May 2020 Galaxy Release (v 20.05)¶

Highlights¶

Tool Recommendations: Anup Kumar has built a tool prediction feature based on machine learning conducted on Galaxy Europe data. Using the connections in workflows, he has built a button which can recommend what tool you should use after a current analysis step. You can read more on UseGalaxy.eu’s blogpost. This feature is not currently available on usegalaxy.org, but can be tried on usegalaxy.eu.

New Interactive Tools: Through the combined efforts of many UseGalaxy.eu admins and developers, as well as the European Galaxy community we have converted a significant number of interactive environments into the new interactive tool specification. Thanks to @bgruening, @hexylena, @jenzopr, @yvanlebras, @annefou, @abretaud, @joachimwolff, and @astrovsky01. You can try them all on live.usegalaxy.eu

Rule Based Uploader: Scrolling!: Many power users have fallen in love with Galaxy’s Rule Builder, allowing you to upload tables of data, and easily tag datasets and build collections on upload. However with too many columns the table did not scroll well for users, but no longer! This has been fixed by one of the Galaxy team members, @assuntad23. If you want to learn more about using the rule builder please see the in-depth tutorial from the developer, @jmchilton.

Social Login: The social login system has seen improvements over the past release, from adding support for Okta, adding and disconnecting OIDC accounts, to logging out. Through CILogon and Custos, users will be able to use existing institutional log in credentials to log into their Galaxy accounts. Different servers support different authentication providers, so ask your admin today if you want to login with CILogon, Custos, ELIXIR AAI, Google, or Globus.

Chira Visualisation: Chira provides a suite of tools and a new visualisation for chimeras, allowing you to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, LIGR-Seq, etc. Read more in EU’s blog. (thanks to @OlegZharkov, Pull Request 9562)

Editor as visualization (thanks to @OlegZharkov). Pull Request 9531
Skip visualization build, if no changes were registered (thanks to @OlegZharkov). Pull Request 9634

new data types for OpenMS (thanks to @bernt-matthias). Pull Request 8109
Add tpr datatype (thanks to @simonbray). Pull Request 9244
Python3 compatible SnpEff and SnpSift metadata detection (thanks to @wm75). Pull Request 9282
Add datatypes for xcms and camera (thanks to @computational-metabolomics). Pull Request 9470
Create csi index for bam files where any region is larger than 2**29 - 1) (thanks to @FredericBGA). Pull Request 9570
Add PAF, GFA1 and odgi datatypes (thanks to @nsoranzo). Pull Request 9592
Add xg, vg and protobuf datatypes (thanks to @bgruening). Pull Request 9593
Sniffer for multi-member zip archives (thanks to @lecorguille). Pull Request 9595
Fix gff3.gz and gff3.bz2 datatypes Pull Request 9731
Use right extension in bz2_to_uncompressed.xml Pull Request 9734
Fix disappearing datatypes after restart Pull Request 9835

Remove deprecated interpreter attribute from tools <command> (thanks to @nsoranzo). Pull Request 9490
Datasource tool for SRA manifest Pull Request 9613
Fix ITs to work in remote Kubernetes Pull Request 9614
fix error in bundled tool: shrimp_color_wrapper (thanks to @bernt-matthias). Pull Request 9665
extract_genomic_dna.py: import Comment, Header from bx.tabular.io instead of bx.intervals.io (thanks to @cat-bro). Pull Request 9748

Please see the full release notes for more details.

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