I have some .gz files, of which i want to run a script on. I need these files to remain in .gz format. When I run my script:
#!#bin#bash
for f1 in $(~/Desktop/hawkfiles17/NG*.fq.gz);
do
echo "${f1}"
done
I want to check the location of the files. The script returns:
bash: /home/amyhouseman/Desktop/hawkfiles1/NG0921017_EKDN210018957-1A_HN2MGDSX2_L2_1.fq.gz: Permission denied`
I have tried using:
chmod u x /home/amyhouseman/Desktop/hawkfiles17/NG0921017_EKDN210018957-1A_HN2MGDSX2_L2_1.fq.gz
, but bash returns:
bash: /home/amyhouseman/Desktop/hawkfiles17/NG0921017_EKDN210018957-1A_HN2MGDSX2_L2_1.fq.gz: cannot execute binary file: Exec format error
I'd be grateful if someone could help, I know that you can't execute .gz files, but I'm not sure what else i can do? I did look through other posts before.
CodePudding user response:
I want to check the location of the files.
You're shebang is incorrect, and several other small strings.
Here is your solution:
$ cat my_script.sh
#!/bin/bash
for item in $(ls ~/Desktop/hawkfiles17/NG*.fq.gz) ; do echo "$item" ; done