--install --path

[lskatz]

Hi, could you clarify in the documentation which things I can put into --path? Like if I have the entire spades package downloaded, do I just run it with --path spades.py=$(which spades.py)? For blast, do I need to consider multiple executables like makeblastdb and blastn?

Thank you!

[lskatz]

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