Don't remove DIA-NN from FragPipe installation.

[reid-wagner]

It's been confirmed with both the FragPipe and DIA-NN authors that their license confers the ability to distribute the DIA-NN package along with the FragPipe download.

---

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[coderabbitai]

📝 Walkthrough

📝 Walkthrough

Walkthrough

The changes in this pull request involve modifications to the FragPipe project, specifically within the scripts and license documentation. The build.sh script has been updated to remove lines that previously handled the DIA-NN tool directories, indicating that the DIA-NN license incompatibility issue is no longer addressed. The script still performs its primary functions, such as copying the FragPipe source and Philosopher installation, and creating a symbolic link to the Philosopher binary.

Additionally, the wrapper script for FragPipe has been simplified by removing a block of code that checked for a specific feature related to the DIA-NN license, streamlining its control flow while retaining checks for license keys for MSFragger and IonQuant. Lastly, a new license agreement for the DIA-NN software has been added, detailing its terms of use, limitations, and requirements for attribution, among other legal stipulations. No alterations were made to the declarations of exported or public entities in any of the modified files.

Possibly related PRs

• Update Earl Grey build.sh #51324: The changes in the build.sh script for Earl Grey involve modifications to executable permissions and symbolic links, which are similar in nature to the updates made in the build.sh script for FragPipe regarding symbolic links and script functionality.

Suggested labels

please review & merge

Suggested reviewers

• mencian
• adamhospital

---

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between 0f38c39 and af0e0e3.

📒 Files selected for processing (1)

• recipes/fragpipe/meta.yaml (1 hunks)

🧰 Additional context used

🔇 Additional comments (2)

recipes/fragpipe/meta.yaml (2)

15-15: LGTM: Build number increment is appropriate.

The build number has been correctly incremented from 3 to 4. This is the standard practice when making changes to a package without altering its version, which aligns with the PR objectives.

---

Line range hint 1-85: Verify if additional changes are needed in meta.yaml

Given the modifications related to DIA-NN handling mentioned in the AI summary (removal of DIA-NN tool directory handling in build.sh and changes to the wrapper script), please verify if any additional changes are needed in this meta.yaml file. For example:

1. Are there any DIA-NN related dependencies that need to be updated or removed?
2. Does the package description or summary need to be updated to reflect the changes in DIA-NN handling?
3. Are there any license files that need to be added or removed as a result of these changes?

To help verify these points, you can run the following script:

✅ Verification successful

Verification Complete: No Additional Changes Needed in meta.yaml

All references to DIA-NN have been successfully removed. No updates are required for dependencies, package descriptions, summaries, or license files related to DIA-NN.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for DIA-NN related entries in meta.yaml and other relevant files

# Check for DIA-NN mentions in meta.yaml
echo "Checking for DIA-NN mentions in meta.yaml:"
rg -i "dia-nn" recipes/fragpipe/meta.yaml

# Check for DIA-NN related files in the recipe directory
echo "Checking for DIA-NN related files in the recipe directory:"
fd -i "dia-nn" recipes/fragpipe

# Check for DIA-NN mentions in build.sh
echo "Checking for DIA-NN mentions in build.sh:"
rg -i "dia-nn" recipes/fragpipe/build.sh

# Check for DIA-NN mentions in the wrapper script
echo "Checking for DIA-NN mentions in the wrapper script:"
rg -i "dia-nn" recipes/fragpipe/fragpipe.py

Length of output: 655

---

Script:

#!/bin/bash
# Description: Locate the current wrapper script and check for DIA-NN mentions

# Find Python scripts in the recipe directory
echo "Searching for Python wrapper scripts in recipes/fragpipe:"
fd -e py recipes/fragpipe --exec echo {}

# If a wrapper script is found, check for DIA-NN mentions within it
# Replace 'wrapper_script.py' with the actual script name if found
# Example:
# rg -i "dia-nn" recipes/fragpipe/wrapper_script.py

Length of output: 539

---

Script:

#!/bin/bash
# Description: Locate the current Python wrapper scripts and check for DIA-NN mentions

# Find Python scripts in the recipe directory
echo "Searching for Python wrapper scripts in recipes/fragpipe:"
fd -e py . recipes/fragpipe --exec echo {}

# Check for DIA-NN mentions within each found Python script
# Replace '{}' with the actual file paths found
fd -e py . recipes/fragpipe --exec rg -i "dia-nn" {}

Length of output: 226

---

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[reid-wagner]

@BiocondaBot please add label

[reid-wagner]

@bgruening Thanks!

[ypriverol]

@reid-wagner @bgruening I talked about the HUPO meeting in Dresden with Vadim from DIANN and nobody is allowed to produce and distribute a valid container singularity or docker with the current license of DIANN 1.9.2. I think is better to double-check with the DIANN developer because this is probably violating the current LICENSE.

[reid-wagner]

@ypriverol - The version that's bundled with FragPipe is 1.8.1, which doesn't have this restriction. We've talked with Vadim as well about this specific package. Thanks for bringing this up, though.