Bash to check directory and create missing folder from file
In the below bash I am trying to ensure that all folders (represented by $folders) in a given directory are created. In the file f1 the trimmed folder will be there somewhere (will be multiple trimmed folders).
When that trimmed folder is found (represented by $S5) the the contents of $2 printed to $STRING. If $STRING is the same as $folders then
that folder is already created in the directory and it can be skipped (this will be the case most of the time). If $STRING is not the same as $folders then the missing is created in the directory. The code seems to work as expected untill the If done, that is the variables are set correctly, but the actual match is portion below is not working and I am not sure how to mkdir. Thank you .
Code:
DIR=/home/cmccabe/folder
for RDIR in "$DIR"/R_2019* ; do ## # matching "R_2019*" to operate on desired directory and expand
TRIMSTR=${RDIR%%-v5.6*} ## trim folder match in RDIR from -v5.6 and store in TRIMSTR
mv "$RDIR" "$TRIMSTR" ## move trimmed folder to directory
S5=${TRIMSTR##*/} ## store run with no path as S5
# Iterate over each sample folder in run directory
cd "$TRIMSTR"
folders=folders=`ls -d *[0-9]*/` ## list only directories begining with digit
done
for f in "$DIR"/f1; do STRING=$(awk -v ref="/$S5/" 'match($0, ref) {print $2}' "$f"); done
nl=" ## added newline boundry seperator
"
if [[ $nl$folders$nl == *$n$STRING/$nl* ]] || continue # only execute file on match
else mkdir $STRING
fi
directory structure where variables come from
Code:
/path/to/run/folder/R_2019_00_00_00_00_00_xxxx_x0-00000-123-v5.6_xxx_xxx_xxx_xxx_xxx_xxx_xxxx
--- /path/to/run/folder/R_2019_00_00_00_00_00_xxxx_x0-00000-123 --- this is $TRIMSTR and the blue is $S5
--- 00-1111-xxx-xxx 00-2222-yyy-yy 00-3333-zz-zz id test --- these are within $TRIMSTER id and test are not stored in $folders
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09-27-2019
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