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This page is a quick start for using the Lonestar cluster at TACC.

Table of Contents
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The Lonestar User Guide

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

Expand
If you've forgotten how to log in, expand this
If you've forgotten how to log in, expand this

Logging In

Code Block

ssh <my_user_name>@lonestar.tacc.utexas.edu

Transferring Files to and from Lonestar

Obtaining the Path

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

...

Code Block
titleTo find the absolute path, needed to pull or push files from/to Lonestar

pwd

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@lonestar.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@lonestar.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@lonestar.tacc.utexas.edu:/...

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

Code Block

 scp -r my_user_name@lonestar.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.

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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.

To see all modules available in the current context, type:

Code Block

 module avail

Then to load a module like gatk for use, type:

Code Block
  module load gatk

Some applications are already loaded when you log in but may not be up to date. Python is already loaded, but only version 2.4.3 is loaded. Version 2.7.1 is in the available list. To load Python 2.7.1, type:

Code Block

 module load python

To automatically load a module when you log in, go to your home directory by typing:

Code Block

 cdh

Let's load R when we log in. Do this by typing:

Code Block
  echo "module load R" >> .profile_user

...

Since module avail only shows modules in the current context (i.e. based on your currently loaded modules), to see all possible modules use:

Code Block

 module spider <freetext>

If you specify some text for <freetext>, you'll see all modules with that text anywhere in their title or description. For example, try to find the transcriptome assembler Trinity.

...