Koen-vdl

Was writing a little tutorial on effectively utilizing the computational resources using shovill as an example when I noticed this inconsistency. Goal was to make the pipeline crash to teach...

fastq-dump parallel error in tutorial

1

Thanks for this great resource. `fastqc-dump` is fairly poorly documented so this workbook was a great starting point for me. I think there is a small error on: https://bioinformaticsworkbook.org/dataAcquisition/fileTransfer/sra.html#gsc.tab=0 `parallel...

`abPOA ` conda installer broken?

7

I believe there is something wrong with the `abPOA `conda installer as the installed version breaks even with the test data (seq.fa). ``` conda create -n abpoa_env -c bioconda abpoa...

Just reporting the conda installer for berokka has a Perl issue. ``` conda create -n berokka_env berokka conda activate berokka_env berokka Can't locate Bio/SeqIO.pm in @INC (you may need to...

Buffer overflow during model fitting

6

Hi Nick, I'm using Gubbins v3.3.5 as indicated below: ``` run_gubbins.py $PREFIX-CLEAN_NoRef.aln --first-tree-builder iqtree \ --tree-builder iqtree \ --tree-args " -T AUTO" \ --first-tree-args " -T AUTO" \ --best-model \...