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Bash to add folder to exsisting folders in directory

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# 1  
Old 10-03-2016
Bash to add folder to exsisting folders in directory
I am trying to create subdirectories in each folder in /home/cmccabe/Desktop/NGS/test/*. When I use echo I can see each folder in the directory, but I can not seem to add the commented out portion in bold. These are the sub-directories and sub-folders I am trying to add to each folder in /home/cmccabe/Desktop/NGS/test/*. Thank you Smilie.

Bash
Code:
 for D in /home/cmccabe/Desktop/NGS/test/*; do
    if [ -d "$D" ]; then
        cd "$D"
        echo "$D"  
#bam/{validation,coverage},bedtools,fastqc,hgmd,igv,panel/{reads,},panel/20x/{base,gene,percent},panel/{reads,},panel/30x/{base,gene,percent},picard,torrent,vcf/overall/{annovar,stats},vcf/panel/{annovar,}} #
    fi
done

Folders in /home/cmccabe/Desktop/NGS/test/[/ICODE]
Code:
 Folder1
 Runfolder2
 Run3

Example:
Code:
 Folder 1 - folder in ]/home/cmccabe/Desktop/NGS/test
 BAM
   -validation
   -coverage
 Bedtools
 FASTQC
 HGMD
 IGV
 Panel
   - 20x
reads  
 base genes percent
   - 30x
reads  
 base genes percent
 Picard
 Torrent
 VCF
    - overall
 annovar, stats
   - Panel
 annovar

Last edited by cmccabe; 10-03-2016 at 03:49 PM.. Reason: fixed format
# 2  
Old 10-03-2016
It seems that you would want to replace the bold code by one or more:
Code:
        mkdir -p "$D/possibly_missing_directory" ...

commands. Given differences in case, differences in leading hyphens and/or spaces, and confusing uses of commas (sometimes separating lists of directories to be created and sometimes apparently being part of the name of a directory being created [<space>annovar,<space>stats]), I am not going to try to guess at which actual mkdir commands you need to do what you really want to do.
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