Please install the following software on your laptop:
TASSEL (https://www.maizegenetics.net/tassel)
FileZilla client (https://filezilla-project.org/download.php)
Text editor You can install any text editor for coding. For example, Windows users can install Notepad++ (https://notepad-plus-plus.org/) . Mac users can install BBEdit (Free Mode, https://www.barebones.com/products/bbedit/download.html)
BioHPC requires two-factor authentication (2FA) for logins outside the Cornell network; both to login machines and the BioHPC webpage (as well as some enhanced security compute machines). The 2FA protocol is different from what is used by other Cornell services. Rather than a push notification, you will need to supply a time-based one-time password (TOTP) as well as your BioHPC username/password. The TOTP is provided by an app installed on your smartphone and linked to your BioHPC account (the app can also be installed on laptops/desktops/browsers if you prefer). To enroll in two-factor authentication, and for more details, visit http://biohpc.cornell.edu/lab/2fa_setup.aspx. This only needs to be done once, though you can re-visit this site to link additional devices to your BioHPC account. When connecting to BioHPC login machines or the BioHPC webpage, you will be prompted for a TOTP after providing your BioHPC password, but this is only required once per week per IP address. There are a few applications that do not support 2FA – such as when using ‘QuickConnect’ in FileZilla. In this case, we recommend first logging into the BioHPC website (https://biohpc.cornell.edu/login_bio.aspx). You will supply your 2-factor code there, and then will be able to use other apps without needing a TOTP from that IP address for the next week.
If you do not already have an account with the Cornell BioHPC, you can request an account through this web site: Request New BioHPC Account (cornell.edu), put "Vitisgen3 workshop" in the Comment field when submitting the request.
If you are not familiar with Linux command line, you can take a virtual workshop at https://biohpc.cornell.edu/workshops.aspx. There are two versions of Linux workshops, a one-hour short version (BioHPC for Beginners) and a three-hour comprehensive version (Linux for Biologists). You can take either one of them.
If you are on Cornell campus network, you can connect directly to cbsuvitisgen2.biohpc.cornell.edu. If from outside Cornell, you need to setup a tunnel to bypass the Cornell firewall.
Open Terminal (Mac) or Command Prompt (Win).
Run this command in terminal to setup a tunnel to cbsuvitisgen2 port 22.
ssh -N -L 8001:cbsuvitisgen2:22 xxxxx@cbsulogin.biohpc.cornell.edu
Replace "xxxxx" in the command with your user ID;
When prompted for password, enter your BioHPC password. When typing the password, you would not see anything on the screen, just finish the typing and then press "Enter". Keep this terminal window open to keep alive the tunnel to Cornell server.
Open a new Terminal (Mac) or Command Prompt (Win) window, and run following command to connect to localhost (port 8001 of localhost is now tunneled into the Cornell Linux server cbsuvitisgen2.biohpc.cornell.edu port 22).
xxxxxxxxxxssh -p8001 xxxxx@localhost
Open Filezilla, enter following information and press "Quickconnect":
xHost: sftp://localhostUsername and password: Your BioHPC user name and passwordPort: 8001
Once connected, the left panel is your laptop, the right panel is the remote server. To upload/download files or directories, just drag the files/directories between the two panels.
3.4.1 Set up another tunnel for Rstudio server, which runs on port 8016 of cbsuvitisgen2
xxxxxxxxxxssh -N -L 8016:cbsuvitisgen2:8016 xxxxx@cbsulogin.biohpc.cornell.edu
3.4.2 Set up Rstudio cache page
xxxxxxxxxxssh -p8001 xxxxx@localhost#after you login, run this command to set up cache directory/programs/rstudio_server/mv_dir
3.4.3 Open a web browser, connect to http://localhost:8016