Copying files to/from UT Box at the command line
If you use SSO (through UT Box), you need to first
set up an external password.
You will need
LFTP installed on your system.
It is already installed on TACC
Open the file
~/.lftp/rc
in a text editor. (You may need to first create the
~/.lftp
folder if it does not exist. Strictly speaking, this step is optional. You could run these commands every time you enter the LFTP shell to temporarily set the options.)
Add these lines to the
~/.lftp/rc
file.
set ftps:initial-prot ""
set ftp:ssl-force true
set ftp:ssl-protect-data true
Now you can use these commands to connect to Box (The second one is run inside the LFTP shell and will prompt you for the password you created.) The user name is the one listed in the account tab of the account settings page on UTBOX.
lftp ftps://ftp.box.com:990
lftp ftp.box.com:~> user YYY@XXX.utexas.edu
LFTP commands are a dialect of FTP commands. If you are not familiar with these, here is a
reference.
Here are some useful commands for working with your local directory from within the LFTP shell:
-
lcd
lets you change local directories.
-
!ls
lets you list the contents of your local directory.
To recursively copy directories
TO BOX, you will need this command:
mirror -R {local dir} {remote dir}
This
does not delete a file from
{remote dir}
if it has been deleted in
{local dir}
since the last backup. You would need to add the
--delete
flag for that type of sync, but be very careful when doing so! You can use the
--dry-run
option to see what would have been deleted before running it.
Note: Sometimes you may get an error looking like this during a
mirror -R
call. The file has been successfully transferred despite this message!
mirror: Access failed: 550 Box: Item with the same name already exists (code=item_name_in_use, request_id=XXXXXXXXXXXXXXX). (FILENAME)
Note: Some TACC servers may not be compiled correctly and might need an extra module loaded (ie Maverick2). Try this in if the above does not work.
For copying all files in subdirectories (but not the directories themselves) from Box to tacc the following may work well:
Note: the above will result in a fairly quick determination and changing message of what is to be transferred followed by a lengthy file transfer which will result in messages such as
pget-chunk: B-A1/B-A1_R1.fastq.gz: seek failed
for each file once each file transferred.
To recursively copy directories
FROM BOX, you will need this command:
This website contains useful examples for both mirroring to and from remote location
Creating a Bookmark File
This only works if you are UT-affiliated.
First, follow these instructions to
set up an external password.
Next, create a bookmark called
utbox
.
Security Note: this saves your external password in clear text in your home directory.
lftp ftps://ftp.box.com:990
set bmk:save-passwords yes
user [your_EID]@eid.utexas.edu
[Enter Password]
bookmark add utbox
quit
Then, you can log in using just one command!
Be sure to test your setup after logging in by running a command like `ls` because it will not give you an error if login failed!
It should list all of your Box file.
This is also the standard way that we make it possible to mass download data as part of
brefito workflows.