Using the Lonestar5 Cluster

This page is a quick start for using the Lonestar5 cluster at TACC.

The Lonestar5 User Guide

For complete up-to-date information, always see: TACC's Lonestar5 User Guide

Start a new terminal window. For MACs this is done by clicking on the magnifying glass on the right hand side of the toolbar at the top of the page and type "terminal". For windows this can be done using putty or cygwin.

Before logging onto TACC servers, multi-factor authentication must be set up. Click here for an overview of this process, and click here to begin setting it up.

You will need to provide your password and a TACC token to successfully log in to lonestar5 or any other TACC cluster.

ssh <my_user_name>@ls5.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

cdh


#If you already have a .bashrc set up, make a backup copy first.
cd
cp .bashrc .bashrc_beforeRNASEQ


#Copy a preconfigured login script
cp /work/projects/BioITeam/projects/courses/Core_NGS_Tools/tacc/bashrc.corengs.ls5 .bashrc
echo "export RNASEQ=/corral-repl/utexas/BioITeam/rnaseq_course_2016" >> .bashrc
#echo "export PATH=\$PATH:/work/projects/BioITeam/common/bin/:/work/01184/daras/bin:/corral-repl/utexas/BioITeam/bin" >> .bashrc
chmod 600 .bashrc
source .bashrc


ls
#See if it took effect
echo $PATH

The chmod 600 .bashrc command marks the file as readable/writable only by you. The .bashrc script file will not be executed unless it has these permissions settings. Note that the well-known filename is .bashrc (or .profile on some systems), which is specific to the bash shell.

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.

Here, you also got a chance to see several routine and important unix commands in use: ls to list all files, mv to move a file to a different location or in this case, to rename a file, cp to make a copy of an existing file. You also saw the concept of wildcards in specifying path: ~ indicating home directory and the use of an already set alias : cdh to change to the home directory.

Transferring Files to and from Lonestar5

Obtaining the Path

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

One logged in on lonestar5 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 lonestar5:

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 Lonestar5

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 Lonestar5

On your computer's side:

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

 scp stuff.fastq my_user_name@ls5.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 Lonestar5.

Transferring files from Lonestar5

On your computer's side:

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

 scp my_user_name@ls5.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 Lonestar5 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@ls5.tacc.utexas.edu:/...

You can also transfer directories from lonestar5 in the same manner:

 scp -r my_user_name@ls5.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. 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.

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

 module avail

 module load bwa

 bwa
 which bwa

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 shows all possible modules on ls5. To see the modules in the current context (i.e. based on your currently loaded modules), use:

 module list

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, you can request for a tool to be installed through TACC consulting. Or you can try to install it locally yourself.

 module spider <freetext>

Now let's go on to look at the directory structure at Lonestar5.

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