Instructions

learn to use three tools: Rstudio server, mobaxterm, filezilla

Install Docker

https://docs.docker.com/engine/install/ubuntu/#install-using-the-repository

Find the Docker image

https://hub.docker.com/r/wallen/arcashla/tags?page=1&ordering=last_updated

Explore image

https://docs.docker.com/engine/reference/run/

Install and configure cromwell and womtool

https://github.com/broadinstitute/cromwell/releases

set environmental variable to .bashrc

Install java jre, if not installed previously

https://ubuntu.com/tutorials/install-jre#1-overview

Test command

https://github.com/RabadanLab/arcasHLA

Install atom editor and wdl language plugin

https://github.com/atom/atom/releases/tag/v1.57.0

D:\Program Files\Atom x64\resources\app\apm\bin> .\apm install language-wdl

Configure the pipeline on the server

Make sure the raw_data_files directory contains the file name in the format of sample_name.xxx.xx.xx.bam

Run scripts one by one

Clean up