Biopython is required in the start of the Snakefile and should be available before you run snakemake.

In the standard Snakefile rules modules are loaded for each rule separately. If these modules are installed on the cluster that you are working on then this should be fine, if some of the modules are not installed or you run into trouble later, you can to see if there are other versions available (e.g. module spider minimap2). (If different rules require different environments (e.g. conda) or modules it can also be solved like this: https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#using-environment-modules )

I have used conda to install Bioperl. It would be helpful also with input on how to quickly check for the availability of SeqIO > and Bio without running the entire script, and what path it should be associated with.

you can quickly check if the bioperl installation works like this: https://stackoverflow.com/questions/1039107/how-can-i-check-if-a-perl-module-is-installed-on-my-system-from-the-command-line

if you create your own conda environment (or multiple depending on snippy) you maybe should use this Snakefile: https://github.com/MigleSur/BacDist/blob/master/Snakefile_non_computerome and maybe modify it accordingly

A small tip with debugging snakemake workflows is to use the -p option to see the commands so you can test them individually.

from my testing the tool:

conda create -n bacdist

conda activate bacdist

conda install -c bioconda -c conda-forge biopython perl-bioperl bwa readseq samclip bedtools freebayes vcflib perl-vcftools-vcf minimap2 seqtk snp-sites snippy vt bcftools samtools raxml snpsift snp-dists conalframeml

# add config.yaml

mv Snakefile Snakefile_tt
mv Snakefile_non_computerome Snakefile

#add 2 samples to fastq/ (I later ran into problems with raxml saying "too few species so I added a few"
#named sample1_R1.fastq.gz ..

snakemake -j4 -p

ran into a problem with snpsift:

snpsift=/services/tools/snpeff/4.3r/snpEff/SnpSift.jar
java -jar $snpsift filter "( GEN[*].GT='0/0' )" BacDist/test/vcf_calls/merged_E110047_raw.vcf > /BacDist/test/vcf_calls/E110047_diff.vcf

Error: Unable to access jarfile /services/tools/snpeff/4.3r/snpEff/SnpSift.jar

snpsift was missing from dependencies and the path to the .jar file was hardcoded in the Snakefile, you have to change this accordingly in the Snakefile (L139 L193 L252). If you installed snpsift with conda:

add snpsift=$WHEREYOUINSTALLEDCONDA/anaconda2/envs/bacdist/share/snpsift-4.3.1t-1/SnpSift.jar

a similar problem with snp-dists that was missing initially from the dependencies. change param in L329 L524 or in the shell part,

also clonalframeml can be installed with conda.

some other issues came with installations, e.g. you cant use conda install vcftools but you need perl-vcftools-vcf

for summary statistics I ran into a problem with awk:

awk: program limit exceeded: maximum number of fields size=32767
    FILENAME="-" FNR=1 NR=1

This might be something ubuntu specific (https://stackoverflow.com/questions/24292787/awk-program-limit-exceeded-maximum-number-of-fields-size-32767) and can be fixed by installing gawk.

All in all it runs through. Hope this helps, let me know if you have questions.