Login or Register to Ask a Question and Join Our Community


Shell Programming and Scripting

Cp command works on command line but not in bash

Login to Discuss or Reply to this Discussion in Our Community

 
Thread Tools Search this Thread
Top Forums Shell Programming and Scripting Cp command works on command line but not in bash
# 1  
Old 02-02-2017
Cp command works on command line but not in bash
The below command moves all the .vcf files into the directory.


Code:
cp /home/cmccabe/Desktop/test/vcf/overall/stats/*.vcf /home/cmccabe/Desktop/NGS/annovar

When I use a bash wrapper the target.txt gets created but the text files do not get copied. All the paths are the same, but not sure why its not working. Thank you Smilie.

Bash
Code:
logfile=/home/cmccabe/Desktop/test/process.log
for file in /home/cmccabe/Desktop/test/vcf/overall/stats/*.vcf ; do
     echo "Start annovar creation: $(date) - file: $file"
     echo ${file##*/} >> /home/cmccabe/Desktop/NGS/annovar/target.txt
     cp /home/cmccabe/Desktop/test/vcf/overall/stats/*.vcf /home/cmccabe/Desktop/NGS/annovar
     echo "End annovar file creation: $(date) - file: $file"
done >> "$logfile"

# 2  
Old 02-02-2017
You are not capturing the errors. Try:

Code:
logfile=/home/cmccabe/Desktop/test/process.log
for file in /home/cmccabe/Desktop/test/vcf/overall/stats/*.vcf ; do
     echo "Start annovar creation: $(date) - file: $file"
     echo ${file##*/} >> /home/cmccabe/Desktop/NGS/annovar/target.txt
     cp /home/cmccabe/Desktop/test/vcf/overall/stats/*.vcf /home/cmccabe/Desktop/NGS/annovar
     echo "End annovar file creation: $(date) - file: $file"
done 2>&1 >> "$logfile"

Also: Why are you copying every single file every loop? If you're trying to copy them one at a time, cp * destination/ isn't the way to do it.
This User Gave Thanks to Corona688 For This Post:
cmccabe
# 3  
Old 02-02-2017
Thank you very much for your help and good point, I appreciate them Smilie
Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. UNIX for Beginners Questions & Answers

Command works interactively but not in bash script

The below command works in the terminal interactively but not as part of a bash script. I though maybe I needed to escape the "$dir" so it isn't interpreted literally, but that's not it. Thank you :). interactively in terminal dir=/path/to new=$(ls "$dir"/*.csv -tr | tail -n 1) && echo... (6 Replies)
Discussion started by: cmccabe
6 Replies

2. Shell Programming and Scripting

Command works at command line but not from cron

Oracle Linux 6. Trying to set up a simple monitoring of memory usage. This command does exactly what I want at the command line: echo $(date +%Y-%m-%d" "%H:%M:%S) $(grep PageTables /proc/meminfo) >> /home/oracle/meminfo.logBut when I put it in my crontab: * * * * * echo $(date +%Y-%m-%d"... (2 Replies)
Discussion started by: edstevens
2 Replies

3. Shell Programming and Scripting

Works on command line but not in script

OSX 10.9 I am building a script that evaluates the difference between 2 files. Here is a command that does not work transparently. Running this command in Terminal yields great results; however when I put that line in a .sh script, I get the errors shown below. Am I doing something silly? ... (1 Reply)
Discussion started by: sudo
1 Replies

4. Shell Programming and Scripting

SH script, variable built command fails, but works at command line

I am working with a sh script on a solaris 9 zone (sol 10 host) that grabs information to build the configuration command line. the variables Build64, SSLopt, CONFIGopt, and CC are populated in the script. the script includes CC=`which gcc` CONFIGopt=' --prefix=/ --exec-prefix=/usr... (8 Replies)
Discussion started by: oly_r
8 Replies

5. Windows & DOS: Issues & Discussions

Command works on CMD line but not in batch?

Hi All, This command works when I type it on but when I run the batch file it doesn't..any ideas why? attrib.exe * | find /c /v "" >filecount.txt (1 Reply)
Discussion started by: Grueben
1 Replies

6. UNIX for Dummies Questions & Answers

Running set options from the command line and bash command

I'm reading about debugging aids in bash and have come across the set command. It says in my little book that an addition to typing set you can also use them "on the command line when running a script..." and it lists this in a small table: set -o option Command Line... (5 Replies)
Discussion started by: Straitsfan
5 Replies

7. UNIX for Dummies Questions & Answers

Works on command line but not in script

Hey guys. Hopefully this is an easy one but having reference similar problems on the web I still can't fix it. I am doing a recursive find and replace from a script. Of course I could just run the damn thing from the command line but it's bugging me now and want to get it working. grep -rl... (4 Replies)
Discussion started by: anthonyjstewart
4 Replies

8. Shell Programming and Scripting

s3cmd works on command line not on cron

Ubuntu 9.10 is my linux distro Based on forums they say that the problem is with environment . here is my case: login as user, then sudo -s using this command: s3cmd put file s3://bucket >>worked! now here is the simple script intended for testing: #! /bin/bash env >/tmp/cronjob.log... (1 Reply)
Discussion started by: qwerty20
1 Replies

9. Shell Programming and Scripting

Zgrep works at command line but not in script?

Hi all- I'm trying to search through some .gz log files to verify certain feeds have passed through our app. I have a small script that I wrote in hopes that I could automate the checking but haven't been able to get the zgrep to work. When I copy it to the command line directly it works... (2 Replies)
Discussion started by: Cailet
2 Replies

10. Shell Programming and Scripting

substring command works but only in BASH shell

I am having trouble running a .sh file. The code 'x=${file_name:0:$z-11}' is giving me a bad substitution error. However when I run in BASH it works. Thing is when this goes to production the .sh will not be running in BASH. Is there a way to substring a string not in BASH or a way to invoke... (2 Replies)
Discussion started by: edwardtk11
2 Replies
Login or Register to Ask a Question