I have a string that contains a command that I want to execute in a bash script. How can I do that?
Sorry for so basic question but I am new in bash.
This is my code:
echo "What is the path to save the result files?"
read out_path
end_cm1=$"fastqc -o "$out_path$" --noextract -fastq "$files1
And I want to execute the instruction that is in the end_cm1 variable.
First, you don't have to put that command in a string at all: you can just do this:
fastqc -o "$out_path" --noextract -fastq $files1
(And I'd recommend putting $out_path in quotes here in case the path has a space in it. I've not put $files1 in quotes because your variable is plural so I assume there's more than one; you should beware spaces in those file names also.)
Second, the answer to the question you asked is eval:
eval $end_cm1
You just have a slight syntax issue in your string:
end_cm1="fastqc -o $out_path --noextract -fastq $files1"
$enc_cm1
Having said that, #ams is right about not needing to assign this
to a string in the first place, and about the risks involved
in not quoting $files1.
Related
I have a text file called OPTIONS.txt storing all flags of Makefile:
arg1=foo arg2="-foo -bar"
I want to pass all flags in this file to make. However,
make `cat OPTIONS.txt`
fails with make: invalid option -- 'a'. It seems that shell interprets it as:
make arg1=foo arg2="-foo -bar"
^argv[1] ^argv[2] ^argv[3]
Is there any way to make it interpreted as:
make arg1=foo arg2="-foo -bar"
^argv[1] ^--------argv[2]
Since you control the options file, store the options one per line:
arg1=foo
arg2="-foo -bar"
Then in the shell, you'll read the file into an array, one element per line:
readarray -t opts < OPTIONS.txt
Now you can invoke make and keep the options whole:
make "${opts[#]}"
If you want the shell to interpret quotes after backtick expansion you need to use eval, like this:
eval make `cat OPTIONS.txt`
however just be aware that this evaluates everything, so if you have quoted content outside of the backticks you'll get the same issue:
eval make `cat OPTIONS.txt` arg4="one two"
will give an error. You'd have to double-quote the arg4, something like this:
eval make `cat OPTIONS.txt` arg4='"one two"'
In general it's tricky to do stuff like this from the command line, outside of scripts.
ETA
The real problem here is that we don't have a set of requirements. Why do you want to put these into a file, and what kind of things are you adding; are they only makefile variable assignments, or are there other make options here as well such as -k or similar?
IF the OP controls (can change) the format of the file AND the file contains content only used by make AND the OP doesn't care about the variables being command line assignments vs. regular assignments AND there are only variable assignments and not other options, then they can just (a) put each variable assignment on its own line, (b) remove all quotes, and (c) use include OPTIONS.txt from inside the makefile to "import" them.
I need to pass further original parameters and also I want to add some others. Something like this:
#!/bin/bash
params="-D FOREGROUND"
params+=" -c Include conf/dev.conf"
/usr/local/apache/bin/apachectl $params "$#"
This code above don't work as expected if params contains of two or more parameters, it treated as one parameter.
The code in your example should work if the following command is valid when executed at the command line written exactly like this :
/usr/local/apache/bin/apachectl -D FOREGROUND -c Include conf/dev.conf "$#"
A quick web search leads me to think that what you want is this (notice the additional double quotes) :
/usr/local/apache/bin/apachectl -D FOREGROUND -c "Include conf/dev.conf" "$#"
Here is how to achieve that simply and reliably with arrays, in a way that sidesteps "quoting inside quotes" issues:
#!/bin/bash
declare -a params=()
params+=(-D FOREGROUND)
params+=(-c "Include conf/dev.conf")
/usr/local/apache/bin/apachectl "${params[#]}" "$#"
The params array contains 4 strings ("-D", "FOREGROUND", "-c" and "Include conf/dev/conf"). The array expansion ("${params[#]}", note that the double quotes are important here) expands them to these 4 strings, as if you had written them with double quotes around them (i.e. without further word splitting).
Using arrays with this kind of expansion is a flexible and reliable to way to build commands and then execute them with a simple expansion.
If the issue is the space in the parameter "-c Include conf/dev.conf" then you could just use a backspace to preserve the space character:
params+="-c Include\ conf/dev.conf"
This question already has answers here:
Why a variable assignment replaces tabs with spaces
(2 answers)
Closed 7 years ago.
I'm having some troubles with the printf function in bash.
I wrote a little script on which I pass a name and two letters (such as "sh", "py", "ht") and it creates a file in the current working directory named "name.extension".
For instance, if I execute seed test py a file named test.py is created in the current working dir with the shebang #!/usr/bin/python3.
So far, so good, nothing fancy: I'm learning shell scripting and I thought this could be a simple exercise to test the knowledge gained so far.
The problem is when I want to create an HTML file. This is the function that I use:
creaHtml(){
head='<!--DOCTYPE html-->\n<html>\n\t<head>\n\t\t<meta charset=\"UTF-8\">\n\t</head>\n\t<body>\n\t</body>\n</html>'
percorso=$CARTELLA_CORRENTE/$NOME_FILE.html
printf $head>>$percorso
chmod 755 $percorso
}
If I run, for instance, seed test ht the correct function (creaHtml) is called, test.html is created but if I try to look into it I only see:
<!--DOCTYPE
And nothing else.
This is the trace for that function:
[sviluppo:~/bin]$ seed test ht
+ creaHtml
+ head='<!--DOCTYPE html-->\n<html>\n\t<head>\n\t\t<meta charset=\"UTF-8\">\n\t</head>\n\t<body>\n\t</body>\n</html>'
+ percorso=/home/sviluppo/bin/test.html
+ printf '<!--DOCTYPE' 'html-->\n<html>\n\t<head>\n\t\t<meta' 'charset=\"UTF-8\">\n\t</head>\n\t<body>\n\t</body>\n</html>'
+ chmod 755 /home/sviluppo/bin/test.html
+ set +x
However, if I try to run printf '<!--DOCTYPE html-->\n<html>\n\t<head>\n\t\t<meta charset=\"UTF-8\">\n\t</head>\n\t<body>\n\t</body>\n</html>' from the terminal, I see the correct output: the "skeleton" of an HTML file neatly displayed with indentation and everything. What am I missing here?
Try echo -e instead of printf. printf is for printing formatted strings. Since you didn't protect $head with quotes, bash splits the string to form the command. The first word (before first white space) forms the format string. The rest are just arguments for things you didn't specify to print.
echo -e "$head" > "$percorso"
The -e evaluates your \n into newlines. I changed your >> to > since it looks like you want this to be the whole file, rather than append to any existing file you might have.
You have to be careful with quotes in bash. One thing can become many things. This actually makes it more powerful, but it can be confusing for people learning. Notice that I also put the file name "$percorso" in double quotes too. This evaluates the variable and makes sure that it ends up as one thing. If you use single quotes, it will be one word, but not evaluated. Unlike Python, there is a big difference between single and double quotes.
If you want to use printf for compatibility as #chepner pointed out, just be sure to quote it:
printf "$head" > "$percorso"
Actually that is much simpler anyway.
I read this question: Makefile: $subst in dependency list, but I still can't make my shell script work correctly.
I have a makefile with a line with the contents:
##public_detailed#|test_create|Syntax: commoncmdsyntax test_create test_name=<test-name>
A target runs a multiline bash script, where the commoncmdsyntax must be replaced by a string containing words and spaces.
In the script, I use cut to assign to a variable desc the following string:
Syntax: commoncmdsyntax test_create test_name=<test-name>
The problem is that commoncmdsyntax is not replaced by new text here:
$(subst commoncmdsyntax,new text,$$desc)
I also tried to replace it by a single word, like XX, but it also does not work.
The subst function (as in $(subst commoncmdsyntax,new text,$$desc)) is a Make function, so Make will perform the substitution before running any rule and therefore before your script assigns a value to desc. So even if secondary expansion worked the way you seem to think it will, this approach would still fail.
If you want to perform a substitution within something made by a shell script (in a recipe), the sensible way is to do so within the recipe:
echo $dest | sed 's/commoncmdsyntax/new text/'
We can give you a more detailed solution if you give us a minimal complete example of the problem.
I have written a small script with which I take the name of a File.
#objectname
echo "objectname"
read ON
Can't get simpler.
I do some processing with the file I get.
gpg -c --no-use-agent "$ON"
For example if I have a file a.exe --> It will encrypt it and give me a file with a different md5 and an extension. Now, the file looks this way a.exe.gpg
Now, if I give it a bind the name of the file directly.
like this for example:
Taken from : this link
# This works
fileName='a.exe.gpg'
md5sum=$(md5sum ${fileName})
echo $md5sum
it returns it properly.
What if I want to do it dynamically.
This is what I tried:
#does not work
gpg -c --no-use-agent "$ON"
fileName= `$ON.gpg`
md5sum= $(md5sum ${fileName})
echo $md5sum
I get this bug here: upload.sh: 1: upload.sh: Fire.exe.gpg: not found and the program does not exit.
May I ask where exactly is the mistake I am doing?
The error is here:
fileName= `$ON.gpg`
There should be no space after =. (Also look at the next line.)
You used back-quotes, which execute $ON.gpg rather than simply evaluating it. Back-quotes are the same as $(...) but less elegant. Use double-quotes for this.
Read Greg's wiki entry on quotes for an ultra-detailed explanation with opinionated commentary. :-)
Be careful when making assignments in shell script. Don't use spaces in any sides of the operator=. Try the following:
fileName="$ON.gpg"
md5sum=$(md5sum ${fileName})
Note that the variable and the assignment operator= are together with no space.
Also, when you use backticks as `expression`, it will be executed by shell like using $(expression), as pointed by user ghoti.
You goofed on fixing the filename.
fileName="$ON.gpg"