MVesuviusC / primerEvalDocker

files to create a docker image for the primer evaluation pipeline

Docker image to run primer evaluation pipeline

Files to create a docker image to run https://github.com/MVesuviusC/primerEvaluation

Documentation is incoming

Kept here: https://hub.docker.com/repository/docker/matthewvc1/primer_eval

Usage:

mkdir evalOut

docker run
-it
-v databases:/usr/local/databases
--mount type=bind,source="$(pwd)"/evalOut,target=/home/runDir/output
--name primerEval
matthewvc1/primer_eval:6_11_2020
bash

###once inside, run setupDatabases.sh which should take a few hours to run

Then start R and run:

rmarkdown::render("primerEvalPipeline.Rmd", output_dir = "output/mam16SOut/", params = list( outDir = "output/mam16SOut", primerFile = "mam16SPrimerInput.txt", taxonomyDb = "/usr/local/databases/tax/taxonomy.db", threads = 8 ) )