This page is a quick start for using the Lonestar cluster at TACC.
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The Lonestar User Guide
For complete up-to-date information, always see: TACC's Lonestar User Guide
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Logging In
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Transferring Files to and from Lonestar
Obtaining the Path
It's a good idea to open 2 terminals for transferring files.
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pwd
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This gives the absolute path to your directory. It might start with "home" or "work" depending on what directory you're in.
Mac/Linux
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Transferring files to LonestarOn 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 LonestarOn 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. Copying DirectoriesSometimes 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:
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Windows
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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:
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module avail
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Then to load a module like gatk for use, type:
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module load gatk
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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:
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module load python
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To automatically load a module when you log in, go to your home directory by typing:
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cdh
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Let's load R when we log in. Do this by typing:
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echo "module load R" >> .profile_user
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Since module avail
only shows modules in the current context (i.e. based on your currently loaded modules), to see all possible modules use:
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module spider <freetext>
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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.
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