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marcelauliano / MitoHiFi

Find, circularise and annotate mitogenome from PacBio assemblies
MIT License
169 stars 29 forks source link

Update CI to build image automatically #109

Open gq1 opened 1 day ago

gq1 commented 1 day ago
  1. Update Github workflow to build base image, either manually on any branch or tag, or tag it with tag name starting with b.
  2. Update Github workflow to build the main image, either manually on any branch or tag, or publish a release, or any push on the master branch.
  3. Make the integration test as the downstream of main docker image building. Run the tests when a new docker image being built.

For all the CI pipeline running examples, see here: https://github.com/gq1/MitoHiFi/actions

gq1 commented 1 day ago

The base container bing re-built, some packages may be a little different, one script failed when running test:

See all contigs and clusters in cdhit.out.clstr
2024-11-22 14:19:51 [INFO] 7. Calculating final stats for final mitogenome and other potential contigs.
    Stats will be saved on contigs_stats.tsv file.
tig00007550_1 list of genes: ['tRNA-Phe', 'tRNA-Glu', 'tRNA-Ser2', 'tRNA-Asn', 'tRNA-Arg', 'tRNA-Ala', 'ND3', 'tRNA-Gly', 'COX3', 'ATP6', 'ATP8', 'tRNA-Asp', 'tRNA-Lys', 'COX2', 'tRNA-Leu2', 'COX1', 'tRNA-Tyr', 'tRNA-Cys', 'tRNA-Trp', 'ND2', 'tRNA-Gln', 'tRNA-Ile', 'tRNA-Met', 'rrnS', 'tRNA-Val', 'rrnL', 'tRNA-Leu', 'ND1', 'tRNA-Ser', 'CYTB', 'ND6', 'tRNA-Pro', 'tRNA-Thr', 'ND4L', 'ND4', 'tRNA-His', 'ND5']
2024-11-22 14:19:51 [INFO] 8. Building annotation plots for all contigs
Traceback (most recent call last):
  File "/opt/MitoHiFi/src/mitohifi.py", line 566, in <module>
    main()
  File "/opt/MitoHiFi/src/mitohifi.py", line 491, in main
    plot_annotation.plot_annotation("final_mitogenome.gb", "final_mitogenome.annotation.png")
  File "/opt/MitoHiFi/src/plot_annotation.py", line 38, in plot_annotation
    graphic_record = MyCustomTranslator().translate_record(in_gb)
  File "/usr/local/lib/python3.6/dist-packages/dna_features_viewer/BiopythonTranslator/BiopythonTranslatorBase.py", line 89, in translate_record
    sequence=str(record.seq) if record.seq.defined else None,
AttributeError: 'Seq' object has no attribute 'defined'

https://github.com/gq1/MitoHiFi/actions/runs/11974247861/job/33385025333