VM Setup - ncbi/workshop-asm-ngs-2022 GitHub Wiki

The image for the VMs used in this workshop was created by first generating a VM the same way we did in the workshop, with the difference that the base image was the Ubuntu 20.04 image and a 100-Gb drive was attached. The following command-line using google cloud CLI should generate a comparable VM:

gcloud compute instances create workshop2-ubuntu --project=ncbi-pd-amr --zone=us-central1-a --machine-type=e2-standard-16 --network-interface=network-tier=PREMIUM,subnet=default --maintenance-policy=MIGRATE --provisioning-model=STANDARD --service-account=[[email protected]](mailto:[email protected]) --scopes=[https://www.googleapis.com/auth/devstorage.read_only,https://www.googleapis.com/auth/logging.write,https://www.googleapis.com/auth/monitoring.write,https://www.googleapis.com/auth/servicecontrol,https://www.googleapis.com/auth/service.management.readonly,https://www.googleapis.com/auth/trace.append](https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.googleapis.com%2Fauth%2Fdevstorage.read_only%2Chttps%3A%2F%2Fwww.googleapis.com%2Fauth%2Flogging.write%2Chttps%3A%2F%2Fwww.googleapis.com%2Fauth%2Fmonitoring.write%2Chttps%3A%2F%2Fwww.googleapis.com%2Fauth%2Fservicecontrol%2Chttps%3A%2F%2Fwww.googleapis.com%2Fauth%2Fservice.management.readonly%2Chttps%3A%2F%2Fwww.googleapis.com%2Fauth%2Ftrace.append&data=05%7C01%7Caprasad%40mail.nih.gov%7Ce19adf9c09f249a3883308dab05fa8f2%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638016225309314236%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C&sdata=yZtlzli1JFpvSSpxnzYqX%2BskvCdZ2Pg2pfuzagxpH%2Fc%3D&reserved=0) --create-disk=auto-delete=yes,boot=yes,device-name=workshop2-ubuntu,image=projects/ubuntu-os-cloud/global/images/ubuntu-2004-focal-v20220823,mode=rw,size=100,type=projects/ncbi-pd-amr/zones/us-central1-a/diskTypes/pd-balanced --no-shielded-secure-boot --shielded-vtpm --shielded-integrity-monitoring --reservation-affinity=any

Once logged into that VM the following commands were used to install software:

Some basics

sudo apt-get update
sudo apt-get -y install git
sudo apt-get install unzip

install RAxML

mkdir -p src/raxml
cd src/raxml
wget [https://github.com/amkozlov/raxml-ng/releases/download/1.1.0/raxml-ng_v1.1.0_linux_x86_64.zip](https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Famkozlov%2Fraxml-ng%2Freleases%2Fdownload%2F1.1.0%2Fraxml-ng_v1.1.0_linux_x86_64.zip&data=05%7C01%7Caprasad%40mail.nih.gov%7Ce19adf9c09f249a3883308dab05fa8f2%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638016225309314236%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C&sdata=bcY6Ab8H6cnF%2Bc%2FKOTCgydrZz%2BIMBuYz2Aa9k4eGkR4%3D&reserved=0)
unzip raxml-ng_v1.1.0_linux_x86_64.zip
sudo cp raxml-ng /usr/local/bin

Work in progress...