Comments (2)
SionBayliss
commented on August 12, 2024
In a future version of PIRATE I will remove the dependency on bioperl. It think it is only used for parsing fasta files and translation. The dependency on bioperl is included in the README. Would you recommend mentioning the core dependencies anywhere?
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tseemann
commented on August 12, 2024
To clarify, you have done everything right. No need to list core modules.
Avoiding Bioperl would make it easier to install in some cases, but ultimately brew and conda take care og it all.
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Related Issues (20)
- Confused with terminology/output HOT 1
- extract_feature_sequences.pl failed HOT 2
- error observed during "aligning all feature sequences" HOT 2
- Missing genome in output HOT 12
- Output gene sequences to run gene alignment separately HOT 4
- PIRATE_plots.pdf created by plot_summary.R HOT 1
- Error after MCL clustering step HOT 5
- How do you tell which gene families are single-copy or multi-copy? HOT 2
- Feature request: Option to include original IDs and annotations in fasta headers for align_features_sequences script HOT 2
- Average_dose =1 is appropriate to determine whether a gene family is a single copy？ HOT 1
- - ERROR: link_clusters.pl failed. HOT 1
- Undefined subroutine &main::translate called HOT 2
- Error when running PIRATE MCL process
- For some single loci, a gene family but for others not. HOT 1
- problem in installation HOT 9
- Bump version in new release HOT 4
- Missing output files and coregenom files HOT 3
- Running on large dataset HOT 2
- stuck at threshold 60 during MCL clustering HOT 3
- PIRATE.pangenome_summary.txt HOT 6
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