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The above example isn't particularly efficient, but it gets the job done. In the above examples, we heavily abuse the Linux "pipe," which is the symbol '|' (probably shares the '\' key on your keyboard above the Enter key). Pipe takes the "standard output" that would normally go to the screen and sends it to the next command.
If we really like this output, we can save it to a file and look through it rather than just printing the first 10 lines:
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head -100000 $TEST_DATA/250k_reads.fastq | grep -A 1 '^@M00' | grep -v '^@M00' | grep -v '^--$' | sort | uniq -c | sort -n -r > my_file.txt
less my_file.txt |
Less lets you look through files. Up and down arrows move one line at a time. 'F' pages down, and 'W' pages up. "Shift+G" takes you to the end of the file, and "G" take you back to the beginning. "Q" exits the program.
Further reading and examples: Scott's list of linux one-liners
Software Modules
TACC has lots of software packages, but most of them are not in your environment. TACC doesn't want to "bloat" your environment with a bunch of software that you don't use, so we put everything in modules. Try this:
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module keyword genomics chemistry biology 2>&1 | grep -v '^[A-Za-z0-9]' | grep -v '^---' | grep -v spider | grep -v '^$' | grep -v " " | sed s/','/' '/g | awk 'BEGIN {print "Module\t\tVersions\nList Updated\t"strftime("%B %d %Y",systime())", "} { prog=$1; prog_vers=$2 "\t" $3 "\t" $4; if (length(prog) < 8) prog="prog\t"; print prog "\t" prog_vers ; }' |
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