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Update Spacepharer to point at the latest version and make sure each YAML file neatly ends with a newline character.
- Update the index, removing old entries and adding new ones. - Fill in links to output file documentation. - Move link to the user manual to the top.
- Include MLST in documentation - Tick box in to do
- Add output to 'rule all' - Include rules to concatenate output in one file - Include PADLOC documentation - Reference additional functions in index
- Add 'extra functions' and 'output files' entries
Necopy-byte
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Aug 29, 2025
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Looks good, there are some minor spelling errors and I remembered that phagescope does not need to take up 320GB as spacepharer should be able to accept it Gzipped
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| The Phagescope database says that it can filter genomes based on criteria, | ||
| but actually downloading these fastas is impossible due to an error. | ||
| Additionally, `wget` and `curl` do not properly download the databases in a way that |
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This has been solved with the script i wrote, apparently the server was just down when i tried to download it originally via wget.
| page cannot be solved using the recommended 'strict channel priority' setting. | ||
| We could only get it to work with the flexible or disabled channel priority. | ||
| We have adapted to YAML so that it can be solved using strict priority mode, | ||
| but this does make strand prediction in CRISPRidentify non-functional. |
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Strand prediction and also apparently the optional cas prediction module CRISPRcasidentifier
| - [PLSDB](spacepharer.md#plsdb-2024_05_31_v2): ~80GB | ||
| - [PLSDB](spacepharer.md#plsdb-2024_05_31_v2): ~80GB | ||
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| - [Phagescope](spacepharer.md#phagescope): ~320GB |
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The file size does remind me that spacepharer should be able to accept gzipped files for its database creation, i will make an issue for this.
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Thanks for checking and suggesting fixes @Necopy-byte ! |
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General workflow refinement, including code updates and expansion of the documentation.