Am I constructing this properly? I can't figure how to debug this.
Basically, I'm trying to pass in a text file (login.info):
foo
bar
To this shell script to be used as parameters like so:
#/usr/bin/ksh
#Base dir
BASEDIR=/home/scripts
export BASEDIR;
#Key
KEY=$BASEDIR/login.info
export KEY;
IFS="
"
arr=( $(<$KEY) )
echo "username=${arr[0]} password=${arr[1]}"
Getting this error:
./tst.sh[12]: Syntax error at line 12 : `(' is not expected.
It seems like your version of ksh doesn't understand (...) in array assignment. Maybe this will work better:
set -A arr $(cat $KEY)
Related
Hi I'm trying to make a function which should get a text file and then do some things on it and then echo. But when I try to execute it, it says syntax error near unexpected token `"$cat"'
#!/bin/usr/bash
cat=$(< cat_dialogue.txt)
function test_cat (){
echo $1
}
test_cat($cat)
desired output:
>meow meow
Your program may look like the following. Note all differences. Check your scripts with shellcheck.
#!/usr/bin/env bash
cat=$(< cat_dialogue.txt)
test_cat() {
echo "$1"
}
test_cat "$cat"
Here is an example BASH function that strips a branchname:
#create function
function strip () {
#create local variable that takes input and fills $TEXT
local TEXT=$1
#stips the branch number from the branchname
echo $TEXT | sed 's/-[0-9]*//2'
}
strip "testbranch-12345-28796"
hope it helps :) also check the BASH documentation as mentioned by #joshmeranda
I'm trying to include a bash script in an AWS SSM Document, via the Terraform templatefile function. In the aws:runShellScript section of the SSM document, I have a Bash for loop with an # sign that seems to be creating an error during terraform validate.
Version of terraform: 0.13.5
Inside main.tf file:
resource "aws_ssm_document" "magical_document" {
name = "magical_ssm_doc"
document_type = "Command"
document_format = "YAML"
target_type = "/AWS::EC2::Instance"
content = templatefile(
"${path.module}/ssm-doc.yml",
{
Foo: var.foo
}
)
}
Inside my ssm-doc.yaml file, I loop through an array:
for i in "$\{arr[#]\}"; do
if test -f "$i" ; then
echo "[monitor://$i]" >> $f
echo "disabled=0" >> $f
echo "index=$INDEX" >> $f
fi
done
Error:
Error: Error in function call
Call to function "templatefile" failed:
./ssm-doc.yml:1,18-19: Invalid character;
This character is not used within the language., and 1 other diagnostic(s).
I tried escaping the # symbol, like \#, but it didn't help. How do I
Although the error is pointing to the # symbol as being the cause of the error, it's the ${ } that's causing the problem, because this is Terraform interpolation syntax, and it applies to templatefiles too. As the docs say:
The template syntax is the same as for string templates in the main Terraform language, including interpolation sequences delimited with ${ ... }.
And the way to escape interpolation syntax in Terraform is with a double dollar sign.
for i in "$${arr[#]}"; do
if test -f "$i" ; then
echo "[monitor://$i]" >> $f
echo "disabled=0" >> $f
echo "index=$INDEX" >> $f
fi
done
The interpolation syntax is useful with templatefile if you're trying to pass in an argument, such as, in the question Foo. This argument could be accessed within the yaml file as ${Foo}.
By the way, although this article didn't give the answer to this exact issue, it helped me get a deeper appreciation for all the work Terraform is doing to handle different languages via the templatefile function. It had some cool tricks for doing replacements to escape for different scenarios.
I have a nextflow script that creates a variable from a text file, and I need to pass the value of that variable to a command line order (which is a bioconda package). Those two processes happen inside the "script" part. I have tried to call the variable using the '$' symbol without any results, I think because using that symbol in the script part of a nextflow script is for calling variables defined in the input part.
To make myself clearer, here is a code sample of what I'm trying to achieve:
params.gz_file = '/path/to/file.gz'
params.fa_file = '/path/to/file.fa'
params.output_dir = '/path/to/outdir'
input_file = file(params.gz_file)
fasta_file = file(params.fa_file)
process foo {
//publishDir "${params.output_dir}", mode: 'copy',
input:
path file from input_file
path fasta from fasta_file
output:
file ("*.html")
script:
"""
echo 123 > number.txt
parameter=`cat number.txt`
create_report $file $fasta --flanking $parameter
"""
}
By doig this the error I recieve is:
Error executing process > 'foo'
Caused by:
Unknown variable 'parameter' -- Make sure it is not misspelt and defined somewhere in the script before using it
Is there any way to call the variable parameter inside the script without Nextflow interpreting it as an input file? Thanks in advance!
The documentation re the script block is useful here:
Since Nextflow uses the same Bash syntax for variable substitutions in
strings, you need to manage them carefully depending on if you want to
evaluate a variable in the Nextflow context - or - in the Bash
environment execution.
One solution is to escape your shell (Bash) variables by prefixing them with a back-slash (\) character, like in the following example:
process foo {
script:
"""
echo 123 > number.txt
parameter="\$(cat number.txt)"
echo "\${parameter}"
"""
}
Another solution is to instead use a shell block, where dollar ($) variables are managed by your shell (Bash interpreter), while exclamation mark (!) variables are handled by Nextflow. For example:
process bar {
echo true
input:
val greeting from 'Hello', 'Hola', 'Bonjour'
shell:
'''
echo 123 > number.txt
parameter="$(cat number.txt)"
echo "!{greeting} parameter ${parameter}"
'''
}
declare "parameter" in the top 'params' section.
params.parameter="1234"
(..)
script:
"""
(...)
create_report $file $fasta --flanking ${params.parameter}
(...)
"""
(...)
and call "nextflow run" with "--parameter 87678"
I'm new at bash script writing and I have this error. I have looked everywhere to find an answer with no success. What is wrong with this script?
#!/bin/bash
exec >> /Users/k_herriage/bin/post-gererate.out 2>&1
date
set -x
mynewfile="~/bin/convert_tst.txt"
myfile=fopen($mynewfile,'w+' );
#echo $myfile
fwrite($myfile, "testing");
fclose($myfile);
exit (0)
line 7: syntax error near unexpected token `('
line 7:`myfile = fopen ( '~/bin/convert_tst.txt','w' );'
Few points:
Calling a function in bash does not require parens, it is syntactically equivalent to a command:
do_something arg1 arg2 arg3
There is no need to do open-append-close sequence in bash, it is perfectly doable with a single command:
echo "testing" >> $mynewfile; ##
>> means "append", where if it was >, it would mean "overwrite" or "discard content". (Both will create the file if it didn't exist.)
I have the following code in my ~/.bashrc:
date=$(which date)
date() {
if [[ $1 == -R || $1 == --rfc-822 ]]; then
# Output RFC-822 compliant date string.
# e.g. Wed, 16 Dec 2009 15:18:11 +0100
$date | sed "s/[^ ][^ ]*$/$($date +%z)/"
else
$date "$#"
fi
}
This works fine, as far as I can tell. Is there a reason to avoid having a variable and a function with the same name?
It's alright apart from being confusing. Besides, they are not the same:
$ date=/bin/ls
$ type date
date is hashed (/bin/date)
$ type $date
/bin/ls is /bin/ls
$ moo=foo
$ type $moo
-bash: type: foo: not found
$ function date() { true; }
$ type date
date is a function
date ()
{
true*emphasized text*
}
$ which true
/bin/true
$ type true
true is a shell builtin
Whenever you type a command, bash looks in three different places to find that command. The priority is as follows:
shell builtins (help)
shell aliases (help alias)
shell functions (help function)
hashed binaries files from $PATH ('leftmost' folders scanned first)
Variables are prefixed with a dollar sign, which makes them different from all of the above. To compare to your example: $date and date are not the same thing. So It's not really possible to have the same name for a variable and a function because they have different "namespaces".
You may find this somewhat confusing, but many scripts define "method variables" at the top of the file. e.g.
SED=/bin/sed
AWK=/usr/bin/awk
GREP/usr/local/gnu/bin/grep
The common thing to do is type the variable names in capitals. This is useful for two purposes (apart from being less confusing):
There is no $PATH
Checking that all "dependencies" are runnable
You can't really check like this:
if [ "`which binary`" ]; then echo it\'s ok to continue.. ;fi
Because which will give you an error if binary has not yet been hashed (found in a path folder).
Since you always have to use $ to dereference a variable in Bash, you're free to use any name you like.
Beware of overriding a global, though.
See also:
http://tldp.org/LDP/Bash-Beginners-Guide/html/sect_03_02.html
An alternative to using a variable: use bash's command keyword (see the manual or run help command from a prompt):
date() {
case $1 in
-R|--rfc-2822) command date ... ;;
*) command date "$#" ;;
esac
}