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API topics are presented in the form of examples that are “recipes” for mastering each of the various topics. The examples are arranged in order, from the.
Configure Torrent Suite Software
Icon Follow these configuration steps only after updating the Torrent Suite Software version.
Torrent Suite Software works out-of-the-box.
- Configure Postfix for nightly email
Configuration tab
Some configuration tasks use the Linux command line and some use the Torrent Browser configuration tab. To access the Torrent Browser configuration tab, use the gear menu near the top right of a Torrent Browser page and select Configure :
Configure disk space notification email address
The Data Management system can automatically notify you when available disk space on a Torrent Server disk partition becomes low. However, in order to receive these notifications, you must configure an email address in the Data Management system . See Data Management Configuration for instructions (search for Email).
Configure contact information
Add the name, email address, and phone number of the person responsible for the server and of an I.T. contact person, and click the Save Contacts button:
Change the hostname
Use the following commands to change the hostname:
Icon The server must reboot after the hostname is changed. The above command automatically reboots the server.
Add an HTTP proxy
Use the following command to add an HTTP proxy:
Set the proxy address and authentication according to the following prompts:
Enter http proxy address:
Enter the proxy address. (If no address is entered, you are prompted to exit the program.)Enter http proxy port number [3128]:
Enter a port number or carriage return to accept the default, 3128, port number.Enter the username for proxy authentication:
Enter a username. If you do not enter a username, no authentication is set.Enter the password for proxy authentication:
Enter a password. If you do not enter a password, no authentication is set.
A proxy address confirmation message is displayed:
The recommended usage is to enter the command sudo TSsetproxy, as shown above, and be prompted for each value. You can however use the TSsetproxy arguments instead:
Configure HTTPS
The Torrent Server is shipped with a self-signed SSL certificate that allows you to enable HTTPS quickly but provides a limited degree of security. Torrent Suite Software administrators who are interested in securing the connection further should read the Ubuntu Server Guide on Certificates and Security, and investigate getting either an SSL certificate signed by their organization or a trusted Root Certificate Authority.
For more information on the level of security provided by Ubuntu, see the following site for 10.04: https://help.ubuntu.com/10.04/serverguide/certificates-and-security.html
or for 14.04: https://help.ubuntu.com/14.04/serverguide/certificates-and-security.html .
or for 14.04: https://help.ubuntu.com/14.04/serverguide/certificates-and-security.html .
With a self-signed SSL certificate, each user sees an error message on his or her first visit to the site and is asked whether or not to trust the certificate.
See also the following apache file for information. This file is installed on your Torrent Server as
Icon /etc/apache2/sites-available/torrent-server-ssl.example
: The Ion PGM and Ion Proton sequencing instruments do not support HTTPS. If you configure HTTPS on the Torrent Server, ensure that Apache is running both HTTPS and HTTP concurrently, so that the sequencing instruments can connect to the Torrent Server over HTTP. If you disable HTTP, the sequencing instruments are not be able to connect to the Torrent Server.
Change the timezone
Use the following commands to change the timezone:
Configure Postfix for nightly email
Preparing Site IT
Adding Email Recipients
Adding Web Root and Site Name to Admin and Global Config
Scheduling the Mail Task (cron job)
Configure Postfix
Adding Email Recipients
Adding Web Root and Site Name to Admin and Global Config
Scheduling the Mail Task (cron job)
Configure Postfix
Postfix is a Linux mail server ('post office') program. It is open-source software and was not designed by Ion Torrent. It is more similar to Exchange than Outlook software in that it is an e-mail server, not an e-mail client. Postfix is designed to work on various infrastructures, so there are many configuration options for IT administrators to adjust mail routing parameters.
You can find the official Postfix documentation here: http://www.postfix.org/documentation.html .
Prepare site IT
It is useful to confirm the following with the site IT administrator:
- Outbound email from the server is allowed Many sites block the ability for machines to send an e-mail message directly to a mail server because this is a common avenue for virus propagation. If the site has such a restriction in place, the IT administrator may need to make an exception for this server.
- Ideally, the domain is configured with a default 'MX record' The 'MX record' is the mail exchange information that automatically knows how to handle any email generated from the Torrent Server. If this is not in place, the nightly email might not work.
Add email recipients
You are cautioned to only add a couple of recipients while testing.
Follow these steps enter destinatione-mail addresses.
Add Web Root and Site Name to Admin and Global Config
Make certain these fields are configured in the database so they will show up correctly on the e-mail message:
- Click the Torrent Browser gear menu and select Configure .
- Scroll down to the Database Administration section and click Admin Interface . If prompted to log in, use your
ionadmin
account. - Click on Global configs :
- Make certain a value is entered in the Web root field and the Site name field, as shown in the example:
The value for Web root should be the main URL that people use to access this Torrent Browser from the desktop.
Schedule the Mail Task (cron job)
The
cron
program is the Linux program that automates tasks to run on a schedule. By default, a cron
job is installed in the Torrent Server to run at 6AM, daily. You can verify this by logging in as ionadmin
and typing the command: crontab -l
. Notice, all cron calls the runnightly.sh script at 6AM.
As a test, without having to wait until 6AM,you can invoke the same script manually from the command-line and see if it generates an e-mail:
If you forgot to enter the Web root setting, you will an error similar to the following:
Configure Postfix
There is no way to know it advance what Postfix configuration settings work for a particular site. The following example procedure shows basic configuration settings that have worked for the servers configured to date.There is no guarantee that these steps work for every situation. If email is still not appearing, you almost certainly require assistance from the site IT administrator, who may or may not have experience with Postfix.
This configuration can be re-executed at anytime:
- Go to the Linux command line and start the Postfix configuration utility:
- Select the type of mail configuration. Typically, Internet with smarthost .
- For System mail name , enter the site domain name. This domain needs to be configured with a default 'MX' (mail exchange) record.
- Leave mail recipient blank.
- Leave other destinations blank.
- Set Force synchronous updates on mail queue to <No> .
- For Local networks , accept the default, and select <OK> .
- For Mailbox size limit , it is recommended that you not have no limit, so enter '51200000' to not consume all disk space.
- Leave Local address extension character blank.
- For Internet protocols to use , accept the default and select <OK> .
- After the last screen, the console returns to text mode and displays the status of the Postfix configuration files update.
This completes Postfix configuration.
Deploy Your System
Prepare Your Site
Install the Server
Network Connectivity
Update Torrent Suite™ Software
Install Analysis Plugins
Configure Torrent Suite™ Software
Verify Functionality
Manage Sequencer Settings from the Torrent Browser
Prepare Your Site
Install the Server
Network Connectivity
Update Torrent Suite™ Software
Install Analysis Plugins
Configure Torrent Suite™ Software
Verify Functionality
Manage Sequencer Settings from the Torrent Browser
Maintain Your System
![Suite Suite](https://patchsearch.com/wp-content/uploads/2019/12/cr2-768x424-1.jpg)
Monitor Your Torrent Server
Monitor Free Disk Space
Back Up and Restore Data
Mount a USB Drive
Boot Into Single-User Mode
Install and Use a UPS
Axeda® Remote System Monitoring (RSM)
Back Up and Restore Data
Mount a USB Drive
Boot Into Single-User Mode
Install and Use a UPS
Axeda® Remote System Monitoring (RSM)
Configure Chips
Configure Experiments
Configure Global Configs
Configure Users
Approve User Account Requests
Configure Basecaller Default Parameters
Configure Experiments
Configure Global Configs
Configure Users
Approve User Account Requests
Configure Basecaller Default Parameters
Upgrade Your Torrent Server Ubuntu® Software
View Network Settings
Shutdown Server
Use a Torrent VM to Evaluate a New Torrent Suite™ Software Release
Shutdown Server
Use a Torrent VM to Evaluate a New Torrent Suite™ Software Release
Update Server
Update the Ion OneTouch™ Device
Update the Ion OneTouch™ Device
Manage your SGE Cluster with QMON
View System Support Diagnostics
View Instrument Diagnostics
View System Support Diagnostics
View Instrument Diagnostics