Skip to content

[26.1] Add kraken2 datatype #22455

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
pvanheus wants to merge 9 commits into
base: release_26.1
Choose a base branch
from
Draft

[26.1] Add kraken2 datatype #22455

Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
77714da
Add kraken2 datatype
pvanheus Apr 10, 2026
7138ae7
Reformat binary.py
pvanheus Apr 10, 2026
41db163
Add tests for kraken2 db compressed archive
pvanheus Apr 20, 2026
10c2d9d
Make Kraken2Database a subclass of Directory
pvanheus Apr 20, 2026
f7c4931
Fix Python linting issues
pvanheus Apr 20, 2026
d87af76
Remove kraken2 datatype test
pvanheus Apr 21, 2026
2b6b9d1
Implement kraken2db and kraken2db.tar.gz datatypes simply using datat…
pvanheus Jun 24, 2026
52101aa
Merge changes from upstream
pvanheus Jun 24, 2026
4c79b75
Remove test file 1.kraken2db.tar.gz
pvanheus Jun 26, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 6 additions & 0 deletions lib/galaxy/config/sample/datatypes_conf.xml.sample
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -359,6 +359,12 @@
<datatype extension="tar" auto_compressed_types="gz,bz2" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true">
<converter file="archive_to_directory.xml" target_datatype="directory"/>
</datatype>
<datatype extension="kraken2db.tar" auto_compressed_types="gz,bz2" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="true" description="Kraken2 database archive">
<converter file="archive_to_directory.xml" target_datatype="kraken2db"/>

@bernt-matthias bernt-matthias Jun 26, 2026

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Does this really work? That is does it produce a kraken2db or a directory.

</datatype>
<datatype extension="kraken2db" type="galaxy.datatypes.data:Directory" subclass="true" description="Kraken2 database directory">
<converter file="directory_to_archive.xml" target_datatype="kraken2db.tar.gz"/>

@bernt-matthias bernt-matthias Jun 26, 2026

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Would this convert any directory?

</datatype>
<datatype extension="directory" type="galaxy.datatypes.data:Directory"/>
<datatype extension="bwa_index" display_in_upload="true" type="galaxy.datatypes.data:Directory" subclass="true"/>
<datatype extension="bwa_mem2_index" display_in_upload="true" type="galaxy.datatypes.data:Directory" subclass="true"/>
Expand Down
Loading