Wow that is awesome...Sorry.. I removed a lot of stuff from the scripts to make it simpler for the post, in mine it uses the current directory. Is there a way to get glob to output just the directory names but not their entire paths (without just regexing it)---> This is the current output of what you posted 

../results//jobs
../results//logs
../results//step0_tophat
../results//step1_2cuffcompare
../results//step1_cufflinks
../results//step2_cuffmerge
../results//step3_cuffdiff
../results//step4_createTranscriptome
../results//step6_bowtie_pe
../results//step7_bowtie_se
../results//step8_bowtie_hg19
../results//step9_tophat_unmapped_hg19

[download]
This is what I was looking for, if it is possible: 
jobs
logs
step0_tophat
step1_2cuffcompare
step1_cufflinks
step2_cuffmerge
step3_cuffdiff
step4_createTranscriptome
step6_bowtie_pe
step7_bowtie_se
step8_bowtie_hg19
step9_tophat_unmapped_hg19

[download]
Thanks so much for your time!

On a side note, I really want to learn more shorthand tricks like this, but they are really hard to find without asking a direct question... are you aware of any resources that instruct specifically on useful shorthand alternatives .. for example the difference between my script and your response.

In reply to Re^2: Most effective bash to perl for directory listing by ZWcarp
in thread Most effective bash to perl for directory listing by ZWcarp

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