Above code is not doing what you explained in your post.
You need to read line by line in out.txt file then find / list the files with *.bam extension , copy etc.
It may be done in oneliner , if you can add more description about structure of Folder1,Folder2 and /home/cmccabe/nfs/exportedReports with clear example.
if not, try like this:
Code:
cat out.txt
DIR1
DIR2
$ ls -a DIR1/
. .. 123.bam abc.bam xyz.log
$ ls -a DIR2/
. .. cool.txt me.bam
Sample code written here to update your script.
Code:
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
Last edited by greet_sed; 09-16-2016 at 01:56 PM..
Reason: Add sample code
Hi Friends,
Below is my requirement and i am not clear how to approach this issue in unix programming.
I have a folder with 2500 files. The files are in below format.
1234_name1.txt
1234_name123.txt
4567_name1.txt
4567_name123.txt
and i need a program which will read each file from this... (5 Replies)
I'm having problems with my bash script. I would like to find a file matching today's date in the filename, i.e. my_file_20120902.txt and then move it to a different directory, i.e. /tmp. Thanks. (1 Reply)
Hi friends,
I have one XML file having below structure :-
INput XML file :-
<?xml version="1.0" encoding="UTF-8"?>
<START>
<A=value1>
<attr name1="a1">
</A>
<B=value2>
<attr name2="b1">
<attr name3="c1">
</B>
</START>
output xml file should be
=== (3 Replies)
I am trying to download all files from a user authentication, password protected https site, with a particular extension (.bam). The files are ~20GB each and I am not sure if the below is the best way to do it. I am also not sure how to direct the downloaded files to a folder as well as external... (7 Replies)
I am trying to move specific folders and subfolders within a directory using the below. I can see the folders to move and they are at the location, but I am getting an error. Thank you :).
mv -v /home/cmccabe/Desktop/NGS/API/6-10-2016{bam/{validation,coverage},bedtools /media/cmccabe/"My... (6 Replies)
Dear Experts
my scenario is as follows...
I have one source folder "Source" and 2 target folders "Target_123456" & "Target_789101". I have 2 series of files. 123456 series and 789101 series. Each series has got 3 types of fiels "Debit", "Refund", "Claims".
All files are getting... (17 Replies)
Hello all,
do you know any way i can i move folders and its content if folder is older than 1,5 days in bash?
I tried:
find /home/xyz/DATA/* -type d -ctime +1.5 -exec mv "{}" /home/xyz/move_data_here/ \;All i got was that Files from DATA /home/xyz/DATA/* ended messed up in... (1 Reply)
Hi Team,
I am new to the linux commands and I really need help . I would be really thankful if I can get some inputs.
I have below folders in the path "/home/temp"
20170428
20170427
20170429
changes
tempI need to get the files generated in the last 15 mins in all the above folders... (4 Replies)
I am trying to mv each of the .vcf files in the variants folder to the folder in /home/cmccabe/f2 that the .vcf id is found in file. $2 in file will always have the id of a .vcf in the variants folder. The line in blue staring with R_2019 in file up to the -v5.6 will always be an exact match to a... (4 Replies)
Discussion started by: cmccabe
4 Replies
LEARN ABOUT DEBIAN
surfraw-update-path
SURFRAW-UPDATE-PATH(1) User Contributed Perl Documentation SURFRAW-UPDATE-PATH(1)NAME
surfraw-update-path - updates PATH in shell config files
SYNOPSIS
surfraw-update-path [-add] [-remove] [-check] [-sys] [-all] [-help] [-shell=SHELL]
DESCRIPTION
surfraw-update-path adds the surfraw elvi directory (/usr/lib/surfraw) to your PATH in your shell's config file.
Currently it supports bash, sh, csh, tcsh, ash, dash, ksh, pdksh, zsh, rc, and es
Don't forget to login again or source your login files for it to take effect.
OPTIONS -check
Checks to see if the surfraw config code is present. This is the default.
-add
Adds the surfraw config code.
-remove
Removes the surfraw config code
-sys
Updates the system-wide shell config instead of the user. Must be done as root.
-shell=SHELL
Selects the shell to configure. Defaults to the value of the $SHELL environment variable.
Currently supported shells are:
sh, ash, bash, dash, csh, tcsh, ksh, pdksh, zsh, rc, and es.
-all
Attempts to configure the startup files for all known shells
-help
Gives a usage message
RETURN VALUE -check returns 0 if the surfraw code is present in the file, 1 if it is not found, or 2 on error.
All other options return 0 on success, or 2 on error.
ENVIRONMENT
SHELL
Used to determine which shell to configure, if -shell is not given.
HOME
Used to find users config files.
ENV Used by posix-compliant shells to specify a startup rc file.
ZDOTDIR
Used to find user config files for zsh. If not set, defaults to HOME.
SEE ALSO surfraw(1), sh(1), ash(1), bash(1), dash(1), csh(1), tcsh(1), ksh(1), pdksh(1), zsh(1), rc(1), es(1)AUTHOR
Ian Beckwith <ianb@erislabs.net>
perl v5.12.4 2011-07-12 SURFRAW-UPDATE-PATH(1)