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…gs-for-releases Tag docker images on github tag creation
They were causing problems for the esl-sfetch step.
Update ribovore to the latest version
Same as in the docs
Bumps [jinja2](https://github.com/pallets/jinja) from 3.1.2 to 3.1.6. - [Release notes](https://github.com/pallets/jinja/releases) - [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst) - [Commits](pallets/jinja@3.1.2...3.1.6) --- updated-dependencies: - dependency-name: jinja2 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com>
Also update pre-commit
s5cmd seems to be required when running R2DT from Nextflow on AWS Batch.
Update Dockerfile for nextflow
Disable 1blast for rnasep
Relaxed version constraints for scikit-image and numpy to allow versions >=0.24.0 and >=2.0.0, respectively. This change enables compatibility with newer releases of these libraries.
Refactored the script to process all models and RNA chains in a PDB file, with options for single or batch processing. Added functions to extract structure info, handle custom output names, clean up invalid dot-bracket pairs, and improved output organization. The script now generates separate FASTA and SVG files for each model/chain combination, and provides better error handling and reporting.
Feature - animated 2Ds showing transition between 2D structures from PDB files
Added the --builder default flag to Docker buildx build commands in the justfile to ensure the default builder is used. This improves consistency and avoids issues when multiple builders are configured.
Ensure that the Rfam seed alignment file starts with the STOCKHOLM header. If the file is invalid, remove it and re-fetch, re-indexing the archive if necessary to handle potential corruption.
Refactored RNA model processing to handle all chains per model, simplified output naming, and updated logic to process only models with RNA chains. Added cleanup_rnaview_files to remove temporary files generated by RNAview after processing. Improved compatibility with multi-model (NMR) structures and ensured colored SVG output is moved to the expected location.
Added logic to replace DNA 'T' with RNA 'U' in the original sequence when updating FASTA files. This ensures correct RNA notation in visualizations, matching template expectations and preventing misinterpretation of edited bases.
Added a new colored SVG example for PZ1_Bujnicki_1 and updated several animated and colored SVGs in test directories to reflect new dimensions, styles, and formatting.
Refactored Runner to use a 'with' statement for subprocess.Popen, ensuring proper resource management and cleanup of the process. This improves code safety and readability.
- New `r2dt.py stitch` command combines R2DT SVGs horizontally - Supports sorting by genomic coordinates, captions, join glyphs - Monochrome mode for publication-ready figures - Auto-detects font sizes from input SVGs - Add --normalize-font-size option documentation
- New `r2dt.py viral-annotate` scans genomes with Rfam cmscan - Generates 2D diagrams for each RNA family hit - Optional stitched output combining all hits - Documentation with SARS-CoV-2, HCV, Dengue examples - Tests for viral annotation pipeline
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This pull request introduces several updates across multiple files, focusing on Docker configuration, workflow triggers, and RNA data adjustments. The most significant changes include updates to
.dockerignoreandDockerfilefor improved build efficiency, enhancements to GitHub Actions workflow triggers, and modifications to RNA-related data files for accuracy and consistency.Docker and Build Configuration Updates:
.dockerignore: Updated to include additional directories (tests/results,tests/html,data/local_data/*/) while removing outdated entries (data/cms,1.4/,2.0/). This optimizes the Docker build context by excluding unnecessary files. [1] [2]Dockerfile: ChangedBASE_IMAGE_VERSIONfromv2.1tov2.2and added commands to set up Rfam and CRW data directories, improving build reproducibility. [1] [2]base_image/Dockerfile: UpdatedRibovore_COMMITto a newer version for dependency consistency.Workflow Enhancements:
.github/workflows/main.yml: Added support for triggering workflows on tag pushes matching the patternv*(e.g.,v1.0), expanding automation coverage.RNA Data Adjustments:
data/rfam/RF00016anddata/rfam/RF00023: Updated sequence and structure data in.fastaand.xmlfiles to correct inaccuracies and improve alignment with current standards. [1] [2] [3] [4] [5]