How to Pass a File Argument to My Bash Script Using a Terminal Command in Linux

Pass content from .txt file as argument for bash script?

$(command) returns the output of the command. If you do $(cat some_file) it will return the text of the file. You can use it to give the content of a file as an argument doing:

cmd1 $(cat args_file)

So when you use echo $(cat file.txt), you get the same output as if you were using cat file.txt because cat sends the content of the file to echo which displays it to the standard output.

$n means argument n passed to the script ($0 being the name of the script). Here you simply have to provide one argument, the name of the file. So $2, $3 and $4 will not contain anything.

So, from the file you can only get a string with the names with $names=$(cat $1). In order to get each field separately, you can use cut:

lname=$(cut -d \  -f 1 $1)
fname=$(cut -d \  -f 2 $1)
mname=$(cut -d \  -f 3 $1)
group=$(cut -d \  -f 4 $1)

NOTES:

The symbol for comments in shell is # NOT //.

head displays the first lines of a file, head -c the first bytes. It does not cut the file.

How do I use the lines of a file as arguments of a command?

If your shell is bash (amongst others), a shortcut for $(cat afile) is $(< afile), so you'd write:

mycommand "$(< file.txt)"

Documented in the bash man page in the 'Command Substitution' section.

Alterately, have your command read from stdin, so: mycommand < file.txt

How to pass arguments to a script invoked by source command?

Create a file test.sh with the following contents:

echo "I was given $# argument(s):"
printf "%s\n" "$@"

and then source it from an interactive shell session:

$ source ./test.sh a 'b c'
I was given 2 argument(s):
a
b c

so you access the arguments just like you would do in a regular bash script, with $@ or $1, $2, $3, etc.

For comparison, run it as a regular script:

$ bash ./test.sh a 'b c'
I was given 2 argument(s):
a
b c

How to pass file path to a function as an argument in bash script?

You haven't defined arg and hence its is empty (undefined). $1 within the function will be the first argument passed.

function mate()
{ 
    arg="$1"
    samtools index "$arg"
    echo "$arg"
}

Propagate all arguments in a Bash shell script

Use "$@" instead of plain $@ if you actually wish your parameters to be passed the same.

Observe:

$ cat no_quotes.sh
#!/bin/bash
echo_args.sh $@

$ cat quotes.sh
#!/bin/bash
echo_args.sh "$@"

$ cat echo_args.sh
#!/bin/bash
echo Received: $1
echo Received: $2
echo Received: $3
echo Received: $4

$ ./no_quotes.sh first second
Received: first
Received: second
Received:
Received:

$ ./no_quotes.sh "one quoted arg"
Received: one
Received: quoted
Received: arg
Received:

$ ./quotes.sh first second
Received: first
Received: second
Received:
Received:

$ ./quotes.sh "one quoted arg"
Received: one quoted arg
Received:
Received:
Received:

using linux how can I pass the contents of a file as a parameter to an executable?

This should do the trick:

./program `cat file`

If you want the entire file content in a single argument, add double quotation (tested in bash. I think It may vary shell to shell) :

./program "`cat file`" 

How can I run a function from a script in command line?

If the script only defines the functions and does nothing else, you can first execute the script within the context of the current shell using the source or . command and then simply call the function. See help source for more information.

How do I parse command line arguments in Bash?

Bash Space-Separated (e.g., --option argument)

cat >/tmp/demo-space-separated.sh <<'EOF'
#!/bin/bash

POSITIONAL_ARGS=()

while [[ $# -gt 0 ]]; do
  case $1 in
    -e|--extension)
      EXTENSION="$2"
      shift # past argument
      shift # past value
      ;;
    -s|--searchpath)
      SEARCHPATH="$2"
      shift # past argument
      shift # past value
      ;;
    --default)
      DEFAULT=YES
      shift # past argument
      ;;
    -*|--*)
      echo "Unknown option $1"
      exit 1
      ;;
    *)
      POSITIONAL_ARGS+=("$1") # save positional arg
      shift # past argument
      ;;
  esac
done

set -- "${POSITIONAL_ARGS[@]}" # restore positional parameters

echo "FILE EXTENSION  = ${EXTENSION}"
echo "SEARCH PATH     = ${SEARCHPATH}"
echo "DEFAULT         = ${DEFAULT}"
echo "Number files in SEARCH PATH with EXTENSION:" $(ls -1 "${SEARCHPATH}"/*."${EXTENSION}" | wc -l)

if [[ -n $1 ]]; then
    echo "Last line of file specified as non-opt/last argument:"
    tail -1 "$1"
fi
EOF

chmod +x /tmp/demo-space-separated.sh

/tmp/demo-space-separated.sh -e conf -s /etc /etc/hosts

Output from copy-pasting the block above

FILE EXTENSION  = conf
SEARCH PATH     = /etc
DEFAULT         =
Number files in SEARCH PATH with EXTENSION: 14
Last line of file specified as non-opt/last argument:
#93.184.216.34    example.com

Usage

demo-space-separated.sh -e conf -s /etc /etc/hosts

---

Bash Equals-Separated (e.g., --option=argument)

cat >/tmp/demo-equals-separated.sh <<'EOF'
#!/bin/bash

for i in "$@"; do
  case $i in
    -e=*|--extension=*)
      EXTENSION="${i#*=}"
      shift # past argument=value
      ;;
    -s=*|--searchpath=*)
      SEARCHPATH="${i#*=}"
      shift # past argument=value
      ;;
    --default)
      DEFAULT=YES
      shift # past argument with no value
      ;;
    -*|--*)
      echo "Unknown option $i"
      exit 1
      ;;
    *)
      ;;
  esac
done

echo "FILE EXTENSION  = ${EXTENSION}"
echo "SEARCH PATH     = ${SEARCHPATH}"
echo "DEFAULT         = ${DEFAULT}"
echo "Number files in SEARCH PATH with EXTENSION:" $(ls -1 "${SEARCHPATH}"/*."${EXTENSION}" | wc -l)

if [[ -n $1 ]]; then
    echo "Last line of file specified as non-opt/last argument:"
    tail -1 $1
fi
EOF

chmod +x /tmp/demo-equals-separated.sh

/tmp/demo-equals-separated.sh -e=conf -s=/etc /etc/hosts

Output from copy-pasting the block above

FILE EXTENSION  = conf
SEARCH PATH     = /etc
DEFAULT         =
Number files in SEARCH PATH with EXTENSION: 14
Last line of file specified as non-opt/last argument:
#93.184.216.34    example.com

Usage

demo-equals-separated.sh -e=conf -s=/etc /etc/hosts

---

To better understand ${i#*=} search for "Substring Removal" in this guide. It is functionally equivalent to `sed 's/[^=]*=//' <<< "$i"` which calls a needless subprocess or `echo "$i" | sed 's/[^=]*=//'` which calls two needless subprocesses.

---

Using bash with getopt[s]

getopt(1) limitations (older, relatively-recent getopt versions):

• can't handle arguments that are empty strings
• can't handle arguments with embedded whitespace

More recent getopt versions don't have these limitations. For more information, see these docs.

---

POSIX getopts

Additionally, the POSIX shell and others offer getopts which doen't have these limitations. I've included a simplistic getopts example.

cat >/tmp/demo-getopts.sh <<'EOF'
#!/bin/sh

# A POSIX variable
OPTIND=1         # Reset in case getopts has been used previously in the shell.

# Initialize our own variables:
output_file=""
verbose=0

while getopts "h?vf:" opt; do
  case "$opt" in
    h|\?)
      show_help
      exit 0
      ;;
    v)  verbose=1
      ;;
    f)  output_file=$OPTARG
      ;;
  esac
done

shift $((OPTIND-1))

[ "${1:-}" = "--" ] && shift

echo "verbose=$verbose, output_file='$output_file', Leftovers: $@"
EOF

chmod +x /tmp/demo-getopts.sh

/tmp/demo-getopts.sh -vf /etc/hosts foo bar

Output from copy-pasting the block above

verbose=1, output_file='/etc/hosts', Leftovers: foo bar

Usage

demo-getopts.sh -vf /etc/hosts foo bar

The advantages of getopts are:

1. It's more portable, and will work in other shells like dash.
2. It can handle multiple single options like -vf filename in the typical Unix way, automatically.

The disadvantage of getopts is that it can only handle short options (-h, not --help) without additional code.

There is a getopts tutorial which explains what all of the syntax and variables mean. In bash, there is also help getopts, which might be informative.

Calling one Bash script from another Script passing it arguments with quotes and spaces

Quote your args in Testscript 1:

echo "TestScript1 Arguments:"
echo "$1"
echo "$2"
echo "$#"
./testscript2 "$1" "$2"

---

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