...
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module load gatk
which gate |
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:
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module spiderlist <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, you can request for a tool to be installed through TACC consulting. Or you can try to install it locally yourself.
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module spider <freetext>
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Now let's go on to look at the directory structure at Lonestar5.