Bash to move specific files from folders in find file
I have a directory /home/cmccabe/nfs/exportedReports that contains multiple folders in it. The find writes the name of each folder to out.txt. A new directory is then created in a new location /home/cmccabe/Desktop/NGS/API, named with the date. What I am trying to do, unsuccessfully at the moment, is copy each specific file type .bam from each folder in out.txt to the new date folder in /home/cmccabe/Desktop/NGS/API/$DATE.
For example, after the find command out.txt:
Code:
Folder1
Folder2
within each of those folders there are 3 .bam files to move to the new directory/home/cmccabe/Desktop/NGS/API/$DATE. Thank you .
Code:
#!/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
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Discussion started by: cmccabe
4 Replies
LEARN ABOUT DEBIAN
ecaccess-file-move
ECACCESS-FILE-MOVE(1p) User Contributed Perl Documentation ECACCESS-FILE-MOVE(1p)NAME
ecaccess-file-move - Move or Rename ECaccess Files
SYNOPSIS
ecaccess-file-move -version|-help|-manual
ecaccess-file-move [-debug] source-ecaccess-file target-ecaccess-file
DESCRIPTION
Allow moving an ECaccess File. When the move occurs within the same ECaccess File System then it is a rename. When the move occurs across
two different ECaccess File Systems then first a copy is done and then a delete of the original file is done (e.g. similar to ecaccess-
file-copy ... -erase).
The source-ecaccess-file and target-ecaccess-file are in the form [domain:][/user-id/]path. Please read the "Shell commands -> File
Management" section of the "ecaccess" guide for more information on the ECaccess File System.
ARGUMENTS
source-ecaccess-file
The source ECaccess File name.
target-ecaccess-file
The target ECaccess File name.
OPTIONS -version
Display version number and exits.
-help Print a brief help message and exits.
-manual Prints the manual page and exits.
-debug Display the SOAP messages exchanged.
EXAMPLES
ecaccess-file-move ec:test1.txt ec:test2.txt
Rename the test1.txt file in the ECFS directory of the authenticated user in test2.txt.
ecaccess-file-move ec:test1.txt home:test2.txt
Copy the test1.txt file from the ECFS directory of the authenticated user to the test2.txt file in the $HOME directory of the authenticated
user, then delete the test1.txt file from ECFS.
SEE ALSO
ecaccess-file-delete, ecaccess-file-get, ecaccess-file-mget, ecaccess-file-modtime, ecaccess-file-mput, ecaccess-file-rmdir, ecaccess-file-
copy, ecaccess-file-dir, ecaccess-file-mdelete, ecaccess-file-mkdir, ecaccess-file-chmod, ecaccess-file-put, ecaccess-file-size and
ecaccess.
perl v5.14.2 2012-04-16 ECACCESS-FILE-MOVE(1p)
09-16-2016
.