Questions tagged [bash]

Questions specific to GNU’s Bourne Again SHell, as opposed to other Bourne/POSIX shells. For questions about Unix shells in general, use the /shell tag instead. For shell scripts with errors/syntax errors, please check them with the shellcheck program (or in the web shellcheck server at https://shellcheck.net) before posting here.

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1
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1answer
27 views

/bin/sh evaluates string while Bash does not

When running the script below, I get two different outputs, depending on whether or not the shell used is sh or bash: regex(){ echo 's/\(.* \)\(!\{0,1\}\)has(/\1\2MOCK_has(/g' } replace_builtins(...
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0answers
26 views

I could not execute my bash shell script -stat is not working

Script: #!/bin/bash USER=$(stat -c '%U' /home/user/Desktop/user_info.sh) I would like to display the name of user who had created the script, but I'm receiving this error: stat: cannot statx '/...
2
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1answer
36 views

Shell parameter expansion on command line does not work in bash script [duplicate]

Consider the following GNU shell parameter expansion on a bash command line, which is explained here: $ a='hello world example' $ echo ${a//+( )/_} hello_world_example However, that very same ...
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23 views

How to change integer in bash script according to written .dat filenames

In my bash script, I want to update a string according to new written filenames with .dat format. Here is what I am trying to do: For example, I use a file named blabla_3200.dat in my bash script, ...
3
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3answers
55 views

Find all executable files excluding certain directories

I'm looking to find all executable files that are NOT in my $PATH. Currently I'm doing this find / \( -path "/opt" -prune -o -path "/var" -prune -o -path "/bin" -prune -o ...
4
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2answers
63 views

Why does quoting not protect filenames that start with “-” against mis-interpretation?

This might be a ridiculous post, but let's say we have a file called -|h4k3r|- , why doesn't this quoting work? cat '-|h4k3r|-' I thought single quotes remove meaning of all special characters? ...
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0answers
12 views

How to have `SPACE: magic-space` in ~/.inputrc without breaking Python 3 REPL?

If I put SPACE: magic-space in my ~/.inputrc file for configuring Readline, then I cannot enter SPACEs in python3 REPL (v3.8.7) How can I use SPACE: magic-space in my ~/.inputrc without breaking ...
1
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1answer
27 views

Print variable value in echo statement

How to pass the variable value in echo statement? testvar="actualvalue" echo 'testing "${testvar}", "testing", "testing" ;' Expected output: testing "...
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0answers
42 views

bash: ls: command not found [duplicate]

I'm using VMWare, and running debian and whenever I run a new terminal my commands like "ls" seem to be lost. I've tried the solutions listed here for instance: https://apple.stackexchange....
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0answers
10 views

Perform loop in HPC within multiple subdirectories one after another

I know this is a repeated question, but none of the suggestions I saw kinda fit what I wanted. I'm working with an HPC cluster that has different modules to perform different actions for high ...
3
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3answers
136 views

How to assign two variables in a single for loop?

I have been running roary pangenome pipeline, where I need to write a script in for loop, For example I have a gff files as follows, a.gff b.gff 5.gff 101.gff clustered_proteins I need to run a ...
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0answers
38 views

Exporting environment variables in `.profile` with a bash and-list construct

I am using gdm3 as my login manager. Upon login, all the PATH modifications in my .profile are set and exported correctly. For example, lines like these below work fine: if [ -d "$HOME/bin" ]...
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0answers
27 views

Is it possible to delete bad whitespace in multiple files of a project?

I have many software projects, in different languages. They are all in git repos. I normally use vim to program. Recently, I enabled the vim spacehi plugin, and started noticing just how much bad ...
1
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3answers
81 views

Pipe result to multiple commands without writing on screen

I have a very big zip file (~10 GB) which I want to unzip, and the result has to be passed to two commands. The results of both subsequent commands have to be appended to a file, and Currently, I run ...
0
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0answers
25 views

User defined function does not override system command

I would like to decorate (python-like) the conda command. To do so, I tried the solution proposed in this Stack Exchange post. It works to decorate other functions that I defined into my ~/.bashrc, ...
4
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3answers
555 views

How to fix infinite bash loop (bashrc + bash_profile) when ssh-ing into an ec2 server?

I mistakenly have source .bash_profile in the bashrc file and vice versa. Now when I tried to ssh into the machine (ec2), it will stuck at loading bash and get connection closed in a second. Is there ...
4
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1answer
309 views

Grep command not returning expected results for testing

I am attempting to do a comparison before I append conditions to a profile.d file A grep -F 'TMOUT' /etc/profile.d/sh.local shows me exactly what I expect however the test is always showing true. In ...
0
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1answer
18 views

Kill tmux session after script is done

I have a bash script that I use to run a script inside a tmux session. It looks like this: #!/bin/bash session="myjob" tmux new-session -d -s $session tmux send-keys 'myscript' 'C-m' The ...
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0answers
19 views

precedence of dircolors

I have a file on 2 servers. The problem is that ls --color do not display them the same way. My file is a binary executable (with +x) and also have a LinuxCapability (CAP_NET_RAW). ls --color on the ...
0
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0answers
44 views

Unable to understand the following shell script

I am trying to run a demo example given in the tutorial for running codes on a cluster computer. Below is the example but I am unable to understand most of the statements - #BSUB -L /bin/bash #BSUB -J ...
3
votes
1answer
208 views

How to expand variables inside read?

In a remote CentOS with Bash 5.0.17(1) where I am the only user via SSH I have executed read web_application_root with: $HOME/www or with: ${HOME}/www or with: "${HOME}"/www or with: &...
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0answers
36 views

Bash simple process respawning daemon

Here is a script called simpled.sh: #!/bin/bash # if top is terminated i want it re-spawn while :; do top & tpid=$! ...
0
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2answers
29 views

Deleting files by checking file size in bash

I have two directories with files, one is the "source", the other "destination". I would like to have a script that checks file in "source". If file name and size matches ...
0
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0answers
24 views

how to exit in bash script from ProFTPD via netcat after some copy operations

I am connecting to a proftpd server via netcat nc 10.10.239.150 21 Then I am doing some copy operations like "The mod_copy module implements SITE CPFR and SITE CPTO commands" After "...
1
vote
1answer
34 views

Can't use variables while feeding commands to bash through stdin

I need to run a small shell script using C popen call (which calls sh -c '<command>'). I can't get my script to work. I isolated the issue to this snippet: #!/bin/bash sh -c 'bash -xev -s <&...
2
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1answer
88 views

Debian 10: Setting PATH variable inside .profile does not work

I'm currently running Debian 10 Xfce and I would like to update my PATH variable to include /opt/bin and ~/.local/bin. As per these - 1 2 answers, I put the following lines in my ~/.profile file: if [ ...
0
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1answer
23 views

write to file with echo/printf [duplicate]

How to write the following to a file printf "*\n!.gitignore\n" > $datadir/.gitignore -bash: !.gitignore\n: event not found
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0answers
23 views

Add WiFi Networks via Command Line

I have some known WiFi networks that I'd like to autoconnect to on Chromium OS. I know that I can add WiFi networks by SSID and password via the GUI, but I'd rather this be done via command line as ...
0
votes
1answer
36 views

bash pass “if” conditions as arguments?

is it possible to pass conditions that are checked in if clauses (https://tldp.org/LDP/Bash-Beginners-Guide/html/sect_07_01.html) as arguments to a function? The following does not work. ...
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0answers
26 views

Use parallel to speed up a recursive shell max function?

I needed a max function, to find the highest value in an array (of 350 int values), and being a friend of recursion, I tried a recursive approach: max () { len=$# a=$1 b=$2 case $len ...
0
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1answer
24 views

Store sqlite3 table names in a bash array

I'm trying to figure out how to store the table names containing a geometry field from a sqlite3 database into a bash array that I can loop on afterwards. Here's what I have but it's empty for the ...
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0answers
25 views

Check if a host exists in ssh/known_hosts in a bash script; add a host only if it doesn't exist

I'm aware about how to check if a host exists in known_hosts ssh-keygen -F github.com I need to do it in a script. Namely, if a host exists - do nothing, otherwise - add it. How would I do it?
3
votes
1answer
79 views

How to not interpret string as command

I'm writing a script which should copy a client system and change some lines in a file. There is a source file which has a line like: $DB_HOST = "LegitDbHost"; And the destination file has ...
4
votes
1answer
331 views

why does tee refuse to work when launched remotely via ssh?

Where is my error? As an answer to a Stackexchange question, I tar a directory and transfer the archive to a remote system, where tee both deposits in a file and pipes it to tar for unpacking. My ...
0
votes
1answer
31 views

Declare non environment variables and print them directly afterwards

I want to declare a few non environment variables and print them directly afterwards. For example: read domain && web_application_root="${HOME}/www" && domain_dir="${...
3
votes
1answer
133 views

#!_ perl is identical for #!/usr/bin/env perl?

My env says: _=/usr/bin/env and I have a question regarding the shebang, will the entry be correct if I type: #!_ perl ?
0
votes
1answer
50 views

how can I remove specific columns and sort

I have a data like this JW_ID ECK number B number T Number M K12 Conc(%) Yield(uM) Yield(ug/ml) JW0002 ECK0003 b0003 thrB thrB 32 2.3 78 JW0003 ...
0
votes
1answer
46 views

awk: how to extract strings directly into bash array?

let's say I have this: ARRAY=() NUM_EXTRACTED=$(cat somefile.txt | awk '/magic/{i++; print > i "_extracted.txt"} END {print i}') for (( i=1; i<=$NUM_EXTRACTED; i++)); do LINE=$(cat &...
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0answers
13 views

Why does the history command show few commands and the .bash_history file is short even if HISTFILESIZE and HISTSIZE are ridiculously high?

I've read these two questions and the accepted answers on StackOverflow: Unlimited Bash History bash HISTSIZE vs. HISTFILESIZE? However, I still don't understand why in any bash session I can see ...
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0answers
34 views

What does echo asterick (*) mean in bash shell [duplicate]

Why does echo * prints all the files in the pwd, and with a leading dash (-)?
-1
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2answers
48 views

How to merge two files based on the matching of one column?

I have two files, B.csv: 1,AD 2,AB 3,AC 5,AF 7,AE and C.csv: 1,x 3,z 5,y How do I get this output: 1,AD,x 2,AB, 3,AC,z 5,AF,y 7,AE, by matching the common column 1 in both of the files?
0
votes
1answer
22 views

In which file should it be best to put full debugging commands such as set -x (and also && complete -r)?

CentOS on a shared website hosting environment (I don't know the version) with Bash 5.0.17(1). I use set -x to get maximal trace which often helps me handle errors; I normally use this command ...
-1
votes
2answers
38 views

How to match regular expression for below string in bash?

Below string I need to compare conditional operator. So only if 81.1.4_r4345 doing some operation or else matching with “done” then execute some operation. vasanth-releases_81.1.4_r4345.tar.gz ...
0
votes
1answer
31 views

Example wanted: here string to fd

man bash features this redirection: [n]<<<word. With this explanation: The result is supplied as a single string, with a newline appended, to the command on its standard input (or file ...
0
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2answers
53 views

XOR in shell globs

Recently my hosting provider changed my public_html directory's name to www without me knowing it so this variable declaration web_application_root="${HOME}/public_html" no longer works. For ...
1
vote
1answer
17 views

Storing for loop value in specific variable

so I've this shell script, where i take simple user input of IPs and store that into a text file. MasterNode(){ echo "Enter number of Master Node below" read -r numESM for ((i=1; i<=${...
0
votes
1answer
27 views

In bash how do I set my path so that it finds the version of a command within the nearest relative path?

I have multiple git repositories on my machine. Each has a subdirectory called scripts/ with a script called cleancode.py. Using bash (really git-bash), when I run cleancode.py I want it to execute ...
0
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0answers
15 views

/usr/share/bash-completion/bash_completion parse error

I am facing an error when run $ source ~/.bashrc. The error is /usr/share/bash-completion/bash_completion:1512: parse error near `|'. bash_completion file (the first line is 1512) : if ! [[ &...
1
vote
2answers
30 views

change permissions with find for specific files

Let's say I have a directory called permissions, that contains several files with different access rights. What I want to do is if a file has access rights for others category, I want to accord the ...
0
votes
1answer
40 views

How to use BASH variable for AWK filtering results

I have this script, I'm getting first letter of my directory name, and I wan't to get directory names that start with the same letter and write to textfile. The for loop is looping list of directory ...

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