Blosum matrix files

[mzueva]

Include blosum matrix files to the software package

[gemini-code-assist]

Summary of Changes

Hello @mzueva, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request integrates essential BLOSUM matrix files into the software package, ensuring they are properly distributed, included in Docker builds, and managed within the project's build process. This enhancement provides necessary data for sequence alignment functionalities, making the software more robust for bioinformatics tasks.

Highlights

• BLOSUM Matrix Files Added: Five new BLOSUM matrix files (blosum40.out, blosum50.out, blosum62.out, blosum80.out, blosum90.out) were added to the data/ directory, providing essential scoring matrices for sequence alignment.
• Build Process Integration: A new prebuild script was added to package.json to automatically copy the data/ directory into each dld/*/data/ subdirectory, ensuring these files are available during the build process.
• Docker Image Update: The Dockerfile was updated to include the newly added data/ directory, copying its contents to /usr/bin/ within the Docker image for proper distribution.
• Git Ignore Configuration: The .gitignore file was modified to exclude dld/*/data/ directories from version control, preventing redundant tracking of copied data.
• Version Bump: A changeset entry was created, indicating a minor version update for @platforma-open/soedinglab.software-mmseqs2 to reflect the inclusion of these new matrix files.

Changelog

• .changeset/early-worlds-deny.md
  • Added a changeset entry for a minor version update, noting the inclusion of matrix files.
• .gitignore
  • Updated to ignore data directories within dld subdirectories.
• Dockerfile
  • Modified to copy the new data directory containing BLOSUM matrices into the Docker image.
• data/blosum40.out
  • Added BLOSUM40 matrix file.
• data/blosum50.out
  • Added BLOSUM50 matrix file.
• data/blosum62.out
  • Added BLOSUM62 matrix file.
• data/blosum80.out
  • Added BLOSUM80 matrix file.
• data/blosum90.out
  • Added BLOSUM90 matrix file.
• package.json
  • Added a prebuild script to copy the data directory to dld subdirectories.

Activity

• No specific activity (comments, reviews, approvals) was provided in the context for this pull request.

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[gemini-code-assist]

Code Review

This pull request adds BLOSUM matrix files to the software package. The changes include adding the data files themselves, updating the .gitignore and package.json to handle them during the build process, and modifying the Dockerfile to include them in the image. While the overall goal is clear and the approach is mostly sound, there are a couple of areas for improvement. The Dockerfile copies the data files to an incorrect location, and the data files themselves are missing a final newline character, which can cause issues with some tools. My review includes suggestions to address these points.

[gemini-code-assist]

Copying data files into /usr/bin is not standard practice, as this directory is reserved for executables. A more appropriate location according to the Filesystem Hierarchy Standard (FHS) is /usr/share. mmseqs2 is known to search for data in standard locations like /usr/share/mmseqs/data, so placing the data in a similar path like /usr/share/mmseqs2/data is recommended. The current COPY command is also likely incorrect as it copies the files directly into /usr/bin rather than into a data subdirectory, due to the trailing slash on the source path.

COPY ./data /usr/share/mmseqs2/data