MiCE 5992 Getting Started Guide
To set up your MSI account for using QIIME, please follow these steps:
Get your login info for MSI
- Click on this link: https://www.msi.umn.edu/user-agreement. After you agree to the user agreement you will get your login information.
Connect to MSI with SSH
Windows users
- Install "Putty" by downloading this file and running the installer: https://the.earth.li/~sgtatham/putty/latest/x86/putty-0.67-installer.msi
- Open the Putty application
- Under the "Hostname" field, enter
login.msi.umn.edu - Under "Port", enter
22 - For "Connection type" click "SSH"
- Click "Open"
- Enter your MSI username and password
- You should now be connected.
- Visual instructions can be found here: http://www.fastcomet.com/tutorials/getting-started/putty#connect and here: http://gabedev.com/3004/software_guide/ (Step 3)
Mac/Linux users
- Open the "Terminal" application. On a Mac you can click the search button (magnifying glass) and type "Terminal" to find the application.
- Enter this command into the terminal, using your username in place of
yourusername:
ssh yourusername@login.msi.umn.edu
- Enter your password
- You should now be connected.
Run the setup command
Copy this command, paste it into your terminal, and press "return"
wget -O setup.sh z.umn.edu/5992setup && chmod +x setup.sh && ./setup.sh
Run this additional command. It's OK to get two "File exists" errors:
mkdir ~/.config; mkdir ~/.config/matplotlib; echo "backend: agg" >> ~/.config/matplotlib/matplotlibrcRun a test script
Run the following commands on the MSI terminal:
isub
module load qiime/1.8.0
print_qiime_config.py
This should print out some details about your QIIME configuration and should not return any errors. If so, you are now ready to use MSI and QIIME.
Install Filezilla to transfer files to/from MSI
Download and install Filezilla from here: https://filezilla-project.org/download.php?type=client
Instructions for connecting to MSI can be found here (Step 4): http://gabedev.com/3004/software_guide/
Thanks to Gabe Al-Ghalith for these instructions!
Get a VPN working
MSI won't let you connect directly unless you are on campus. To access your files from home, you will need to set up a VPN (Virtual Private Network).
Windows users see step 7 in Gabe's instructions here: http://gabedev.com/3004/software_guide/
Mac users try the "Native Client for MAC using IPSec" instructions here: https://it.umn.edu/downloads-guides-install-ipsec-native
If those don't work, see more options here: https://it.umn.edu/downloads-guides