I want to pass a command to a shell script. This command is a grep command. While executing I am getting the following errors, please help:
myscript.sh "egrep 'ERROR|FATAL' \*20100428\*.log | grep -v aString"
myscript.sh is a simple script:
#!/bin/ksh
cd log
$1
the errors are:
egrep: can't open |
egrep: can't open grep
egrep: can't open -v
egrep: can't open aString
Error is because egrap sees |, grep, -v and aString as arguments.
try this:
eval $1
You can call sh -c $1 to invoke the first argument as commands in a new shell so that the shell special characters will be expanded.
Related
As title. It seems that my .zshrc last line has some problem. No matter what the last line is, I receive the .zshrc:119: parse error near \n'` error. I'm using MAc M1 Max. Have googled some threads but all didn't work.
Example aliases
# alias zshconfig="mate ~/.zshrc"
# alias ohmyzsh="mate ~/.oh-my-zsh"
DEFAULT_USER="amber-moe"
if brew list | grep coreutils > /dev/null ; then PATH="$(brew --prefix coreutils)/libexec/gnubin:$PATH" alias ls='ls -F --show-control-chars --color=auto' eval `gdircolors -b $HOME/.dir_colors` fi
# The next line updates PATH for the Google Cloud SDK.
#if [ -f '/Users/xiaolang/google-cloud-sdk/path.zsh.inc' ]; then . '/Users/xiaolang/google-cloud-sdk/path.zsh.inc'; fi
# The next line enables shell command completion for gcloud.
if [ -f '/Users/xiaolang/google-cloud-sdk/completion.zsh.inc' ]; then . '/Users/xiaolang/google-cloud-sdk/completion.zsh.inc'; fi
This is the last line of my .zshrc. Thanks for helping me.
Are you using MSDOS endings? Seems like this is the problem
The problem isn't the last line; it's that your first if statement isn't terminated correctly, so zsh is still looking for the fi but finds the EOF instead.
The line
if brew list | grep coreutils > /dev/null ; then PATH="$(brew --prefix coreutils)/libexec/gnubin:$PATH" alias ls='ls -F --show-control-chars --color=auto' eval `gdircolors -b $HOME/.dir_colors` fi
Should actually be several lines:
if brew list | grep coreutils > /dev/null ; then
PATH="$(brew --prefix coreutils)/libexec/gnubin:$PATH"
alias ls='ls -F --show-control-chars --color=auto' eval `gdircolors -b $HOME/.dir_colors`
fi
(You can also add semicolons before alias and fi to achieve the same without breaking the line.)
I wrote a script in R that has several arguments. I want to iterate over 20 directories and execute my script on each while passing in a substring from the file path as my -n argument using sed. I ran the following:
find . -name 'xray_data' -exec sh -c 'Rscript /Users/Caitlin/Desktop/DeMMO_Pubs/DeMMO_NativeRock/DeMMO_NativeRock/R/scipts/dataStitchR.R -f {} -b "{}/SEM_images" -c "{}/../coordinates.txt" -z ".tif" -m ".tif" -a "Unknown|SEM|Os" -d "overview" -y "overview" --overview "overview.*tif" -p FALSE -n "`sed -e 's/.*DeMMO.*[/]\(.*\)_.*[/]xray_data/\1/' "{}"`"' sh {} \;
which results in this error:
ubs/DeMMO_NativeRock/DeMMO_NativeRock/R/scipts/dataStitchR.R -f {} -b "{}/SEM_images" -c "{}/../coordinates.txt" -z ".tif" -m ".tif" -a "Unknown|SEM|Os" -d "overview" -y "overview" --overview "overview.*tif" -p FALSE -n "`sed -e 's/.*DeMMO.*[/]\(.*\)_.*[/]xray_data/\1/' "{}"`"' sh {} \;
sh: command substitution: line 0: syntax error near unexpected token `('
sh: command substitution: line 0: `sed -e s/.*DeMMO.*[/](.*)_.*[/]xray_data/1/ "./DeMMO1/D1T3rep_Dec2019_Ellison/xray_data"'
When I try to use sed with my pattern on an example file path, it works:
echo "./DeMMO1/D1T1exp_Dec2019_Poorman/xray_data" | sed -e 's/.*DeMMO.*[/]\(.*\)_.*[/]xray_data/\1/'
which produces the correct substring:
D1T1exp_Dec2019
I think there's an issue with trying to use single quotes inside the interpreted string but I don't know how to deal with this. I have tried replacing the single quotes around the sed pattern with double quotes as well as removing the single quotes, both result in this error:
sed: RE error: illegal byte sequence
How should I extract the substring from the file path dynamically in this case?
To loop through the output of find.
while IFS= read -ru "$fd" -d '' files; do
echo "$files" ##: do whatever you want to do with the files here.
done {fd}< <(find . -type f -name 'xray_data' -print0)
No embedded commands in quotes.
It uses a random fd just in case something inside the loop is eating/slurping stdin
Also -print0 delimits the files with null bytes, so it should be safe enough to handle spaces tabs and newlines on the path and file names.
A good start is always put an echo in front of every commands you want to do with the files, so you have an idea what's going to be executed/happen just in case...
This is the solution that ultimately worked for me due to issues with quotes in sed:
for dir in `find . -name 'xray_data'`;
do sampleID="`basename $(dirname $dir) | cut -f1 -d'_'`";
Rscript /Users/Caitlin/Desktop/DeMMO_Pubs/DeMMO_NativeRock/DeMMO_NativeRock/R/scipts/dataStitchR.R -f "$dir" -b "$dir/SEM_images" -c "$dir/../coordinates.txt" -z ".tif" -m ".tif" -a "Unknown|SEM|Os" -d "overview" -y "overview" --overview "overview.*tif" -p FALSE -n "$sampleID";
done
I`m going to delete all files from directory that contains "2" in their name.
this command work well
ls | grep [*2*]
but when i try to pipe the output from that command to command rm
ls | grep [*2*] | rm
there is error "Try `rm --help' for more information."
please help
Why not use the wildcarding in the shell directly ?
e.g.
$ rm *2*
I don't think you need the ls or the grep. Your above problem stems from the fact that you're piping output into the stdin of rm, whereas you want to supply command line arguments to rm. rm doesn't read from stdin.
To pipe output from another command to rm you must use xargs commant for rm
Try this
ls | grep [*2*] | xargs rm
the output will send like arguments of rm command
you need to feed every line to rm command as an input. For this you need xargs along with pipe.
so modify the command like ls -1 | grep [*2*] | xargs rm -rf
just complementing on other answers, instead of running ls then grep, you could use find.
find . -name "*2*" | xargs rm
I'm using tcsh, and I'm trying to grep a path from a file with several ID, I'm doing:
grep I241149 $ENV_CASTRO/ALL_CMD_LINES.BAK | grep -o \$"ENV_CASTRO.*.asm"
that gets me:
$ENV_CASTRO/central/WS678/test_do_all.asm
but if I try
cp `grep I241149 $ENV_CASTRO/ALL_CMD_LINES.BAK | grep -o \$"ENV_CASTRO.*.asm"` .
it prompts
cp: cannot stat `$ENV_CASTRO/central/WS678/test_do_all.asm': No such file or directory
How do I tell tcsh that the output of grep contains a $ that means it is an environment variable and is not plain text?
Thanks in advance.
eval is your friend ....
eval cp `grep I241149 $ENV_CASTRO/ALL_CMD_LINES.BAK | grep -o \$"ENV_CASTRO.*.asm"` .
I don't have the time to create files to test this.
I hope this helps.
The problem is that the output of the grep command is not being evaluated by the shell, and so variable substitution is not happening.
One way to solve this would be to execute the desired command within another shell, for example,
sh -c "cp `grep I241149 $ENV_CASTRO/ALL_CMD_LINES.BAK | grep -o '$ENV_CASTRO.*.asm'` ."
I was given this syntax by user phi
find . | awk '!/((\.jpeg)|(\.jpg)|(\.png))$/ {print $0;}' | xargs grep "B206"
I would like to suppress the output of grep: can't open..... and find: cannot open lines from the results.sample output to be ignored:
grep: can't open ./cisc/.xdbhist
find: cannot open ./cisc/.ssh
Have you tried redirecting stderr to /dev/null ?
2>/dev/null
So the above redirects stream no.2 (which is stderr) to /dev/null. That's shell dependent, but the above should work for most. Because find and grep are different processes, you may have to do it for both, or (perhaps) execute in a subshell. e.g.
find ... 2>/dev/null | xargs grep ... 2>/dev/null
Here's a reference to some documentation on bash redirection. Unless you're using csh, this should work for most.
The option flag grep -s will suppress these messages for the grep command