 +01:00
Nicola Soranzo
26e6a17a17
Fix skipping of empty lines in gtf_filter_by_attribute_values_list tool
...
Introduced in https://github.com/galaxyproject/galaxy/pull/11365 .
2025-09-10 03:45:54 +01:00
Nicola Soranzo
bafa6de88e
Fix incorrect test for Grep1 tool
2025-09-10 03:22:09 +01:00
Nicola Soranzo
eb0a33ff39
Fix gff_filter_by_attribute and gff_filter_by_feature_count tools for recent Python
...
Original fix by @natefoo in
https://github.com/galaxyproject/galaxy/pull/20840 .
2025-09-10 03:21:14 +01:00
Nicola Soranzo
0abc2f7d97
Fix ldtools if tool path contains spaces
2025-09-10 02:14:50 +01:00
Nicola Soranzo
4768d3d1db
Drop Python helper script from sort1 tool
...
Also:
- Incidentally address the deprecation of the `argparse.FileType` type
converter in Python 3.14 , see
https://docs.python.org/3.14/whatsnew/3.14.html#deprecated
https://github.com/galaxyproject/galaxy/issues/16854
- Drop the now unnecessary Python requirement.
- Use CDATA.
2025-09-08 23:47:46 +01:00
mvdbeek
30af8fb6ea
Merge branch 'release_25.0' into dev
2025-08-29 20:00:19 +02:00
mvdbeek
4225e4b0fa
Merge branch 'release_24.2' into release_25.0
2025-08-29 19:59:33 +02:00
mvdbeek
541d70acf6
Include galaxy user agent in data source tools
...
Closes https://github.com/galaxyproject/galaxy/issues/20833
2025-08-29 17:22:28 +02:00
Björn Grüning
a08f04e5e1
Merge branch 'dev' into cleaner_wording
2025-06-12 22:55:03 +02:00
Enis Afgan
dc248bb980
Add icons for many ITs
2025-05-12 10:07:25 -04:00
Dannon Baker
3bf1e0400e
Add a set of logos for interactive tools
2025-05-12 10:07:24 -04:00
Dannon Baker
312c134493
Square-ify jupyter logo
2025-05-12 10:07:24 -04:00
Dannon Baker
452f3e402c
Logo for jupyter notebook
2025-05-12 10:07:24 -04:00
Björn Grüning
46c35f3234
Merge branch 'dev' into cleaner_wording
2025-04-27 09:03:08 +02:00
Nate Coraor
cf1333a148
Also chown R lib in RStudio BioC tool
2025-04-16 11:39:38 -04:00
Nate Coraor
9e43a5788d
Merge pull request #19924 from afgane/rstudio32
...
RStudio IT updates to work on .org
2025-04-10 10:11:39 -04:00
Daniel Blankenberg
491f415173
Merge pull request #19689 from jaidevjoshi83/DICED
...
Data-source tool for DICED database (https://diced.lerner.ccf.org/ ) added.
2025-04-09 15:33:49 -04:00
Björn Grüning
bedf19baa4
change description of the export tool
2025-04-05 22:25:22 +02:00
mvdbeek
b0c197c9e6
Drop unnecessary global statements
2025-04-05 09:55:42 +02:00
Enis Afgan
d7bddb5116
RStudio IT updates to work on .org
2025-03-27 19:46:10 -04:00
mvdbeek
de7b0ed7da
Merge branch 'release_24.2' into dev
2025-03-21 19:09:05 +01:00
John Chilton
ff011fbe01
Handle directories with percents in export_remote.xml.
2025-03-20 16:25:09 -04:00
Jayadev Joshi
52a9eca51c
tool xml fixed
2025-03-18 21:47:57 -04:00
Enis Afgan
1d215a7d2d
Add RStudio IT based on upstream image from Bioconductor
2025-03-18 16:45:14 -04:00
Jayadev Joshi
c14c2a0ee9
data type added
2025-03-04 22:54:17 -05:00
Jayadev Joshi
d1dae72ad5
tool issues fixed
2025-03-04 22:50:27 -05:00
Jayadev Joshi
20ac054683
renamed the data source tool file
2025-02-27 16:01:05 -05:00
Enis Afgan
c6e553be71
Update RStudio IT
2025-02-26 16:01:00 -05:00
Jayadev Joshi
155b198f8a
Data-source tool for DICED databased added, DICED_Datasetbrowser.xml
2025-02-24 10:31:41 -05:00
Nicola Soranzo
7ce76af796
Format code with black 25.1.0
2025-02-16 18:07:51 +00:00
Nicola Soranzo
faa752ed03
Fix type annotations
2025-02-09 01:54:55 +00:00
Nicola Soranzo
aa49793ecf
Make CompressedFile a context manager
...
to ensure that the archive is closed.
2025-01-18 14:40:30 +00:00
Marius van den Beek
9960c31265
Merge pull request #16837 from lldelisle/ilastik
...
Add Interactive Tool Ilastik
2024-11-15 18:44:09 +01:00
Marius van den Beek
e34f6ade2f
Merge pull request #18861 from natefoo/jupyter-24.07
...
Jupyter Interactive Tool 1.0.1/24.07
2024-11-12 16:33:26 +01:00
Nicola Soranzo
178a1efb30
Remove outdated fimo wrapper and galaxy-sequence-utils dependency
...
The fimo tool was removed from `tool_conf.xml.sample` in 2014
(commit fa11d10c8bhttps://github.com/galaxyproject/tools-iuc/pull/499 ).
This bundled version doesn't probably work any more and is not
available on the UseGalaxy.* servers.
This allows us to remove `galaxy-sequence-utils` from the project
dependencies, since the other 2 tools
(`lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml`
and `tools/maf/vcf_to_maf_customtrack.xml`) correctly specify it as a
requirement.
2024-10-04 12:33:26 +01:00
Nate Coraor
615bd19718
Keep Jupyter 1.0.1 IT as a separate tool
2024-10-01 12:21:29 -04:00
Nicola Soranzo
79a4ebd28d
Enable `ignore-without-code` mypy error code
2024-09-26 11:02:33 +01:00
Nate Coraor
1e0f928809
Jupyter Interactive Tool 1.0.1/24.07
2024-09-20 13:07:10 -04:00
mvdbeek
ac71c06854
Merge branch 'release_24.1' into dev
2024-09-13 16:59:22 +02:00
mvdbeek
00f6482387
Merge branch 'release_24.0' into release_24.1
2024-09-13 16:57:45 +02:00
Delphine Lariviere and Björn Grüning
3dddfb1eb6
Apply suggestions from code review
...
Co-authored-by: Björn Grüning <bjoern@gruenings.eu >
2024-09-06 09:34:29 +10:00
Delphine Lariviere
83c2e706a6
add blob toolkit to the list of interactive tools
2024-09-06 09:34:29 +10:00
Marius van den Beek
c42710a403
Merge pull request #18630 from Delphine-L/blobtoolkit
...
Add BlobToolkit to the list of interactive tools
2024-09-05 16:40:12 +02:00
mvdbeek
48ebf3122b
Update ENA url in ebi_sra tool
...
I think this fixes https://github.com/galaxyproject/galaxy/issues/18770
? I did manage to get the redirect to Galaxy, however the user interface
looks pretty weird to me, so I'm not sure this is how it is meant to be
?
2024-09-04 12:29:31 +02:00
John Chilton
e530227ac6
Implement group tag testing in tools.
2024-08-09 11:54:19 -04:00
mvdbeek
0d1f74e4dd
Merge branch 'release_24.1' into dev
2024-08-08 17:43:04 +02:00
davelopez and Marius van den Beek
7d00202034
Fix export_remote include metadata flag
...
We were passing 'false' to --export-metadata-files, but it was
considered True (non-zero length string), and the metadata was
always included in the export.
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com >
2024-08-07 14:46:57 +02:00
mvdbeek