I am using an ssh account that connects to an external server, i have downloaded through guix some software like samtools and bedtools but when i try to use them in my directory it gives me this error:
-bash: samtools: command not found
In my direcory, however, there is the directry guix.profile and if I go into the bin folder of this, I have everything I downloaded.
What am I doing wrong?
Thank you
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To run a file from the shell you need two things:
The shell must find the file
Being in the same directory does not enable the shell to find the file. You have to either supply an absolute or relative path the file, or have the directory in your PATH environment variable
In simplest terms this means instead of
$ samtools
try
$ ./samtools
The relative path tells the shell it wants that file
To run it from another directory, either use the whole absolute path, e.g. /home/yourname/samtools , or move the file into a directory that is on your $PATH
The file needs to be executable
If the file is not executable you will need
$ chmod +x ./samtools
Related
I am on Windows.
I have a script file named basics.sh and here is what it contains:
cd opt-out-exam/abduvosid_malikov/IT
mkdir made_by_my_script
cd made_by_my_script
echo "Hello World" > hello.txt
so basically, basics.sh script file is responsible to:
go to folder opt-out-exam/abduvosid_malikov/IT
make a directory made_by_my_script
create hello.txt file with content Hello World
Right now. to execute this basics.sh script, I am going to IT folder and writing this command in the terminal:
./basics.sh
In order to execute this basics.sh script, is it compulsory for me to go to IT folder
OR
is it possible to execute this script file even if I am staying in another folder (lets say currently working directory is opt-out-exam)
The first line is a change directory command followed by a relative path, not absolute. In such cases, it is important where you run the script. (An absolute path would start with the filesystem root, i. e. /.)
If you run this script from a directory (I wouldn't call it a folder in this context) where the relative path opt-out-exam/abduvosid_malikov/IT does not exist, it won't cd into it. But it will make a new directory without any problem, it will also create the file and write a line into it.
So only the first line will fail if it's run somewhere else.
UPD: As Gordon Davisson pointed out, this means that you want to check whether the directory change actually took place or not.
I have project structure like this
project
|app
|script
inside script folder, there are files such as 'run'
run file content:
#!/bin/bash
npm start
I want to run the file 'run' while I'm at the root of my project by typing only command 'run'. How would you do this?
This is sh file. In order to execute sh file on linux this file has to be executable.
Make sure this file has X permission.
If there is no x permission on file simply execute the command
chmod +x run.sh
Then execute the file by typing
./run.sh
For windows you need to create .bat file.
I'm not quite sure what you want but assuming you need a way to execute a file from node.js, you can use child_process module and child_process.exec method to start any executable.
Assuming the run file in the script directory is executable (if not, run chmod +x script/run), it can be executed by running ./script/run.
If you want to avoid having to type the name of the directory (script), you could append the script directory to your PATH environment variable. If you’re running a POSIX compatible shell (not csh or tcsh), this can be done using:
export PATH="$PATH:/path/to/project/script"
This will allow you to run any executable command in the script directory without having to specify the name of the directory, e.g., run.
NB: be sure that there aren’t common command names in the script directory as these commands can be run from any directory (including outside the project directory) after it has been added to the PATH. That’s also why I suggest adding it to the end of the PATH (so it’s the last directory that’s searched for executable commands).
I have a shell script which calls for different executables from it.
The shell script and the executables are within same directory and I am trying to run it from there. Still, on running, I get the error, "executable" not found- No file/directory exists.
What should I do???
First, You need to provide permission to the File :
chmod +x filename
Then, execute the binary file by,
./filename
The current directory is typically not in your command path, for security reasons. You need to provide the path explicitly, that is
./mycommand
instead of
mycommand
(Keep in mind, though, that this will break if you run the script from a different directly. ./mycommand is relative to the directory you run from, not the directory where the script is stored.)
I am very new to bash and using .sh files. I am trying to run the program aescrypt by calling it in a .sh file as follows (aescrypt is in the same directory as the .sh file) :
./aescrypt -e -p password file.txt
It throws the following error:
./aescrypt no such file or directory
Am I doing it wrong?
ps- I realy don't want to add it to the PATH variable as I will be using this on more than one computer that resets every day.
The location of the script is irrelevant. The thing that matters is the working directory of the process executing the script. The simplest solution really is to add aescrypt to a standard location like /bin or /usr/bin. If neither of those is acceptable, perhaps /usr/local/bin is an option. Otherwise, just use the full path of aescrypt in your script. Either hard code it, or if it is in the same directory as the script, try:
$(dirname $0)/aescrypt ...
(Note that hardcoding is more reliable, but less flexible. If you move the executable, the script will break. But using dirname will break if the script changes directory during execution.)
how about if you call the program like ./aescrypt.sh, thats the way to call an .sh programm througt the terminal
First off all, you have also to change the permissions of the file to make it executable, the way to make that is to write in the terminal, the command:
sudo chmod 765 aescrypt.sh
For that you have to be located where the file is
I have a command which is not working if I log-in to Unix using my ID.
$ db2licm -l
-bash: db2licm: command not found
But if the root gives the same command in the format ./db2licm -l, he gets valid results.
How can root publish the command so that it can be used by me also?
The ./ at the beginning of root's version of the command indicates that it is in the current directory (presumably root's home directory). To make it accessible to other users it should be moved or copied to a directory that is in their executable search path, such as /usr/bin, and its permission bits should be set so that anyone can execute it (normally mode 0755).
Usually that sort of thing should be done via the program's installer, not manually.
Your question doesn't have a single answer, because this depends on a lot of factor.
Access
First of all, in order to run a program from your account, you need to have execution privilege on the executable. You can check that you indeed have execution rights using ls -l :
$ ls -l /bin/bash
-rwxr-xr-x 1 root root 934336 2014-09-27 04:01 /bin/bash
Here, the characters rwxr-xr-x are respectively for user (root), group (root) and others access (three characters/flags for each). In my case, anybody can execute /bin/bash because the x flag is set on the last three character block (rwxr-xr-x).
Finding the executable
Secondly, the system needs to be able to find the executable. In your example, you specify that root launches the executable by prepending ./ before the command name, which basically mean "execute this program located in the current directory". Navigate anywhere else in your filesystem's tree structure and the command won't execute anymore.
To execute a command without specifying its exact path, this command must be in a directory included in your PATH environment variable. You can either add your command's directory to your PATH variable, move that command into a directory already present in your PATH variable (like /usr/bin) or create a symbolic link into a directory already present in your PATH variable, pointing to your command in its current directory.
Adding to PATH
If you'd like to add your executable's directory to your PATH environment variable on a permanent basis, you only need to modify your profile (usually ~/.bashrc if you are using bash or ~/.profile) by adding the following line :
export PATH="/the/directory/to/add:$PATH"
Note the : between your path and the $PATH variable.