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
I need to copy a directory from a remote host to my local laptop. I have seen from previous posts that in order to do that I type,
scp -r user#remotehost.ac.uk:/path/to/dirtory/ /home/user/Desktop
But I get,
/home/user/Desktop: No such file or directory
why is that happening?
When you do:
scp -r user#remotehost.ac.uk:/path/to/dirtory/ /home/user/Desktop
The following will happen:
the command will connect to user#remotehost.ac.uk
it will try to copy this folder "/path/to/dirtory/" to the specified location "/home/user/Desktop"
The thing is that folder "/home/user/Desktop" must exist on your computer. You should check that the "/user/" actually exists, maybe you mistyped.
I am working on a script to copy a custom user profile over to the default. Part of the script uses rsync to copy the contents of the customized profile, named "profile" to the default profile located in: /System/Library/User Template/English.lproj. Each time I run the command interactively, it fails indicating "No such file or directory." I can browse to the directory in the Finder. I can navigate to the directory via the terminal. Why can't rsync find it? Here is the command:
rsync -av /Users/profile/* /System/Library/User\ Template/English.lproj
I tried a similar approach using cp -R instead of rsync and got a whole bunch of file not found error messages. Using the cd command to that same path also fails. I can step through each individual directory and arrive at English.lproj but I can't do it in one command. Any ideas where I am going wrong with my command?
Thanks
Jason
I feel like I am missing some fundamental concept as to how the .ssh directory works in windows. I have had no issues when working in OSX/Linux like I am having now. My end goal is simply to move my existing ssh key into the default ~/.ssh directory, and update the config if I so choose (you know, normal ssh key related tasks).
However, any time I have tried to move my existing SSH key over to the ~/.ssh directory, or open it, or even create a config file I just get the following error (in either gitbash, puttygen, etc...):
Puttygen (saving the key to disk):
Overwrite existing file C:\Users\me\.ssh?
or in gitbash (attempting to do anything, including just create the config file):
touch: creating `/c/Users/me/.ssh/config': No such file or directory
cd ~/.ssh
sh.exe": cd: /c/Users/me/.ssh: Not a directory
What am I missing/not understanding?
Kind Regards,
u353
This answer for Windows environment:
At the beginning, Windows didn't have .ssh folder.
Create an ssh key file pair like this (ssh-keygen is nowadays a native Windows command, that comes with Windows 10+11):
ssh-keygen -t rsa -b 4096 -C "your_email#example.com" (must run your terminal as administrator).
Your is_rsa and id_rsa.pub files will be placed under C:\Users\your_username\
So, you need to create the folder C:\Users\your_username\.ssh then copy your ssh files (the extensionless private key and the public key ending in .pub) to there.
You also have to create file C:\Users\your_username\.ssh\config and edit it for the first time.
Next ssh will be placed in the .ssh folder automatically.
Note: ~/ under Linux is the equivalent of C:\Users\your_username\ on Windows
I have created and regularly use a ".ssh" directory on Windows 7; as mentioned in the above comments, Windows Explorer doesn't support them, or more specifically, the error-checking in Windows Explorer does not allow you to give a file name that starts with a period. That same restriction does not exist in the command prompt or powershell.
Also, as mentioned above, it appears you have a file called ".ssh" in your home directory, which must be removed before you can create a folder named ".ssh".
Once such a folder exists, you can open it and change/create files in it using Windows Explorer; it just won't let you name a folder/file ".ssh" directly.
Gitbash should directly allow you to run "rm .ssh" and "mkdir .ssh", at which point everything else should work.
It is quite possible to add a . in the beginning of a directories name using File Explorer, it can be easily done by adding a . at the end of the directory name as well. For example:
To create a directory named .shh, just add the name as .ssh. and it will be created without any error.
And as #Bryson mentioned, this can be done from the cli as well, without appending a . at the end.
Coming to this in 2018, given that on Windows 10 you have the Optional Feature OpenSSH client installed it appears that on Windows a .ssh folder is created for you under C:\Users\<your_username>\.ssh
This is a feature that allows you to use PowerShell to SSH into remote hosts, and seems to be pretty similar in usage to the Linux/Unix equivalent. It was already installed for me when I setup my computer, but you can read the following for how to verify it's installed or install it:
You can check if it's installed by going to Settings -> Manage Optional Features, and then checking if you see OpenSSH in the list. If it is then your .ssh folder is probably in your home directory C:\Users\<your_username>\.ssh. If you need to install it then click "Add a feature", locate OpenSSH Client, click it and click install to install it.
Use git bash on windows
go to home directory as
$ cd
then to check .ssh folder on home directory use
$ ls -A
you will be able to see a ./ssh folder there
$ cd ./ssh
$ ls
you will be able to see the config files if exists
To transfer any key-pair or any files to this folder use below command
First to that directory in which you already have key-pair
$ cp name_of_key-pair_file.pem ~/.ssh/
First of all, if you want to generate SSH files, all you need to do is run this command:
ssh-keygen
Once you did, .ssh folder will be generated in this path:
C:\Users\your_username\
For checking what files are in .ssh folder you can easily run this command:
ls ~/.ssh
with this above command, you can see all your ssh files which would be like this:
id_rsa id-rsa.pub
Please note that:
id_rsa : It's a private file and
id-rsa.pub : It's a public file
so, if you like to see inside of that file or whatever you like just type this command :
cat ~/.ssh/id_rsa.pub
To solve this problem I used git batsh console
This isn't supported as Windows doesn't recognize dot files as directories.
I used SSH to connect to a server and navigate to the folder where I want to store some files from my Mac. I think what I need to do is use SCP to do the copy but I'm not sure exactly about the terminology in the command parameters. And so far everything I've tried gets some sort of "not found" error.
Before logging on to the server the prompt is :
Apples-MacBook-Pro-2:~ neiltayl$
After logging in and navigating to the folder I want to store things in it is :
[neiltayl#cs136 Tracer]$
I need to copy several files from the Tracer folder on my local computer to the Tracer folder on cs136 and cannot fathom the correct parts of the respective FROM and TO parts of SCP to make it work.
This is the nearest I got so far;
Apples-MacBook-Pro-2:~ neiltayl$ ls
Applications Downloads Music Tracer
Desktop Library Pictures c151
Documents Movies Public dwhelper
Apples-MacBook-Pro-2:~ neiltayl$ scp ./Tracer/*.* neiltayl#cs136.cs.iusb.edu:Tracer
neiltayl#cs136.cs.iusb.edu's password:
./Tracer/*.*: No such file or directory
The scp command is -
$ scp File1 username#someting:DIRNAME
Here File 1 is the file that you are sending over to the other computer.
DIRNAME is the path to the directory where you want the file to be stored.
In your case the command would be
scp -r Tracer neiltayl#cs136:New_Tracer
Here Tracer is the folder that contains all the files that you want to copy.