Add a wrapper script for command-line predictions#3
Open
TJN25 wants to merge 2 commits intopatrickbryant1:mainfrom
Open
Add a wrapper script for command-line predictions#3TJN25 wants to merge 2 commits intopatrickbryant1:mainfrom
TJN25 wants to merge 2 commits intopatrickbryant1:mainfrom
Conversation
Adds `run_rarefold_predict.sh`, a wrapper script that provides a command-line interface for the prediction workflow. It accepts flags for all primary inputs, including `--id`, `--fasta`, `--outdir`, `--params`, and `--hhblitsdb`. Key implementation details: - Resolves the script's absolute path at runtime to correctly locate internal Python scripts and default data files from any working directory. - Checks for hhblits on the system PATH before using the hardcoded fallback path.The original predict.sh script is not modified. This provides a new, parallel entry point for executing predictions.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Thank you for creating and sharing this useful tool. I've been working on installing it and during the setup, I found that I wanted to run predictions from different directories and within automated pipelines. To make that easier, I wrote a wrapper script,
run_rarefold_predict.sh, that provides a more flexible command-line interface.I thought this might be useful to others in the community, so I wanted to contribute it back in case you find it helpful.
What this PR adds:
run_rarefold_predict.sh: A new Bash script that wraps the existing prediction workflow. It allows a user to specify all inputs (like FASTA file, output directory, and prediction ID) using command-line flags.README.mdexplaining how to use the new script for custom predictions.The original
predict.shscript is left completely unchanged, so this is a purely additive contribution.Thanks again for your hard work on RareFold!