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

The Lonestar User Guide

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

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

Logging In

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.

  • One logged in on Lonestar with the current directory set to where you want to transfer files to or from
  • One on your computer with the current directory set to where you want to transfer files to or from

On Lonestar:

Go to the directory where you want your files to be or where you want to copy from.

Type

To 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

 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.

 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.

 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:

 scp -r my_folder my_user_name@lonestar.tacc.utexas.edu:/...

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

 scp -r my_user_name@lonestar.tacc.utexas.edu:/home/.../my_folder ./

Windows

 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.

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:

 module avail

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

 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:

 module load python

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

 cdh

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

 echo "module load R" >> .profile_user

This writes the command to load R to your profile. Now whenever you log in, R will automatically load.

Why not load all the modules by default? Well, you actually may want to add many of the moduels that you encounter in later tutorials to be loaded on login. The reason they are not loaded by default is to keep things lean for those people simulating hurricanes who don't want to load Bioperl every time they log in. Occasionally two different modules also don't play nice together and you will get messages that you have to "swap" one for another.

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

 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.

Can't find a program that you need? No worries, we will learn how to install other linux programs on TACC in a later lesson.

Now let's go on to look at the directory structure at Lonestar.

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