...
Code Block |
---|
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:/corral-replwork/utexasprojects/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 ls $RNASEQ |
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.
...
Code Block |
---|
module avail |
Code Block |
---|
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:
Code Block |
---|
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.
Code Block |
---|
module spider <freetext>
|
Now let's go on to look at the directory structure at Lonestar5.
BACK TO THE COURSE OUTLINE