Comments (1)
Multiple --path
seems to make the usage menu pop up
(etoki) [gzu2@monolith3 EToKi]$ python EToKi.py configure --install --path kraken2=$(which kraken2) --path samtools=$(which samtools) --usearch `which usearch`
usage: EToKi [-h] {configure,prepare,assemble,MLSTdb,MLSType,MLSTsum,cgMLST,align,phylo,EBEis,uberBlast,clust,isCRISPOL} ...
options:
-h, --help show this help message and exit
sub-commands:
{configure,prepare,assemble,MLSTdb,MLSType,MLSTsum,cgMLST,align,phylo,EBEis,uberBlast,clust,isCRISPOL}
configure install and/or configure 3rd party programs
prepare trim, collapse, downsize and rename the short reads.
assemble de novo or reference-guided assembly for genomic or metagenomic reads
MLSTdb Set up exemplar alleles and database for MLST schemes
MLSType MLST nomenclature using a local set of references
MLSTsum Summarise MLSType results and assign new allele designations
cgMLST Select a list of genes for the cgMLST scheme
align align multiple queried genomes to a single reference
phylo infer phylogeny and ancestral states from genomic alignments
EBEis in silico serotype prediction for Escherichia coli and Shigella spp.
uberBlast Use Blastn, uBlastp, minimap2 and/or mmseqs to identify similar sequences
clust linear-time clustering of short sequences using mmseqs linclust
isCRISPOL in silico prediction of CRISPOL array for Salmonella enterica serovar Typhimurium
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Related Issues (10)
- Make pip installable HOT 1
- Usearch is proprietary HOT 2
- Need documentation on cgMLST HOT 1
- Use a single tool with subcommands
- requests HOT 1
- Doesn't handle Help when no module is given HOT 1
- Comparing the names of programs to those described in Enterobase docs HOT 2
- Error when running example script EToKi.py MLSTdb
- Error when downloading spades dependency
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