2017-cicese-metagenomics
1.0
Site
Environmental Metagenomics Workshop
Welcome!
Start an Amazon Web Services computer:
Intro to Shell Lesson
The Shell
For Future Reference
Finding files
Running command-line BLAST
Short read quality and trimming
Run the MEGAHIT assembler
Evaluating Metagenomic Assemblies
Annotation with Prokka
Comparing datasets using sourmash
A sourmash tutorial
K-mers, k-mer specificity, and comparing samples with k-mer Jaccard distance.
Binning a Metagenomic Assembly
Gene Abundance Estimation with Salmon
Mapping
Slicing and dicing with k-mers
Using Anvi’o to Knit Everything Together
Using and Installing Circos
Workflow and repeatability discussion
Data
Building this site on your own
2017 / September / Environmental Metagenomics
Day 2 - installation instructions
K-mer Spectral Error Trimming
Page
Starting up an Amazon Web Services machine
Start here:
boot
Full table of contents:
Indices and tables
Source
Starting up an Amazon Web Services machine
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Start here:
Start an Amazon Web Services computer:
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Full table of contents:
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Start an Amazon Web Services computer:
0. Select “EC2 - virtual servers in the cloud”
1. Switch to zone US West (N California)
2. Click on “Launch instance.”
3. Select “Community AMIs.”
4. Search for ami-05384865 (ubuntu-wily-15.10-amd64-server)
5. Click on “Select.”
6. Choose m4.xlarge.
7. Click “Review and Launch.”
8. Click “Launch.”
9. Select “Create a new key pair.”
10. Enter name ‘amazon-key’.
11. Click “Download key pair.”
12. Click “Launch instance.”
13. Select View instances (lower right)
14. Bask in the glory of your running instance
Log into your instance with the UNIX shell
Log into your instance via the UNIX shell (Mac/Linux)
Log into your instance via MobaXTerm (Windows)
Log into your instance from a Mac or Linux machine
Change permissions and execute ssh
Successful login
Log into your instance from a Windows machine
Configure your instance firewall
1. Select ‘Security Groups’
2. Select ‘Inbound’
3. Select ‘Edit’
4. Select ‘Add Rule’
5. Enter rule information
6. Select ‘Save’.
7. Return to the Instances page.
Creating your own Amazon Machine Image
1. Actions, Create image
2. Fill out name and description
3. Wait for it to become available
Working with persistent storage: volumes and snapshots
Creating persistent volumes to store data
Creating snapshots of volumes
Terminating your instance
1. Select Actions, Instance State, Terminate
2. Agree to terminate.
3. Verify status on your instance page.
Things to mention and discuss
When do disks go away?
What are you charged for?
Regions vs zones:
Running RStudio Server in the cloud
1. Start up an Amazon instance
2. Configure your network firewall
3. Log in via the shell
4. Set a password for the ‘ubuntu’ account
5. Install R and the gdebi tool
6. Download & install RStudio Server
7. Open your RStudio Server instance
Indices and tables
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Index
Module Index
Search Page
LICENSE:
This documentation and all textual/graphic site content is released under
Creative Commons - 0 (CC0)
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fork @ github
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