I quickly searched for this before posting, but could not find any similar posts. Let me know if they exist.
The commands being executed seem very simple. A directory listing is used as the input for a function.
The directory contains a bunch of files named "epi1_mcf_0###.nii.gz"
Command-line version (bash is running when this is executed):
fslmerge -t output_file `ls epi1_mcf_0*.nii.gz`
Shell script version:
#!/bin/bash
fslmerge -t output_file `ls epi1_mcf_0*.nii.gz`
The command-line version fails, but the shell script one works perfectly.
The error message is specific to the function, but it's included anyway.
** ERROR (nifti_image_read): failed to find header file for 'epi1_mcf_0000.nii.gz'
** ERROR: nifti_image_open(epi1_mcf_0000.nii.gz): bad header info
Error: failed to open file epi1_mcf_0000.nii.gz
Cannot open volume epi1_mcf_0000.nii.gz for reading!
I have been very frustrated with this problem (less so after I figured out that there was a way to get the command to work).
Any help would be appreciated.
(Or is the general consensus that the problem should be looked for in the "fslmerge" function?)
`ls epi1_mcf_0*.nii.gz` is better written as simply epi1_mcf_0*.nii.gz. As in:
fslmerge -t output_file epi1_mcf_0*.nii.gz
The `ls` doesn't add anything.
Note: Posted as an answer instead of comment. The Markdown-lite comment parser choked on my `` `ls epi1_mcf_0*.nii.gz` `` markup.
(I mentioned this in a comment first, but I'll make an answer since it helped!)
Do you have any shell aliases defined? (Type alias) Those will affect commands typed at the command line, but not scripts.
Linux often has ls defined as ls --color. This may affect the output since the colour codes are sent as escape codes through the regular output stream. If you use ls --color=auto it will auto-detect whether its output is a terminal or not. From man ls:
By default, color is not used to distinguish types of files. That is
equivalent to using --color=none. Using the --color option without the
optional WHEN argument is equivalent to using --color=always. With
--color=auto, color codes are output only if standard output is connected to a terminal (tty).
Related
This question already has answers here:
How to trick an application into thinking its stdout is a terminal, not a pipe
(9 answers)
Closed 5 years ago.
Various bash commands I use -- fancy diffs, build scripts, etc, produce lots of color output.
When I redirect this output to a file, and then cat or less the file later, the colorization is gone -- presumably b/c the act of redirecting the output stripped out the color codes that tell the terminal to change colors.
Is there a way to capture colorized output, including the colorization?
One way to capture colorized output is with the script command. Running script will start a bash session where all of the raw output is captured to a file (named typescript by default).
Redirecting doesn't strip colors, but many commands will detect when they are sending output to a terminal, and will not produce colors by default if not. For example, on Linux ls --color=auto (which is aliased to plain ls in a lot of places) will not produce color codes if outputting to a pipe or file, but ls --color will. Many other tools have similar override flags to get them to save colorized output to a file, but it's all specific to the individual tool.
Even once you have the color codes in a file, to see them you need to use a tool that leaves them intact. less has a -r flag to show file data in "raw" mode; this displays color codes. edit: Slightly newer versions also have a -R flag which is specifically aware of color codes and displays them properly, with better support for things like line wrapping/trimming than raw mode because less can tell which things are control codes and which are actually characters going to the screen.
Inspired by the other answers, I started using script. I had to use -c to get it working though. All other answers, including tee, different script examples did not work for me.
Context:
Ubuntu 16.04
running behavior tests with behave and starting shell command during the test with python's subprocess.check_call()
Solution:
script --flush --quiet --return /tmp/ansible-output.txt --command "my-ansible-command"
Explanation for the switches:
--flush was needed, because otherwise the output is not well live-observable, coming in big chunks
--quiet supresses the own output of the script tool
-c, --command directly provides the command to execute, piping from my command to script did not work for me (no colors)
--return to make script propagate the exit code of my command so I know if my command has failed
I found that using script to preserve colors when piping to less doesn't really work (less is all messed up and on exit, bash is all messed up) because less is interactive. script seems to really mess up input coming from stdin even after exiting.
So instead of running:
script -q /dev/null cargo build | less -R
I redirect /dev/null to it before piping to less:
script -q /dev/null cargo build < /dev/null | less -R
So now script doesn't mess with stdin and gets me exactly what I want. It's the equivalent of command | less but it preserves colors while also continuing to read new content appended to the file (other methods I tried wouldn't do that).
some programs remove colorization when they realize the output is not a TTY (i.e. when you redirect them into another program). You can tell some of those to use color forcefully, and tell the pager to turn on colorization, for example use less -R
This question over on superuser helped me when my other answer (involving tee) didn't work. It involves using unbuffer to make the command think it's running from a shell.
I installed it using sudo apt install expect tcl rather than sudo apt-get install expect-dev.
I needed to use this method when redirecting the output of apt, ironically.
I use tee: pipe the command's output to teefilename and it'll keep the colour. And if you don't want to see the output on the screen (which is what tee is for: showing and redirecting output at the same time) then just send the output of tee to /dev/null:
command| teefilename> /dev/null
I have a problem regarding an alias file in /etc/profile.d/. This isn't anything important. I'm just interested why it isn't working as expected.
So basically I have the file 00-alias.sh at the path mentioned above and I wanted to make a shortcut which reads a specific line of a file. So this is my code:
alias lnn='sed -n "${1}p" < "${2}"'
With that code I should be able to perform a command like
$ lnn 4 test.txt
However, this doesn't work. I simply get the error
-bash: : No such file or directory
Now I thought, ok, maybe relative paths aren't working because the file is located at the path /etc/profile.d/00-alias.sh
So I went ahead and made a new alias like
alias pwd2='echo $(pwd)'
Then updated the profile.d with
source /etc/profile.d/00-alias.sh
And just tried pwd2 but that echoed the path I was currently in. So in theory the file can be found with the command I wrote. I still tried to pass the file to my alias with absolute path like
$ lnn 4 /var/test.txt
Still same error as above.
But, if I enter the command of the alias in the terminal like
sed -n "4p" < test.txt
It works perfectly fine. No matter if I put quotes around test.txt
And here is another weird thing: If I write
alias lnn='sed -n "${1}p" < ${2}'
without the quotes around ${2} I get the error
-bash: ${2}: ambiguous redirect
In the terminal it works just fine...
So, what am I doing wrong? Does anyone have an idea on this? I'd love to know my mistake. But as I said, this isn't a real problem as I'm just curious why bash behaves like that.
Aliases in bash do not take parameters of any form. Save the pain and use a function instead.
function lnn() {
sed -n "${1}p" < "${2}"
}
Add the function to the file 00-alias.sh and source it once before calling the function from command-line.
source /etc/profile.d/00-alias.sh
lnn 4 test.txt
See more information at BashFAQ/80: How can I make an alias that takes an argument?
You can't. Aliases in bash are extremely rudimentary, and not really suitable to any serious purpose. The bash man page even says so explicitly:
An excerpt from the GNU bash man page, about aliases
.. There is no mechanism for using arguments in the replacement text. If arguments are needed, a shell function should be used.
On a side note the problem has nothing to do with relative paths (or) so, just remember aliases are not allowed in scripts. They're only allowed in interactive shells. If you're writing a script, always use a function instead.
I'm pretty new to Bash and Linux in general. I've created a couple scripts that I would like to be able to use by typing the command, rather than the directory and the executable file. I'm using Debian Jessie if that makes a difference.
The path to one of my scripts is ~/Scripts/DIR_1/My_Script.sh while another is in ~Scripts/DIR_2/My_Other_Script.sh. I would like ALL of the scripts contained withing the Scripts directory to be indexed as commands regardless of directory/path depth.
I've appended this text to the end of my .bashrc file...
PATH=${PATH}:$(find ~/Scripts -type d | sed '/\/\\./d' | tr '\n' ':' | sed 's/:$//')
Since I'm pretty new to this kind of thing, I had to steal that line from here.
When I try to run My_Script from the command line withing a sub directory of my home folder (or anywhere else for that matter) I get My_Script: command not found
I will readily admit that I might have misunderstood the process of adding a bash script to the command line.
How do I recursively add bash scripts as commands? What is wrong with the process I'm currently using?
I think your issue is that you're not putting the .sh, that is part of your file name.
Normally, pressing tab after having typed only the first letter should complete the command up to the point where there is an ambiguity (or completely if there's none). In case of ambiguity, pressing tab a second time shows the options. So in your case, if you type My<tab><tab> you should have options My_Script.sh and My_Other_Script.sh displayed. And if you type My_Script<tab> it should complete by putting My_Script.sh
Edit
I forgot to precise that you can check the value of PATH by doing echo $PATH. This will allow you to check that the command you copied did what you wanted.
Every time I run a script using bash scriptname.sh from the command line in Debian, I get Command Not found and then the result of the script.
The script works but there is always a Command Not Found statement printed on screen for each empty line. Each blank line is resulting in a command not found.
I am running the script from the /var folder.
Here is the script:
#!/bin/bash
echo Hello World
I run it by typing the following:
bash testscript.sh
Why would this occur?
Make sure your first line is:
#!/bin/bash
Enter your path to bash if it is not /bin/bash
Try running:
dos2unix script.sh
That wil convert line endings, etc from Windows to unix format. i.e. it strips \r (CR) from line endings to change them from \r\n (CR+LF) to \n (LF).
More details about the dos2unix command (man page)
Another way to tell if your file is in dos/Win format:
cat scriptname.sh | sed 's/\r/<CR>/'
The output will look something like this:
#!/bin/sh<CR>
<CR>
echo Hello World<CR>
<CR>
This will output the entire file text with <CR> displayed for each \r character in the file.
You can use bash -x scriptname.sh to trace it.
I also ran into a similar issue. The issue seems to be permissions. If you do an ls -l, you may be able to identify that your file may NOT have the execute bit turned on. This will NOT allow the script to execute. :)
As #artooro added in comment:
To fix that issue run chmod +x testscript.sh
This might be trivial and not related to the OP's question, but I often made this mistaken at the beginning when I was learning scripting
VAR_NAME = $(hostname)
echo "the hostname is ${VAR_NAME}"
This will produce 'command not found' response. The correct way is to eliminate the spaces
VAR_NAME=$(hostname)
On Bash for Windows I've tried incorrectly to run
run_me.sh
without ./ at the beginning and got the same error.
For people with Windows background the correct form looks redundant:
./run_me.sh
If the script does its job (relatively) well, then it's running okay. Your problem is probably a single line in the file referencing a program that's either not on the path, not installed, misspelled, or something similar.
One way is to place a set -x at the top of your script or run it with bash -x instead of just bash - this will output the lines before executing them and you usually just need to look at the command output immediately before the error to see what's causing the problem
If, as you say, it's the blank lines causing the problems, you might want to check what's actaully in them. Run:
od -xcb testscript.sh
and make sure there's no "invisible" funny characters like the CTRL-M (carriage return) you may get by using a Windows-type editor.
use dos2unix on your script file.
for executing that you must provide full path of that
for example
/home/Manuel/mywrittenscript
Try chmod u+x testscript.sh
I know it from here:
http://www.linuxquestions.org/questions/red-hat-31/running-shell-script-command-not-found-202062/
If you have Notepad++ and you get this .sh Error Message: "command not found"
or this autoconf Error Message "line 615:
../../autoconf/bin/autom4te: No such file or directory".
On your Notepad++, Go to Edit -> EOL Conversion then check Macinthos(CR).
This will edit your files. I also encourage to check all files with this command,
because soon such an error will occur.
Had the same problem. Unfortunately
dos2unix winfile.sh
bash: dos2unix: command not found
so I did this to convert.
awk '{ sub("\r$", ""); print }' winfile.sh > unixfile.sh
and then
bash unixfile.sh
Problems with running scripts may also be connected to bad formatting of multi-line commands, for example if you have a whitespace character after line-breaking "\". E.g. this:
./run_me.sh \
--with-some parameter
(please note the extra space after "\") will cause problems, but when you remove that space, it will run perfectly fine.
I was also having some of the Cannot execute command. Everything looked correct, but in fact I was having a non-breakable space right before my command which was ofcourse impossible to spot with the naked eye:
if [[ "true" ]]; then
highlight --syntax js "var i = 0;"
fi
Which, in Vim, looked like:
if [[ "true" ]]; then
highlight --syntax js "var i = 0;"
fi
Only after running the Bash script checker shellcheck did I find the problem.
I ran into this today, absentmindedly copying the dollar command prompt $ (ahead of a command string) into the script.
Make sure you haven´t override the 'PATH' variable by mistake like this:
#!/bin/bash
PATH="/home/user/Pictures/"; # do NOT do this
This was my mistake.
Add the current directory ( . ) to PATH to be able to execute a script, just by typing in its name, that resides in the current directory:
PATH=.:$PATH
You may want to update you .bashrc and .bash_profile files with aliases to recognize the command you are entering.
.bashrc and .bash_profile files are hidden files probably located on your C: drive where you save your program files.
Can I execute command within another command in UNIX shells?
If impossible, can I use the output of the previous command as the input of next command, as in:
command x then command y,
where in command y I want use the output of command x?
You can use the backquotes for this.
For example this will cat the file.txt
cat `echo file.txt`
And this will print the date
echo the date is `date`
The code between back-quotes will be executed and be replaced by its result.
You can do something like;
x=$(grep $(dirname "$path") file)
here dirname "$path" will run first and its result will be substituted and then grep will run, searching for the result of dirname in the file
What exactly are you trying to do? It's not clear from the commands you are executing. Perhaps if you describe what you're looking for we can point you in the right direction. If you want to execute a command over a range of file (or directory) names returned by the "find" command, Colin is correct, you need to look at the "-exec" option of "find". If you're looking to execute a command over a bunch of arguments listed in a file or coming from stdin, you need to check out the "xargs" commands. If you want to put the output of a single command on to the command line of another command, then using "$(command)" (or 'command' [replace the ' with a backquote]) will do the job. There's a lot of ways to do this, but without knowing what it is you're trying it's hard to be more helpful.
Here is an example where I have used nested system commands.
I had run "ls -ltr" on top of find command. And it executes
it serially on the find output.
ls -ltr $(find . -name "srvm.jar")