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This page is a quick start for using the Lonestar Lonestar6 cluster at TACC.

Table of Contents
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The

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Lonestar6 User Guide

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

Logging in

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

Setting up up a profile

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Copy a preconfigured "profile" to use with your account



 

 

Code Block
cdh
mv ~/.profile ~/.profile.old
cp /corral-replwork2/utexasprojects/BioITeam/scripts/rnaseq_profile_user 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

 


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

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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@lonestarname@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@lonestarname@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@lonestarname@ls6.tacc.utexas.edu:/...

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

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


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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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