Update Trinity requirements

[avani-bhojwani]

Added coreutils to the requirements as it may be needed to use the sort command. Currently, running Trinity results in this being shown repeatedly:

BusyBox v1.32.1 (2021-04-13 11:15:36 UTC) multi-call binary.
Usage: sort [-nrugMcszbdfiokt] [-o FILE] [-k start[.offset][opts][,end[.offset][opts]] [-t CHAR] [FILE]...
Sort lines of text
    -o FILE    Output to FILE
    -c    Check whether input is sorted
    -b    Ignore leading blanks
    -f    Ignore case
    -i    Ignore unprintable characters
    -d    Dictionary order (blank or alphanumeric only)
    -n    Sort numbers
    -g    General numerical sort
    -M    Sort month
    -V    Sort version
    -t CHAR    Field separator
    -k N[,M] Sort by Nth field
    -r    Reverse sort order
    -s    Stable (don't sort ties alphabetically)
    -u    Suppress duplicate lines
    -z    Lines are terminated by NUL, not newline

---

Please read the guidelines for Bioconda recipes before opening a pull request (PR).

General instructions

• If this PR adds or updates a recipe, use "Add" or "Update" appropriately as the first word in its title.
• New recipes not directly relevant to the biological sciences need to be submitted to the conda-forge channel instead of Bioconda.
• PRs require reviews prior to being merged. Once your PR is passing tests and ready to be merged, please issue the @BiocondaBot please add label command.
• Please post questions on Gitter or ping @bioconda/core in a comment.

Instructions for avoiding API, ABI, and CLI breakage issues

Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify run_exports (see here for the rationale and comprehensive explanation).
Add a run_exports section like this:

build:
  run_exports:
    - ...

with ... being one of:

Case	run_exports statement
semantic versioning	{{ pin_subpackage("myrecipe", max_pin="x") }}
semantic versioning (0.x.x)	{{ pin_subpackage("myrecipe", max_pin="x.x") }}
known breakage in minor versions	{{ pin_subpackage("myrecipe", max_pin="x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
known breakage in patch versions	{{ pin_subpackage("myrecipe", max_pin="x.x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
calendar versioning	{{ pin_subpackage("myrecipe", max_pin=None) }}

while replacing "myrecipe" with either name if a name|lower variable is defined in your recipe or with the lowercase name of the package in quotes.

Bot commands for PR management

Please use the following BiocondaBot commands:

Everyone has access to the following BiocondaBot commands, which can be given in a comment:

@BiocondaBot please update	Merge the master branch into a PR.
@BiocondaBot please add label	Add the please review & merge label.
@BiocondaBot please fetch artifacts	Post links to CI-built packages/containers. You can use this to test packages locally.

Note that the @BiocondaBot please merge command is now depreciated. Please just squash and merge instead.

Also, the bot watches for comments from non-members that include @bioconda/<team> and will automatically re-post them to notify the addressed <team>.

[coderabbitai]

📝 Walkthrough

📝 Walkthrough

📝 Walkthrough

Walkthrough

The pull request modifies the recipes/trinity/meta.yaml file for the Trinity package. The key changes include an increment in the build number from 0 to 1 and the addition of coreutils to the run requirements section under the requirements key. This change indicates that coreutils is now a required dependency at runtime. No other structural or logical alterations are present in the file.

Possibly related PRs

• Update lofreq to add bcftools dependency #51672: This PR adds a new dependency (bcftools) to the lofreq package's meta.yaml, similar to how the main PR adds coreutils as a runtime requirement in the trinity package's meta.yaml.

Suggested labels

please review & merge

Suggested reviewers

• druvus

---

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?

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

🪧 Tips

Chat

There are 3 ways to chat with CodeRabbit:

• Review comments: Directly reply to a review comment made by CodeRabbit. Example:
  • I pushed a fix in commit <commit_id>, please review it.
  • Generate unit testing code for this file.
  • Open a follow-up GitHub issue for this discussion.
• Files and specific lines of code (under the "Files changed" tab): Tag @coderabbitai in a new review comment at the desired location with your query. Examples:
  • @coderabbitai generate unit testing code for this file.
  • @coderabbitai modularize this function.
• PR comments: Tag @coderabbitai in a new PR comment to ask questions about the PR branch. For the best results, please provide a very specific query, as very limited context is provided in this mode. Examples:
  • @coderabbitai gather interesting stats about this repository and render them as a table. Additionally, render a pie chart showing the language distribution in the codebase.
  • @coderabbitai read src/utils.ts and generate unit testing code.
  • @coderabbitai read the files in the src/scheduler package and generate a class diagram using mermaid and a README in the markdown format.
  • @coderabbitai help me debug CodeRabbit configuration file.

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 using PR comments)

• @coderabbitai pause to pause the reviews on a PR.
• @coderabbitai resume to resume the paused reviews.
• @coderabbitai review to trigger an incremental review. This is useful when automatic reviews are disabled for the repository.
• @coderabbitai full review to do a full review from scratch and review all the files again.
• @coderabbitai summary to regenerate the summary of the PR.
• @coderabbitai resolve resolve all the CodeRabbit review comments.
• @coderabbitai configuration to show the current CodeRabbit configuration for the repository.
• @coderabbitai help to get help.

Other keywords and placeholders

• Add @coderabbitai ignore anywhere in the PR description to prevent this PR from being reviewed.
• Add @coderabbitai summary to generate the high-level summary at a specific location in the PR description.
• Add @coderabbitai anywhere in the PR title to generate the title automatically.

CodeRabbit Configuration File (.coderabbit.yaml)

• You can programmatically configure CodeRabbit by adding a .coderabbit.yaml file to the root of your repository.
• Please see the configuration documentation for more information.
• If your editor has YAML language server enabled, you can add the path at the top of this file to enable auto-completion and validation: # yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json

Documentation and Community

• Visit our Documentation for detailed information on how to use CodeRabbit.
• Join our Discord Community to get help, request features, and share feedback.
• Follow us on X/Twitter for updates and announcements.

[coderabbitai]

Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (1)

recipes/trinity/meta.yaml (1)

43-43: Consider adding a minimum version constraint for coreutils.

While not strictly necessary, specifying a minimum version constraint (e.g., coreutils >=8.32) would ensure reproducibility and compatibility across different environments.

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between f76dedf and 8323a25.

📒 Files selected for processing (1)

• recipes/trinity/meta.yaml (1 hunks)

🔇 Additional comments (1)

recipes/trinity/meta.yaml (1)

43-43: LGTM! Addition of coreutils addresses the BusyBox sort limitation.

The addition of coreutils as a runtime dependency is appropriate and will resolve the reported issues with BusyBox's limited sort functionality.

[avani-bhojwani]

@BiocondaBot please add label