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License: GNU General Public License v3.0
Arundinaria SNP calling for phylogenies
License: GNU General Public License v3.0
Paths in scripts are relative to the UC Riverside HPC directories. This will break anywhere else
re-write to be relative to the repo
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
./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 figuresThe FASTQ files in this repo simply take up space since they are backed uploaded to SRA.
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
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.
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.
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)
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