3 Exercises

3.1 Launch Terra

Open anvilproject.org and click on “Launch” Terra

3.2 Clone HPRC Workspace

At anvil.terra.bio/#workspaces

Enter hprc in the search box
Click on the “Public” tab
Click on AnVIL_HPRC
Click on the circle with three vertical dots in the upper right corner and select “Clone”

3.3 Start a Cloud Environment

Click on the Environment Configuration (cloud icon)
Select Jupyter Settings
Scroll down and click “Create”

3.4 Find Tidbits

In the Dashboard tab, what are three types of sequencing data that are available?
In the Data tab participant table, what two superpopulations have the most participants?
In the Data tab sample table, how many samples lack any ilmn data?
In the Data tab assembly_sample table, what is the command to download the HG002 mat_fasta file?

3.5 Enter Terminal

In the Analysis tab, click on Terminal
Make a working copy of the HG002 mat_fasta
- NOTE: Requester pays buckets require -u <google-project-id> [ref]
Examine file with ls -l and zcat *.fa.gz | head

gsutil cp 'gs://fc-4310e737-a388-4a10-8c9e-babe06aaf0cf/working/HPRC_PLUS/HG002/assemblies/year1_f1_assembly_v2_genbank/HG002.maternal.f1_assembly_v2_genbank.fa.gz' .

3.6 Shut Down

Click on the Environment Configuration (cloud icon)
Select Jupyter Settings
Scroll down and click “Delete Environment”
Select “Delete” after deciding to keep or delete your persistent disk
Click “hamburger” icon in the upper left, expand your name, select Cloud Environments and confirm no unnecessary resources are running