I am having a problem with something seemingly very simple in Unix. I used the following code to move a file to another directory:
mv genes.gtf ./ ../..
The file is no longer in the original directory, but it has not shown up in the destination directory either! Has anyone experienced a similar thing before? What is causing the problem? Is it possible for it to take a while for a file to be moved, so it shows up in the destination directory with a big delay?
When 3 arguments are passed to mv, the first two are considered sources, and the last one is considered the destination. It seems you moved both genes.gtf and the current directory (./) to ../..
I think what you meant to write was mv genes.gtf ../..
As far as what happened to your file, I have no idea; I've never attempted to move ./ anywhere in unix/linux before.
Related
I recently attempted to move some files by running an -exec mv command with find (command linked below). When I did this, I mistyped the destination directory path (so the directory did not yet exist) and mv created what appears to be an executable instead of a directory?
When I run "Get Info" one image renders and the file size is about the correct size for an image, but hundreds of files were supposed to be copied. Have I lost this data for good? Is there any way to get macOS to recognize this "executable" as a directory?
This is the command I used:
find . -type f -name "*.JPG" -exec mv {} ../../DestinationFolderName \;
Here's an image showing a successful mv into an existing directory, and what happened when I put a path to a directory that did not yet exist.
Unfortunately "mv" to a name that doesn't exist is interpreted as a filename rather than a directory. So the OS has, one-by-one, copied your JPG file on top of each other. The resulting file is most likely whatever JPG happened to be the one it moved last (if you rename it to JPG extension you can check which one).
So, very unfortunately, you probably need to investigate a data recovery tool for MacOS quickly (and do so before you've done things that make more files on your disk, as much a possible). The "ghosts" of the files are for now at least mostly still present on your hard drive (as deallocated segments), but are back in the pool to be overwritten as you create new files (even when your browser creates temporary cache files, and things like that). It's a conundrum.
If you don't have a backup/time-machine of the files, the best thing to do is get a MacOS data recovery program QUICKLY.
VERY sorry not to have a happier answer.
Is it possible to have rsync copy "unsafe" symlinks (that is, those that refer to files/dirs outside of the copied tree, see docs here) but not update the times on them?
I'm using rsync -a --delete --omit-dir-times to copy a bunch of files from /home/somebody/foo/bar to a destination machine, but running into the following error: rsync: failed to set times on "/home/somebody/foo/bar/symlink": Operation not permitted (1), where /home/somebody/foo/bar/smylink refers to something in /usr/lib/ owned by root at the destination and lacking proper permission for the rsync user to update it.
Essentially rsync tries to update the time on the symlink like all other files it copies, but gets blocked by permissions because it's not root at the destination.
What I'd like to do is copy the link, but not touch the symlink target at all during the copy. I just want the link. I could change permissions on the target file, but I'd like to avoid that.
Is this achievable? Is this a terrible idea and I'd be abusing rsync? Suggestions for alternative approaches in the latter case?
There is another option for rsync --omit-link-times which will probably do what you are looking for. See man page at:
http://manpages.ubuntu.com/manpages/bionic/man1/rsync.1.html
Suddenly grep command stopped working. When I did the ls -l ~/grep showing the one file in my home directory.But this file has been present for ages. If I give command which grep --> pointing to /bin/grep and with /bin/grep it is working fine. Can anyone please suggest.
Thanks,
Regards,
Shiv
You can delete the zero-byte file in your home directory. It's not doing anything. (I don't know how it got there.) The problem is that the first entry in PATH, ".", points to whatever directory you're in. So when you're in your home directory, the shell (bash, I assume) looks for grep in the current directory, and finds the file that's there, which can't do anything.
I consider it a bad idea to have "." in your path. It's convenient, and natural if you're coming from the Windows world, but it means that what gets executed can change depending on what directory you're in (as you have now seen). It also means that if you're on a multiuser system, someone can put an executable in one of their directories, and then when you cd into their directory, all of a sudden you're executing their code, which might not be what you want, and could be dangerous.
Instead, remove ".:" (dot colon) from your PATH. When you need to run a script in the current directory, add "./" to its name to execute it. "/bin" and "/usr/bin" should usually be at the front of the list. Some people prefer to put "/usr/local/bin" at the front of the list, or something else.
You can change your PATH by editing .profile or .bash_profile or .bashrc. It depends on how you have your shell set up. Be careful to separate each directory path in PATH with one ":" character.
I started an online Unix course. I entered the course kinda late and I'm having a little trouble getting caught up. We had a homework question (I got it wrong) it said to:
Change the current working directory to directory WT5 using a single command line and starting at the home path.
How in the world am I supposed to do that? I know how to change a directory from your current directory just $ cd WT5 And if I wanted to list all of the contents in the home directory I would use $ ls ~/nameofhomedirectory And, if I wanted to change the current working directory to the home directory I would use $ cd ~ or just $ cd
So how would I combine all of that in one single command line to change the current directory to another directory using a path that includes the home directory?
Thank you for all of your help in advance!
UPDATE: Okay. I can see now that this maybe a little confusing. So let me try to make it a little bit more clear where I am going wrong or getting mixed up.
Let's say this is a tree of directories you have.
Tree of Directories
Now, your home directory is user And your current working directory is work But you want to change your current working directory to play. How would you change the directory using a single command line and starting at your home direcotry and not your current working directory work
Thanks again!
I'm not quite sure I understand your question, but you could try:
cd ~/WT5
or:
cd $HOME/WT5
or if you absolutely need to be long-winded about it:
cd /user/homedirectory/subdirectory/currentworkingdirectory/WT5
These all include your home directory in the path. The short-hands are to be preferred.
This might do the trick:
cd ~/../users/carol/play
The idea is that you can go upwards from a home directory too.
I originally had three files: makefile, readme.txt, and hashtable.c in my directory, where I am writing my code in emacs. I noticed that some new files: #hashtable.c#, #readme.txt#, hashtable.c~, and makefile~ have been created. I was wondering what these files were. Are these important, and if not, how do I tell emacs to stop making them? I'm also curious why readme.txt doesn't get a tilde file and makefile doesn't get a sharp file.
The file with the ~ is a backup file that automatically gets created when you save a file. The #readme.txt# is the file being currently edited/in use (i.e., the autosave version). That will usually go away (unlike the ~ file) when you exit emacs normally (if it crashes or gets killed the # files may stay around).
You might find this page about emacs backup files of interest, and this SO question: How do I control how Emacs makes backup files?
You can prevent backup files from being created with this:
(setq make-backup-files nil)
I recommend installing no-littering. It automatically puts backup files (file~) in ~/.emacs.d/var/backup/. It doesn't do anything about autosaves (#file#), but there is a note about putting those files in a specified directory in the README:
(setq auto-save-file-name-transforms
`((".*" ,(no-littering-expand-var-file-name "auto-save/") t)))
Neither of these things actually prevents Emacs from creating these files, but I'm assuming most people actually want these files (in case of a crash), but don't want them strewn all over the filesystem.
For #files# you have to do rm "#file#" from the terminal, because rm #file# doesn't work.
For ~file you can simply digit rm ~file.
Maybe you could try:
find . -name \\#*\\# | xargs rm
Warning: this will remove those files matching in subdirectories.