I am very new to programing, especially in bash.
I often run the same long command filled with many arguments each day but with different file names and one other argument, the bulk of the string remains the same. This is the case for Clonezilla server.
I want to be able to run a script that only asks for the for the portions I want to change, then substitutes those values into the original string and pass it along to the shell.
For example:
I have a set of file names: a.img b.img c.img
the command I run: drbl-ocs -b -g auto -e1 auto -e2 -r -x -j2 -sc0 -p poweroff --clients-to-wait <number value here> -l en_US.UTF-8 startdisk multicast_restore <name of file> nvme0n1
My goal is to be able to type: sudo sh myscript.sh arga argb
where "arga" is a number that replaces <number value here> and "argb" replaces <name of file> in the above string.
Thanks for any help!
The command line arguments to a script can be found in the positional parameters, parameters whose names are positive integers.
#!/bin/sh
drbl-ocs -b -g auto -e1 auto -e2 -r -x -j2 -sc0 \
-p poweroff --clients-to-wait "$1" -l en_US.UTF-8 \
startdisk multicast_restore "$2" nvme0n1
Related
As the title says, within linux how can I feed input to the bash when I do sudo bash
Lets say I have a bash script that reads the name.
The way I execute the script is through sudo using:
cat read-my-name-script.sh | sudo bash
Lets just say this is how I execute the script throught the network.
Now I want to fill the name automatically, is there a way to feed the input. I tried doing this: cat read-my-name-script.sh < name-input-file | sudo bash where the name-input-file is a file for the input that the user will be using to feed the script.
I am new to linux and learning to automate the input and wanted to create a file for input where the user can fill it and feed it to my script.
This is convoluted, but might do what you want.
sudo bash -c "$(cat read-my-name.sh)" <name-input-file
The -c says the next quoted argument are the commands to run (so, read the script as a string on the command line, instead of from a file), and the calling shell interpolates the contents of the file inside the double quotes before the sudo command gets evaluated. So if read-my-name.sh contains
#!/bin/bash
read -p "I want your name please"
then the command gets expanded into
sudo bash -c '#!/bin/bash
read -p "I want your name please"' <name-input-file
(where of course at this time the shell has actually removed the outer double quotes altogether; I put in single quotes in their place instead to show how this would look as actually executable, syntactically valid code).
I think you need that:
while read -r arg; do sudo bash read-my-name-script.sh "$arg";done <name-input-file
So each line of name-input-file will be passed as argument to sudo bash read-my-name-script.sh
If your argslist located on http server, you can do that:
while read -r arg; do sudo bash read-my-name-script.sh "$arg";done < <(wget -q -O- http://some/address/in/internet/name-input-file)
UPD
add [[ -f name-input-file ]] && readarray -t args <name-input-file
to read-my-name-script.sh
and use "${args[#]}" as arguments of command in the script.
For example echo "${args[#]}" or cmd "${args[0]}" "${args[1]}" ... "${args[100]}" in any order.
In this case you can use
wget -q -O- http://some/address/in/internet/read-my-name-script.sh | bash
for run your script with arguments from name-input-file whitout saving script to the local machine
I have a bash script like below. First it will take sorted.bam files as input and use "stringtie" tool give each sample gtf as output. Then path for each sample gtf will be given into mergelist.txt. and then use "stringtie merge" on them to get "stringtie_merged.gtf".
I totally have 40 sorted.bam files.
for sample in /path/*.sorted.bam
do
dir="/pathto/hisat2_output"
dir2="/pathto/folder"
base=`basename $sample '.sorted.bam'`
"stringtie -p 8 -G gencode.v27.primary_assembly.annotation_nochr.gtf -o ${dir2}/stringtie_output/${base}/${base}_GRCh38.gtf -l ${dir2}/stringtie_output/${base}/${base} ${dir}/${base}.sorted.bam; ls ${dir2}/stringtie_output/*/*_GRCh38.gtf > mergelist.txt; stringtie --merge -p 8 -G gencode.v27.primary_assembly.annotation_nochr.gtf -o ${dir2}/stringtie_output/stringtie_merged.gtf mergelist.txt"
done
I separated the commands with ; After running the script on all sorted.bam files and after completing the job I see that mergelist.txt has paths only for 33 sample gtf's. Which means the path for other 7 sample gtfs is missing in merge list.txt.
Is Separating the commands with ; right one or is there any other way?
The script should use one command first and with the output the paths need to be given in the text file and then use the other command.
You haven't separated the commands with semi-colons; you've invoked a single command that has semi-colons embedded in it. Consider the simple script:
"ls; pwd"
This script does not call ls followed by pwd. Instead, the shell will search the PATH looking for a file named ls; pwd (that is, a file with a semi-colon and a space in its name), probably not find one and respond with an error message. You need to remove the double quotes.
What's wrong with multiple lines, as you already have more than one line:
dir="/pathto/hisat2_output"
dir2="/pathto/folder"
for sample in /path/*.sorted.bam ;do
base=$(basename ${sample} '.sorted.bam')
stringtie -p 8 -G gencode.v27.primary_assembly.annotation_nochr.gtf -o ${dir2}/stringtie_output/${base}/${base}_GRCh38.gtf -l ${dir2}/stringtie_output/${base}/${base} ${dir}/${base}.sorted.bam
ls ${dir2}/stringtie_output/*/*_GRCh38.gtf > mergelist.txt
stringtie --merge -p 8 -G gencode.v27.primary_assembly.annotation_nochr.gtf -o ${dir2}/stringtie_output/stringtie_merged.gtf mergelist.txt
done
Anyway, I don't see the point in having the second stringtie command inside the loop, it should work fine just after.
If stringtie is able process STDIN you might get away without the mergelist.txt by using:
stringtie --merge -p 8 -G gencode.v27.primary_assembly.annotation_nochr.gtf -o ${dir2}/stringtie_output/stringtie_merged.gtf <<< $(echo ${dir2}/stringtie_output/*/*_GRCh38.gtf)
you should double quote your variables and use $( command ) instead backticks
base=$( basename $sample '.sorted.bam' ) :
you have a space in filenames??
prefer:
base=$( basename "$sample.sorted.bam" ) # with or without space
if you have spaces, you must double quote:
stringtie -p 8 \
-G gencode.v27.primary_assembly.annotation_nochr.gtf \
-o "$dir2/stringtie_output/$base/$base_GRCh38.gtf" \
-l "$dir2/stringtie_output/$base/$base" \
"$dir/$base.sorted.bam"
ls "$dir2"/stringtie_output/*/*_GRCh38.gtf > mergelist.txt
...
I am currently working on a Text-to-speech project and I need to write bash script which will, when it is called, execute two commands. If the first command returns the proper answer (if returns an answer at all), the second command will be called and executed.
My question is, how can I write a script, that executes shell commands in a specific certain file system location?
For example, I need to be in the directory /opt/text/example and execute this command:
sudo ./bin/sample_read -I ../languages/ -I ../languages -v dave -T 2 \
-i /opt/text/example.txt -F 22 -O embedded-pro -o out_file.pcm
and then to wait for the answer, then (if it is good) execute the second command.
The second command is
aplay -f S16_LE -r 22050 -c 1 out_file.pcm
This should help:
pushd /path/to/directory
my_var=$(command1)
if [ "$my_var" == "expected_result" ]; then
command2
fi
popd
You basically run command1 and store its output in my_var. Then you compare the content of $my_var with whatever you're expecting.
Also pushd <path>/popd allow you to move to a directory and back.
I don't have a lot of experience with scripting.
I have a directory that contains, among many other files, a set of *.phylip files I need to analyze with a program. I would like to automate this task. I think a loop bash shell script would be appropriate, although I could be wrong.
If I was to perform the analysis manually on one .phylip file, I would use the following command in terminal:
./raxmlHPC-SSE3 -m GTRCAT -y -s uce-5.phylip --print-identical-sequences -p 12345 -n uce-5_result
For the bash shell script, I think it would be close to:
#!/bin/sh
for i in $( ls ); do
./raxmlHPC-SSE3 -m GTRCAT -y -s uce-5.phylip --print-identical-sequences -p 12345 -n test_5 $i
done
The issue I'm aware of, but don't know how to fix, is the -s option, which specifies the input phylip file. Any suggestions on how to modify the script to do what I need done?
Try the below code:
#!/bin/bash
for i in *.phylip
do
./raxmlHPC-SSE3 -m GTRCAT -y -s "$i" --print-identical-sequences -p 12345 -n ${i%.phylip}_result
done
-s option will be passed $i which has the file name with .phylip extension in the current directory.
${i%.phylip}_result replaces the .phylip extension with _result which i guess is what you expect. (Ref: Parameter Substitution)
I'm trying to write a shell script that calls another script that then executes a rsync command.
The second script should run in its own terminal, so I use a gnome-terminal -e "..." command. One of the parameters of this script is a string containing the parameters that should be given to rsync. I put those into single quotes.
Up until here, everything worked fine until one of the rsync parameters was a directory path that contained a space. I tried numerous combinations of ',",\",\' but the script either doesn't run at all or only the first part of the path is taken.
Here's a slightly modified version of the code I'm using
gnome-terminal -t 'Rsync scheduled backup' -e "nice -10 /Scripts/BackupScript/Backup.sh 0 0 '/Scripts/BackupScript/Stamp' '/Scripts/BackupScript/test' '--dry-run -g -o -p -t -R -u --inplace --delete -r -l '\''/media/MyAndroid/Internal storage'\''' "
Within Backup.sh this command is run
rsync $5 "$path"
where the destination $path is calculated from text in Stamp.
How can I achieve these three levels of nested quotations?
These are some question I looked at just now (I've tried other sources earlier as well)
https://unix.stackexchange.com/questions/23347/wrapping-a-command-that-includes-single-and-double-quotes-for-another-command
how to make nested double quotes survive the bash interpreter?
Using multiple layers of quotes in bash
Nested quotes bash
I was unsuccessful in applying the solutions to my problem.
Here is an example. caller.sh uses gnome-terminal to execute foo.sh, which in turn prints all the arguments and then calls rsync with the first argument.
caller.sh:
#!/bin/bash
gnome-terminal -t "TEST" -e "./foo.sh 'long path' arg2 arg3"
foo.sh:
#!/bin/bash
echo $# arguments
for i; do # same as: for i in "$#"; do
echo "$i"
done
rsync "$1" "some other path"
Edit: If $1 contains several parameters to rsync, some of which are long paths, the above won't work, since bash either passes "$1" as one parameter, or $1 as multiple parameters, splitting it without regard to contained quotes.
There is (at least) one workaround, you can trick bash as follows:
caller2.sh:
#!/bin/bash
gnome-terminal -t "TEST" -e "./foo.sh '--option1 --option2 \"long path\"' arg2 arg3"
foo2.sh:
#!/bin/bash
rsync_command="rsync $1"
eval "$rsync_command"
This will do the equivalent of typing rsync --option1 --option2 "long path" on the command line.
WARNING: This hack introduces a security vulnerability, $1 can be crafted to execute multiple commands if the user has any influence whatsoever over the string content (e.g. '--option1 --option2 \"long path\"; echo YOU HAVE BEEN OWNED' will run rsync and then execute the echo command).
Did you try escaping the space in the path with "\ " (no quotes)?
gnome-terminal -t 'Rsync scheduled backup' -e "nice -10 /Scripts/BackupScript/Backup.sh 0 0 '/Scripts/BackupScript/Stamp' '/Scripts/BackupScript/test' '--dry-run -g -o -p -t -R -u --inplace --delete -r -l ''/media/MyAndroid/Internal\ storage''' "