Problem

Paths in scripts are relative to the UC Riverside HPC directories. This will break anywhere else

Solution

re-write to be relative to the repo

Problem

The current directory structure is mostly a historical hodge-lodge for when I was writing this up during my PhD. The locations of inputs, outputs, scripts, references, etc is just whatever was convenient at the time, but it has no objective structure to an outside

Solution

• Create an organized set of directories including:
  • ./References to capture Picard and boa refs along with tables of samples names, etc
  • ./FASTQ, but we should pull directly from NCBI instead
  • ./Logs to replace ./history, and also not include these in git
  • ./Results
  • ./Results/Phylo to capture phylogenetic results (.nex, .phy.) from MrBayes, RAxML, jModelTest, SplitsTree, etc
  • ./Results/SNP to capture results from GATK, WhatsHap, SpeedSeq, bcftools, etc
  • ./Figures to contain both intermediate plots and manuscript figures
  • others?
• Change paths, see #2

Problem

The FASTQ files in this repo simply take up space since they are backed uploaded to SRA.

Solution

Add a script to pull these files to a local directory. The files will need to either be renamed to match the old names from Purdue, or (better) the scripts changed so that they reference standard file names

Follow the #5 PR a lot of the points in the README have changed. I had added some small news updates to the top, but it needs a re-write

Problem

All of the scripts here depend on the UC Riverside HPCC infrastructure in terms of install software like MrBayes, GATK, etc. In addition there are a number of rather off-the-map R packages.

From a reproducibility standpoint, it would be nice to wrap all of this into a single docker container with all dependencies pre-installed.

Solution

Create a Dockerfile to include in the repo that specifies how to build a container to house the analysis. Subsequently, this container should be built and made publicly available in Dockerhub.

Additional considerations

Inside the scripts, file paths will need to be changed. Submission scripts will need to either be removed or reworked to call Docker instead. Removal is probably better since most HPC environments would require Singularity over docker and the submission itself is likely to be very environment-specific (Slurm vs PBS, etc)