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
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
Go to the directory where you want your files to be or where you want to copy from.
This gives the absolute path to your directory. It might start with "home" or "work" depending on what directory you're in.
Transferring files to Lonestar
On your computer's side:
Go to the directory where you want to copy files from.
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.
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.
Sometimes you may want to transfer more than one file.
If you wanted to transfer a directory, use the -r option like so:
You can also transfer directories from Lonestar in the same manner:
SSH Secure File Transfer (Windows) is available as part of the SSH Secure Shell client which can be downloaded from Bevoware.
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:
Then to load a module like gatk for use, type:
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:
To automatically load a module when you log in, go to your home directory by typing:
Let's load R when we log in. Do this by typing:
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.
module avail only shows modules in the current context (i.e. based on your currently loaded modules), to see all possible modules use:
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.