Comments (4)
SionBayliss
commented on August 12, 2024
Great! Shall I wait for your PR before dealing with the most recent issues that you have raised? Or should I address the xargs and exit 0 --checks fixes?
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tseemann
commented on August 12, 2024
Someone accepted the PR despite the bug... maybe you can try it and see if it works?
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SionBayliss
commented on August 12, 2024
The main functionality works but the plotting script has some issues. The later versions of the r-packages do not install their own dependencies. I checked the versions I tested previously and they work fine. I will make a pull request for the fixed package versions and submit it (pending Natasha's input). Thanks again for you help with this!
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tseemann
commented on August 12, 2024
That is frustrating re: badly written R conda pkgs....
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Related Issues (20)
- 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
- understanding pirate results
- question on presente/absence gene table data
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