perf: autobump bio/trinity #3121
Conversation
![snakedeploy-bot[bot]](https://avatars.githubusercontent.com/u/1858646?s=60&v=4){kind=small}
WalkthroughThe updates reflect significant enhancements in package dependencies for a Linux 64-bit environment, including major version upgrades, package replacements, and the removal of obsolete components. Notably, various R packages and core libraries like Changes
Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media? TipsChatThere are 3 ways to chat with CodeRabbit:
Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments. CodeRabbit Commands (invoked as PR comments)
Additionally, you can add CodeRabbit Configuration File (
|
![mergify[bot]](https://avatars.githubusercontent.com/in/10562?s=60&v=4){kind=small}
![coderabbitai[bot]](https://avatars.githubusercontent.com/in/347564?s=60&v=4){kind=small}
There was a problem hiding this comment.
Actionable comments posted: 0
Review details
Configuration used: CodeRabbit UI
Review profile: ASSERTIVE
Files selected for processing (2)
- bio/trinity/environment.linux-64.pin.txt (2 hunks)
- bio/trinity/environment.yaml (1 hunks)
Additional comments not posted (8)
bio/trinity/environment.yaml (1)
6-6: Approve the trinity version update.The update from
trinity =2.15.1totrinity =2.15.2is a minor version bump. Ensure compatibility with your existing setup and test for any changes in behavior or performance improvements.bio/trinity/environment.linux-64.pin.txt (7)
8-8: Update to ca-certificates.The update to
ca-certificates-2024.7.4ensures the latest set of trusted certificates, which is crucial for secure communications.
12-12: Update to font-ttf-ubuntu.The update to
font-ttf-ubuntu-0.83-h77eed37_2reflects a change in font package management, potentially improving rendering or compatibility.
15-16: Upgrade to libgcc and libstdcxx.The upgrade to
libgcc-devel_linux-64-14.1.0andlibstdcxx-ng-14.1.0is essential for compatibility with newer compilers and libraries.
17-17: Update to pandoc.The update to
pandoc-3.3is important for document conversion tasks, providing new features and improvements.
18-18: Upgrade to python_abi.The upgrade to
python_abi-3.12indicates a shift to a newer Python ABI, which may affect compatibility with Python packages.
170-170: Upgrade to R base and related packages.The update to
r-base-4.3.3and related R packages ensures access to the latest features and bug fixes in the R ecosystem.
381-381: Approve trinity version update.The update to
trinity-2.15.2is consistent with the changes in theenvironment.yamlfile. Ensure that this version is compatible with your workflows.
🤖 I have created a release \*beep\* \*boop\* --- ## [4.1.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v4.0.0...v4.1.0) (2024-08-21) ### Features * Allow outputting of rendered yte config in Datavzrd wrapper ([#3123](https://www.github.com/snakemake/snakemake-wrappers/issues/3123)) ([e74be78](https://www.github.com/snakemake/snakemake-wrappers/commit/e74be7843299478a276febfacb52825a9762500c)) ### Bug Fixes * Correctly handle non str index list for bwa-mem2/mem ([#3101](https://www.github.com/snakemake/snakemake-wrappers/issues/3101)) ([6f46508](https://www.github.com/snakemake/snakemake-wrappers/commit/6f46508aa99663930e70c82114205929aee2dfcb)) ### Performance Improvements * autobump bio/gatk3/baserecalibrator ([#3119](https://www.github.com/snakemake/snakemake-wrappers/issues/3119)) ([6c2bdfd](https://www.github.com/snakemake/snakemake-wrappers/commit/6c2bdfdca79c7037448bc601a4aeb3d578ea0980)) * autobump bio/gatk3/realignertargetcreator ([#3118](https://www.github.com/snakemake/snakemake-wrappers/issues/3118)) ([ba219e7](https://www.github.com/snakemake/snakemake-wrappers/commit/ba219e7698eb078fe22c703a9662c8cb6deee0eb)) * autobump bio/genomescope ([#3117](https://www.github.com/snakemake/snakemake-wrappers/issues/3117)) ([6292229](https://www.github.com/snakemake/snakemake-wrappers/commit/62922298404397c7b23dc5b8fb01bc33e445e97f)) * autobump bio/igv-reports ([#3120](https://www.github.com/snakemake/snakemake-wrappers/issues/3120)) ([fe33c2c](https://www.github.com/snakemake/snakemake-wrappers/commit/fe33c2c27328212c528e94f995fd0bc26d7fde39)) * autobump bio/trinity ([#3121](https://www.github.com/snakemake/snakemake-wrappers/issues/3121)) ([62b0231](https://www.github.com/snakemake/snakemake-wrappers/commit/62b0231c99920200e3fa6794f87578869cc35bd5)) * Update Datavzrd wrapper ([#3122](https://www.github.com/snakemake/snakemake-wrappers/issues/3122)) ([5101461](https://www.github.com/snakemake/snakemake-wrappers/commit/51014613939bfc5e48e0b2ae619e283cf36bfd88)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Automatic bump of bio/trinity.
Summary by CodeRabbit
New Features
ca-certificates,libgcc, andlibstdcxx.pandocfor enhanced document processing capabilities.Bug Fixes
trinitypackage to potentially resolve issues and improve functionality.