Use a web browser to connect at:
https://hgsc-sftp1.hgsc.bcm.tmc.edu
Help using the web browser interface
For instructions on using the web client interface, log in and then click on the "help" link that is located near the top, right-hand corner of the interface.
Notes about using the web browser interface
The web browser interface client offers two interfaces: enhanced and basic.
Macintosh users: use the basic interface
Windows users: use the enhanced interface (gives a better UI and the ability of automatic checksums)
SFTP settings:
Host: sftp://hgsc-sftp1.hgsc.bcm.tmc.edu:9910
Your SFTP client may require you to enter the host name and port number seperately, as follows:
Host: sftp://hgsc-sftp1.hgsc.bcm.tmc.edu
Port: 9910
Please be sure that the hostname that you are typing begins with sftp:// and not http://, https://, or ftp://.
SFTP client products
While we do not endorse a particular SFTP client, here are a few that are available:
You can use command line SFTP by using the following command:
sftp -oPort=9910 username@hgsc-sftp1.hgsc.bcm.tmc.edu
Replace "username" with your actual username provided by BCM-HGSC.
Commands
cd somedirectory |
- can move into a directory if needed |
get * |
- download all files in current directory to your local machine |
get somefilename.bam |
- to download a specific file |
put * |
- to upload all files from your current directory on your client machine to HGSC |
put somefilename.bam |
- to upload a specific file |
exit |
- exit command will close the connection |
Although the SFTP protocol will work for you, the stock "sftp" client that ships with most Linux distributions is inefficient, because the sftp command is geared to downloading one file per subcommand.
The solution is to use lftp which is a terminal client that supports multiple protocols and has a more modern perspective.
https://en.wikipedia.org/wiki/Lftp
For Redhat & Centos systems you can install lftp like this:
sudo yum install lftp
For Ubuntu (Debian) systems you can install lftp like this:
sudo apt-get install lftp
This is a sample session:
[ec2-user@ip-xx-xxx-xx-xxx ~]$ sudo yum install lftp [ec2-user@ip-xx-xxx-xx-xxx ~]$ mkdir test1 [ec2-user@ip-xx-xxx-xx-xxx ~]$ cd test1 [ec2-user@ip-xx-xxx-xx-xxx test1]$ lftp sftp://username@hgsc-sftp1.hgsc.bcm.tmc.edu:9910 [^] Password: lftp username@hgsc-sftp1.hgsc.bcm.tmc.edu:~> mirror Interrupt lftp username@hgsc-sftp1.hgsc.bcm.tmc.edu:/> mirror -c Total: 52 directories, 102 files, 0 symlinks New: 73 files, 0 symlinks 9050 bytes transferred in 7 seconds (1.3K/s) lftp username@hgsc-sftp1.hgsc.bcm.tmc.edu:/> exit [ec2-user@ip-xx-xxx-xx-xxx test1]$ logout