Page Comparison

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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#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.

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 module avail

 module load gatk
 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.

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

 module spider <freetext>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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