数据检索

基因组学 Next-Gen Sequence Retrieval

The RTSF 基因组学 Core FTP server now requires secure (FTPS) connections.

To protect the integrity and security of the MSU network and its systems, and to permit users from outside of the MSU network to once again access the RTSF 基因组学 Core file distribution server we will be enforcing secure (encrypted) connections only. This change ensures that usernames and password are no longer passed between the client and host in clear text.

For you this will mean using an FTP client application capable of Secure FTP (FTPS) using TLS and configuring it to use an 明确的 TLS connection. Nearly every current FTP client software is capable of FTPS using TLS. When configuring your software for FTPS used 明确TLS 只是,从来没有 隐式TLS. We cannot provide configurations instructions for every FTP client software but below are examples for two popular ones.

文件Zilla (Windows/Mac/Linux)

Open the Site Manager and create a New Site for your RTSF FTPS account.

 
  1. 输入 the host name titan.BCH.365bet体育.EDU
  2.  
  3. 选择 协议 FTP-文件 传递 协议
  4.  
  5. 选择 加密 要求 明确的 FTP通过TLS

输入 the username and password provided to you. The settings should look like:

filezillaTLSConfig

Transmit (Mac OS X)

Click on the FTP tab in a new connection window to get the “Connect to FTP Server” dialog.

 
  1. 输入 the host name titan.BCH.365bet体育.EDU
  2.  
  3. 选择 the radio button FTP TLS/SSL

输入 the username and password provided to you. The settings should look like:

transmitTLSConfig

After clicking Connect with whatever client software you are using you may be presented 同 a notice that it is unable to verify the server’s certificate. This is normal and you may proceed be clicking OK or Connect, etc.

传递ring data from the RTSF FTP server using the command line program wget

500 Internal Server Error

Internal Server Error

The server encountered an internal error and was unable to complete your request. Either the server is overloaded or there is an error in the application.

If you attempt to run wget as described below and you receive an error message which states: 'Unsupported scheme "ftps"' it means that the version of wget you are using does not support FTPS.


Special considerations for using wget on the MSU HPCC cluster:

You will need to log into the file transfer host and load two software modules to perform FTPS file transfers to the HPCC.

- log in via ssh using your MSUNetID to rsync.hpcc.365bet体育.EDU

$的ssh @rsync.hpcc.365bet体育.EDU

Your log in prompt should indicate that your are logged in to the globus-01 host ([username@globus-01 ~]$)

Do not ssh out to any of the development nodes. FTPS transfer from the RTSF FTP server to the HPCC only works if you are currently working from the rsync login node. Once you have transferred your data to your home directory on the HPCC it will of course be available anywhere on the HPCC.

- load the modules GCCcore v6.4.0 and wget v1.19.4

[username@globus-01]$ module load GCCcore/6.4.0 wget/1.19.4

- execute the wget command

[username@globus‑01]$ wget -r -np -nH --ask-password ftps://@/

输入 your password when prompted.

Username, password and hostname are the ones provided to you (usually via email) when you first received data from the MSU RTSF 基因组学 Core. directory_name is the name of the subdirectory in you FTP account which contains the data for your current run(s) that you want to download. This subdirectory name is provided in the email notifying you that your data is available.

This command will create a new subdirectory named at your current working directory containing all of the FastQ files for that run.