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The Lonestar6 User Guide

For complete up-to-date information, always see: TACC's Lonestar User Guide

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Code Block
ssh <my_user_name>@ls6.tacc.utexas.edu

Setting up up a profile

There are many flavors of Linux/Unix shells. The default for TACC's Linux (and most other Linuxes) is bash (bourne againshell), which we will use throughout.

Whenever you login via an interactive shell as you did above, a well-known script is executed by the shell to establish your favorite environment settings. We've set up a common profile for you to start with that will help you know where you are in the file system and make it easier to access some of our shared resources. To set up this profile, do the following steps after logging in:

Copy a preconfigured "profile" to use with your account

Code Block

cdh
mv ~/.profile ~/.profile.old
cp /work2/projects/BioITeam/projects/courses/Core_NGS_Tools/tacc/bashrc.corengs.ls6.light_bg ~/.profile
echo "export PATH=\$PATH:/work2/projects/BioITeam/common/bin/" >> ~/.profile
chmod 600 .profile
source .profile
ls -a

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Notice that when you do a normal ls to list the contents of your home directory, this file doesn't appear. That's because it's a hidden "dot file" – a file that has no filename, only an extension. To see these hidden files, use the -a (all) switch for ls.

Transferring Files to and from Lonestar

Obtaining the Path

It's a good idea to open 2 terminals for transferring files.

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This gives the absolute path to your directory. It might start with "home" or "work" depending on what directory you're in.

Mac/Linux

Expand

	On a local Mac or Linux machine
	On a local Mac or Linux machine

Transferring files to Lonestar

On your computer's side:

Go to the directory where you want to copy files from.

Code Block
scp stuff.fastq my_user_name@ls6.tacc.utexas.edu:/home/.../

Replace the "/home/.../" with the "pwd" information obtained earlier.

This command would transfer "stuff.fastq" in your current directory to a specified directory on Lonestar.

Transferring files from Lonestar

On your computer's side:

Go to the directory where you want to copy files to.

Code Block
scp my_user_name@ls6.tacc.utexas.edu:/home/.../stuff.fastq ./

Replace the "/home/..." with the "pwd" information obtained earlier.

This command would transfer "stuff.fastq" from the specified directory on Lonestar to your current directory on your computer.

Copying Directories

Sometimes you may want to transfer more than one file.

If you wanted to transfer a directory, use the -r option like so:

Code Block
scp -r my_folder my_user_name@ls6.tacc.utexas.edu:/...

You can also transfer directories from Lonestar in the same manner:

Code Block
scp -r my_user_name@ls6.tacc.utexas.edu:/home/.../my_folder ./

Windows

Expand

	On a local Windows machine
	On a local Windows machine

SSH Secure File Transfer (Windows) is available as part of the SSH Secure Shell client which can be downloaded from Bevoware. You can also use winscp (free to download).

Modules

Modules are programs or sets of programs that have been set up to run on TACC. They make managing your computational environment very easy. All you have to do is load the modules that you need and a lot of the advanced wizardry needed to set up the linux environment has already been done for you. New commands just appear.

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Versions Compared

Old Version 24

New Version 25

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