Shell Programming and Scripting

Folder1
Folder2

#!/bin/bash

cd /home/cmccabe/nfs/exportedReports
find . -maxdepth 1 -type d | cut -c 3- | awk -F _ 'NF > 1' > out.txt

DATE=`date +%-m-%-d-%Y` 
        mkdir -p /home/cmccabe/Desktop/s5/$DATE

MY_DIR="/home/cmccabe/nfs/exportedReports/out.txt"
DEST="/home/cmccabe/Desktop/NGS/API/$DATE"
FILEEXT=".bam"

NEWEST=`ls -tr1d "${MY_DIR}/"*.${FILEEXT} 2>/dev/null | tail -1`

if [ -z "${NEWEST}" ] ; then
    echo "No file to copy"
    exit 1
elif [ -d "${NEWEST}" ] ; then
    echo "The most recent entry is a directory"
    exit 1
else
    echo "Copying ${NEWEST}"
    cp -p "${NEWEST}" "${DEST}"
fi

NEWEST=`ls -tr1d "${MY_DIR}/"*.${FILEEXT} 2>/dev/null | tail -1`

cat out.txt
DIR1
DIR2
$ ls -a DIR1/
.  ..  123.bam  abc.bam  xyz.log
$ ls -a DIR2/
.  ..  cool.txt  me.bam

a=/home/cmccabe/nfs/exportedReports;DEST="/home/cmccabe/Desktop/NGS/API/$DATE";
while read line; do find $a/$line -name "*.bam" -exec cp {} $DEST \;
done < out.txt 
$ ls -a $DEST
.  ..  123.bam  abc.bam  me.bam

cp: cannot stat ‘/home/cmccabe/nfs/exportedReports/Auto_user_S5-00580-5-Medexome_66_030/plugin_out/coverageAnalysis_out.39/IonXpress_007/scraper/link.summary.bam': No such file or directory

#!/bin/bash

cd /home/cmccabe/nfs/exportedReports
find . -maxdepth 1 -type d | cut -c 3- | awk -F _ 'NF > 1' > out.txt

DATE=`date +%-m-%-d-%Y` 
        mkdir -p /home/cmccabe/Desktop/s5/$DATE

a=/home/cmccabe/nfs/exportedReports;DEST="/home/cmccabe/Desktop/s5/$DATE";
while read line; do find $a/$line -name "*.bam" -exec cp {} $DEST \;
done < out.txt

find . -maxdepth 1 -name "test*" -exec echo "cp -t /tmp" {} \+

DATE=`date +%-m-%-d-%Y` 
FROM="/home/cmccabe/nfs/exportedReports"
DEST="/home/cmccabe/Desktop/s5/$DATE"
if
  cd "$FROM" &&
  mkdir -p "$DEST"
then
  cp *_*/*.bam "$DEST"
fi

find . -maxdepth 2 -type d -name "again_test*" -prune -o -type f -name "test*" -print

find . -maxdepth 2 -type d -name "again_test*" -prune -o -type f -name "test*" -exec cp -t /tmp {} \+