lynnlangit/teamteri

Bioinformatics on GCP, AWS or Azure

Team Teri

How this Repo is Organized

This Repo contains my own 'study notes' as I learn genomic-scale cloud bioinformatics. It includes descriptions of common tools, platforms and summaries of my work with clients. I update this Repo frequently. It is organized via the folder structure shown below.

• 🗒️ Concepts and Terms (genomics files types, use cases, terminology and also whitepapers)
• 🔬 Lab Testing (Illumina and more)
• ⚒️ Genomic Tools (GATK, VariantSpark, HAIL and many more - this section updates OFTEN)
• 📦 Genomics Platforms (Terra.bio, Galaxy Project, IDSeq and others)
• ☁️ Public Cloud Genomics (Alibaba Cloud, AWS, Azure or GCP). The general approach is to implement a cloud-native Data Lake pattern for scalable genomic analysis. A conceptual rendering of this pattern is shown below.
• 📚 LLMs for Bioinformatics (Reading List). So many papers and tools are being published in this area. Here's what I am reading now.

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More Cloud/Genomics Reources

In addition to this Repo, I have a number of other Repos with cloud bioinformatics information. Also, I've included two of my favorite link aggregator resources here for additional learning.

My GitHub Open Source Courses

• GENERAL CLOUD - my learn-cloud Repo - https://github.com/lynnlangit/learning-cloud
• GCP - my gcp-for-bioinformatics open source course - https://github.com/lynnlangit/gcp-for-bioinformatics
• AWS - my aws-for-bioinformatics open source course - https://github.com/lynnlangit/aws-for-bioinformatics
• WDL language - my learn-wdl open source course - https://github.com/openwdl/learn-wdl

Repos with Links

• a link Collection : link to Repo (awesome bioinformatics) with large number of curated links for learning about bioinformatics tools and topics
• bioinformatics benchmark papers - link links to published benchmark papers for bioinformatics

Data Lake Pattern

The Data Lake (or Data Mesh [Lake of Lakes]) pattern is key for implementing bioinformatics workloads effectively on any public cloud. Shown below is a simple conceptual explanation of this key concept.

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Who is Teri?

Teri is the impetus for my movement into the world of genomic research. She was diagnosed with breast cancer in 2016. She survived, but suffered a long course of intense and painful treatment due in part to the lack of availability of personalized treatment options at the time of her diagnosis.

teamteri's Issues

Error when bash 1_gce-standup.sh

When setup Galaxy VMs
I use $bash 1_gce-standup.sh command
something wrong!

deb0612@cloudshell:~/TeamTeri/Galaxy/Setup_VMs (galaxy-test-project-250916)$ bash 1_gce-standup.sh
Importing configuration from cli.rc...
./0_cli.rc: line 1: syntax error near unexpected token newline' ./0_cli.rc: line 1: ACCOUNT=<account_email>'
authenticate to GCP from your working directory via Terminal
will not launch if already has credentials

You are already authenticated with gcloud when running
inside the Cloud Shell and so do not need to run this
command. Do you wish to proceed anyway?

Do you want to continue (Y/n)? Y

Go to the following link in your browser:

https://accounts.google.com/o/oauth2/auth?code_challenge=fShCtOGMhFd92W9mwBqpRdLVO9d_a5LgKqf245aLEr8&prompt=select_account&code_challenge_method=S256&access_type=offline&redirect_uri=urn%3Aietf%3Awg%3Aoauth%3A2.0%3Aoob&response_type=code&client_id=32555940559.apps.googleusercontent.com&scope=https%3A%2F%2Fwww.googleapis.com%2Fauth%2Fuserinfo.email+https%3A%2F%2Fwww.googleapis.com%2Fauth%2Fcloud-platform+https%3A%2F%2Fwww.googleapis.com%2Fauth%2Fappengine.admin+https%3A%2F%2Fwww.googleapis.com%2Fauth%2Fcompute+https%3A%2F%2Fwww.googleapis.com%2Fauth%2Faccounts.reauth

Enter verification code: 4/qQEEP8bQWudtvgKyY-yMfI4HUeph9tLdQvkQOkk8oo2WigUiMQjQDSc
Creating firewall rule...
Creating client image, please wait...
Waiting for image to become available...
ERROR: (gcloud.compute.firewall-rules.create) argument --target-tags: expected one argument
Usage: gcloud compute firewall-rules create NAME (--action=ACTION | --allow=PROTOCOL[:PORT[-PORT]],[...]) [optional flags]
optional flags may be --action | --allow | --description |
--destination-ranges | --direction | --disabled |
--enable-logging | --help | --network | --priority |
--rules | --source-ranges | --source-service-accounts |
--source-tags | --target-service-accounts |
--target-tags
For detailed information on this command and its flags, run:
gcloud compute firewall-rules create --help
ERROR: (gcloud.compute.images.create) argument --project: expected one argument
Usage: gcloud compute images create IMAGE_NAME (--source-disk=SOURCE_DISK | --source-image=SOURCE_IMAGE | --source-image-family=SOURCE_IMAGE_FAMILY | --source-snapshot=SOURCE_SNAPSHOT | --source-uri=SOURCE_URI) [optional flags]
optional flags may be --csek-key-file | --description | --family | --force |
--guest-os-features | --help | --kms-key |
--kms-keyring | --kms-location | --kms-project |
--labels | --licenses | --require-csek-key-create |
--source-disk | --source-disk-zone | --source-image |
--source-image-family | --source-image-project |
--source-snapshot | --source-uri

For detailed information on this command and its flags, run:
gcloud compute images create --help
Creating client instances, please wait...
Waiting for instances to become available...
ERROR: (gcloud.compute.instances.create) argument --machine-type: expected one argument
ERROR: (gcloud.compute.instances.create) argument --machine-type: expected one argument
Usage: gcloud compute instances create INSTANCE_NAMES [INSTANCE_NAMES ...] [optional flags]
optional flags may be --accelerator | --address | --no-address | --async |
--boot-disk-auto-delete | --boot-disk-device-name |
--boot-disk-kms-key | --boot-disk-kms-keyring |
--boot-disk-kms-location | --boot-disk-kms-project |
--boot-disk-size | --boot-disk-type |
--can-ip-forward | --create-disk | --csek-key-file |
--custom-cpu | --custom-extensions | --custom-memory |
--custom-vm-type | --deletion-protection |
--description | --disk | --help | --hostname |
--image | --image-family | --image-project | --labels |
--local-ssd | --machine-type | --maintenance-policy |
--metadata | --metadata-from-file |
--min-cpu-platform | --network | --network-interface |
--network-tier | --node | --node-affinity-file |
--node-group | --preemptible | --private-network-ip |
--node-group | --preemptible | --private-network-ip |
--public-ptr | --no-public-ptr | --public-ptr-domain |
--no-public-ptr-domain | --require-csek-key-create |
--restart-on-failure | --scopes | --no-scopes |
--service-account | --no-service-account |
--shielded-integrity-monitoring |
For detailed information on this command and its flags, run:
gcloud compute instances create --help

Update Galaxy section for Docker containers