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LEARNING MATERIALS
Maintenance Notification

CyVerse systems will be unavailable on Tuesday, September 18th, from 7:00am to 5:00pm MST.
Check your local timezone here https://goo.gl/CHqLph

Keep up to date with our maintenance schedules on the CyVerse public calendar
http://www.cyverse.org/maintenance-calendar

ACCESS TO OR USAGE OF THE FOLLOWING SERVICES WILL BE UNAVAILABLE OR DISRUPTED:

Discovery Environment:        7:00am to 5:00pm MST

The Discovery Environment will be unavailable while patches and updates are applied.
        ** Currently running analyses will be terminated. Please plan accordingly.

DataStore                    
7:00am to 5:00pm MST
The DataStore will be unavailable during the maintenance period.

Atmosphere                    7:00am to 5:00pm MST
Atmosphere instances will continue to run.
Commonly-used images will be available for launching instances, but users will be unable to create new images, or launch instances from rarely-used images, while we perform Atmosphere and DataStore maintenance.

User Portal                   7:00am to 5:00pm MST
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Agave/Science API             7:00am to 5:00pm MST
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Please contact suppport@cyverse.org for any questions, or concerns.

 

 

 

 

 

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Code Block
upendra_35@vm142-34:~$ sudo usermod -aG docker $USER
upendra_35@vm142-34:~$ exit

Close the terminal and log-in again.

 

Part 2: Running QIIME-2 2018.4 on the command line

Code Block
$ alias qiime='docker run -t -i -v $(pwd):/data qiime2/core:2018.4 qiime’
$ qiime --version
q2cli version 2018.4.0
Run `qiime info` for more version details.

Part 3: Running QIIME-2 2018.4 Jupyter notebook

Code Block
upendra_35@vm142-34:~$ ezj
/usr/bin/python3
DEBUG: using python version 3
DEBUG: downloading anaconda binary, may take a few minutes
DEBUG: Anaconda already installed to /opt/anaconda3
/opt/anaconda3/bin/python3
DEBUG: using python version 3
[I 08:20:25.161 NotebookApp] JupyterLab beta preview extension loaded from /opt/anaconda3/lib/python3.6/site-packages/jupyterlab
[I 08:20:25.161 NotebookApp] JupyterLab application directory is /opt/anaconda3/share/jupyter/lab
[I 08:20:25.167 NotebookApp] Serving notebooks from local directory: /home/upendra_35
[I 08:20:25.167 NotebookApp] 0 active kernels
[I 08:20:25.167 NotebookApp] The Jupyter Notebook is running at:
[I 08:20:25.167 NotebookApp] http://128.196.142.34:8888/?token=3e13e7c44c7ea797fd064ee3e4cc1fc88d8929f0ca48c541
[I 08:20:25.167 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 08:20:25.168 NotebookApp] 
    
    Copy/paste this URL into your browser when you connect for the first time,
    to login with a token:
        http://128.196.142.34:8888/?token=3e13e7c44c7ea797fd064ee3e4cc1fc88d8929f0ca48c541

Step 1. Copy/paste the above URL into your browser when you connect for the first time. Click the New tab and then bash kernel to launch new Jupyter notebook page

Step 2. Now you can copy and paste the commands from the below notebook to run Qiime2 moving sample tutorial. Here is an example..