I want to mimic copying a directory structure recursively (as in cp -r or rsync -a), but only touch the copied files, i.e. make all the copied files empty.
The specific use case is for a Snakemake pipeline; Snakemake looks for existing files in order to decide whether to re-run a pipeline step, and I want to make it believe the steps have already been run while avoiding fully downloading all the files.
This is a little kludgy, but you could pipe the output of find or rsync -nv into a little bash loop with mkdir -p and touch:
find /some/dir -type f | while read FILE; do
mkdir -p $(dirname $FILE)
touch $FILE
done
In makefile, I am doing something like this -
#while read -r file; do \
if [ ! -z "$$file" ]; then \
cp -R path/to/someplace/$$file path/to/someplace/else/$$file \
fi \
done <filename.txt
filename.txt contains files and folders like -
abc/*.txt
folder1/
folder2/
textfile.txt
I am able to copy files and folders but in the case of abc/*.txt it shows an error:
cp: target `/path/to/someplace/else/*.txt' is not a directory.
Is there some way possible to copy these files with wildcard characters?
Actually the problem is not in the pattern expansion. That bit would appear to work as expected. The error is actually due to the resulting cp command. You end up with for instance:
cp abc/a.txt abc/b.txt other/path/abc/*.txt
However, for multiple source files cp expect destination to be a directory, which other/place/abc/* is not (it could be if you created it, but is unlikely what you wanted).
That said. You could for instance create the target directory by calling mkdir -p other/path/`dirname $$file` (escaped $ for make) and with cp use `dirname $$file` as well for destination.
There are few caveats. For instance if absolute paths were to be encountered or globing characters where also used on directories leading up to the files themselves (dir?/*.txt, some/*/file). It would perhaps be safer to use for instance tar or cpio:
tar cf - -C /source/path src/*.txt | tar xf - -C /target/path/
My script is designed to gather files and back them up across the network using ssh (because it is the only thing unblocked by the firewall) and then delete any backups that are over 30 days old. However, when the code is run I receive this error message:
receiving incremental file list rsync: mkdir
"/var/home/username_local/BackupTo/username/2015-08-10" failed: No such
file or directory (2) rsync error: error in file IO (code 11) at
main.c(576) [receiver=3.0.6]
The code I am using is below:
#!/bin/bash
#User who's files are being backed up
BNAME=username
#directory to back up
BDIR=/home/username/BackThisUp
#directory to backup to
BackupDir=/var/home/username_local/BackupTo
#user
RUSER=$USER
#SSH Key
KEY=/var/home/username_local/.ssh
#Backupname
RBackup=`date +%F`
#Backup Server
BServ=backup.server
#Path
LPATH='Data for backup'
#date
DATE=`date +%F`
#Transfer new backups
rsync -avpHrz -e "ssh -i $KEY" $BNAME#$BServ:$BDIR $BackupDir/$BNAME/$DATE
find $BackupDir/$BNAME -type d -ctime +30 -exec rm -rf {} \;
EDIT: The problem was solved when I added:
mkdir $BackupDir/$BNAME > /dev/null 2>&1
before the rsync
I think rsync will not writ to non existing destination directories.
You could prepend your rsync with an
ssh $BNAME#$BServ "mkdir $BackupDir/$BNAME/$DATE"
but only if the variables for mkdir are known safe. This can be a code injection if e.g. your $BackupDir is provided externally from the script.
Another trick would be to prepend the actual rsync (started on the remote server) with... mkdir:
rsync -avpHrz --rsync-path "mkdir -m 700 $BackupDir/$BNAME/$DATE && rsync" -e "ssh -i $KEY" $BNAME#$BServ:$BDIR $BackupDir/$BNAME/$DATE
Let's say I have a bunch of *.tar.gz files located in a hierarchy of folders. What would be a good way to find those files, and then execute multiple commands on it.
I know if I just need to execute one command on the target file, I can use something like this:
$ find . -name "*.tar.gz" -exec tar xvzf {} \;
But what if I need to execute multiple commands on the target file? Must I write a bash script here, or is there any simpler way?
Samples of commands that need to be executed a A.tar.gz file:
$ tar xvzf A.tar.gz # assume it untars to folder logs
$ mv logs logs_A
$ rm A.tar.gz
Here's what works for me (thanks to Etan Reisner suggestions)
#!/bin/bash # the target folder (to search for tar.gz files) is parsed from command line
find $1 -name "*.tar.gz" -print0 | while IFS= read -r -d '' file; do # this does the magic of getting each tar.gz file and assign to shell variable `file`
echo $file # then we can do everything with the `file` variable
tar xvzf $file
# mv untar_folder $file.suffix # untar_folder is the name of folder after untar
rm $file
done
As suggested, the array way is unsafe if file name contained space(s), and also doesn't seem to work properly in this case.
Writing a shell script is probably easiest. Take a look at sh for loops. You could use the output of a find command in an array, and then loop over that array to perform a set of commands on each element.
For example,
arr=( $(find . -name "*.tar.gz" -print0) )
for i in "${arr[#]}"; do
# $i now holds each of the filenames output by find
tar xvzf $i
mv $i $i.suffix
rm $i
# etc., etc.
done
So, if I'm in my home directory and I want to move foo.c to ~/bar/baz/foo.c , but those directories don't exist, is there some way to have those directories automatically created, so that you would only have to type
mv foo.c ~/bar/baz/
and everything would work out? It seems like you could alias mv to a simple bash script that would check if those directories existed and if not would call mkdir and then mv, but I thought I'd check to see if anyone had a better idea.
How about this one-liner (in bash):
mkdir --parents ./some/path/; mv yourfile.txt $_
Breaking that down:
mkdir --parents ./some/path
# if it doesn't work; try
mkdir -p ./some/path
creates the directory (including all intermediate directories), after which:
mv yourfile.txt $_
moves the file to that directory ($_ expands to the last argument passed to the previous shell command, ie: the newly created directory).
I am not sure how far this will work in other shells, but it might give you some ideas about what to look for.
Here is an example using this technique:
$ > ls
$ > touch yourfile.txt
$ > ls
yourfile.txt
$ > mkdir --parents ./some/path/; mv yourfile.txt $_
$ > ls -F
some/
$ > ls some/path/
yourfile.txt
mkdir -p `dirname /destination/moved_file_name.txt`
mv /full/path/the/file.txt /destination/moved_file_name.txt
Save as a script named mv.sh
#!/bin/bash
# mv.sh
dir="$2" # Include a / at the end to indicate directory (not filename)
tmp="$2"; tmp="${tmp: -1}"
[ "$tmp" != "/" ] && dir="$(dirname "$2")"
[ -a "$dir" ] ||
mkdir -p "$dir" &&
mv "$#"
Or put at the end of your ~/.bashrc file as a function that replaces the default mv on every new terminal. Using a function allows bash keep it memory, instead of having to read a script file every time.
function mvp ()
{
dir="$2" # Include a / at the end to indicate directory (not filename)
tmp="$2"; tmp="${tmp: -1}"
[ "$tmp" != "/" ] && dir="$(dirname "$2")"
[ -a "$dir" ] ||
mkdir -p "$dir" &&
mv "$#"
}
Example usage:
mv.sh file ~/Download/some/new/path/ # <-End with slash
These based on the submission of Chris Lutz.
You can use mkdir:
mkdir -p ~/bar/baz/ && \
mv foo.c ~/bar/baz/
A simple script to do it automatically (untested):
#!/bin/sh
# Grab the last argument (argument number $#)
eval LAST_ARG=\$$#
# Strip the filename (if it exists) from the destination, getting the directory
DIR_NAME=`echo $2 | sed -e 's_/[^/]*$__'`
# Move to the directory, making the directory if necessary
mkdir -p "$DIR_NAME" || exit
mv "$#"
It sounds like the answer is no :). I don't really want to create an alias or func just to do this, often because it's one-off and I'm already in the middle of typing the mv command, but I found something that works well for that:
mv *.sh shell_files/also_with_subdir/ || mkdir -p $_
If mv fails (dir does not exist), it will make the directory (which is the last argument to the previous command, so $_ has it). So just run this command, then up to re-run it, and this time mv should succeed.
The simpliest way to do that is:
mkdir [directory name] && mv [filename] $_
Let's suppose I downloaded pdf files located in my download directory (~/download) and I want to move all of them into a directory that doesn't exist (let's say my_PDF).
I'll type the following command (making sure my current working directory is ~/download):
mkdir my_PDF && mv *.pdf $_
You can add -p option to mkdir if you want to create subdirectories just like this: (supposed I want to create a subdirectory named python):
mkdir -p my_PDF/python && mv *.pdf $_
Making use of the tricks in "Getting the last argument passed to a shell script" we can make a simple shell function that should work no matter how many files you want to move:
# Bash only
mvdir() { mkdir -p "${#: -1}" && mv "$#"; }
# Other shells may need to search for the last argument
mvdir() { for last; do true; done; mkdir -p "$last" && mv "$#"; }
Use the command like this:
mvdir foo.c foo.h ~/some/new/folder/
rsync command can do the trick only if the last directory in the destination path doesn't exist, e.g. for the destination path of ~/bar/baz/ if bar exists but baz doesn't, then the following command can be used:
rsync -av --remove-source-files foo.c ~/bar/baz/
-a, --archive archive mode; equals -rlptgoD (no -H,-A,-X)
-v, --verbose increase verbosity
--remove-source-files sender removes synchronized files (non-dir)
In this case baz directory will be created if it doesn't exist. But if both bar and baz don't exist rsync will fail:
sending incremental file list
rsync: mkdir "/root/bar/baz" failed: No such file or directory (2)
rsync error: error in file IO (code 11) at main.c(657) [Receiver=3.1.2]
So basically it should be safe to use rsync -av --remove-source-files as an alias for mv.
The following shell script, perhaps?
#!/bin/sh
if [[ -e $1 ]]
then
if [[ ! -d $2 ]]
then
mkdir --parents $2
fi
fi
mv $1 $2
That's the basic part. You might want to add in a bit to check for arguments, and you may want the behavior to change if the destination exists, or the source directory exists, or doesn't exist (i.e. don't overwrite something that doesn't exist).
Sillier, but working way:
mkdir -p $2
rmdir $2
mv $1 $2
Make the directory with mkdir -p including a temporary directory that is shares the destination file name, then remove that file name directory with a simple rmdir, then move your file to its new destination.
I think answer using dirname is probably the best though.
This will move foo.c to the new directory baz with the parent directory bar.
mv foo.c `mkdir -p ~/bar/baz/ && echo $_`
The -p option to mkdir will create intermediate directories as required.
Without -p all directories in the path prefix must already exist.
Everything inside backticks `` is executed and the output is returned in-line as part of your command.
Since mkdir doesn't return anything, only the output of echo $_ will be added to the command.
$_ references the last argument to the previously executed command.
In this case, it will return the path to your new directory (~/bar/baz/) passed to the mkdir command.
I unzipped an archive without giving a destination and wanted to move all the files except demo-app.zip from my current directory to a new directory called demo-app. The following line does the trick:
mv `ls -A | grep -v demo-app.zip` `mkdir -p demo-app && echo $_`
ls -A returns all file names including hidden files (except for the implicit . and ..).
The pipe symbol | is used to pipe the output of the ls command to grep (a command-line, plain-text search utility).
The -v flag directs grep to find and return all file names excluding demo-app.zip.
That list of files is added to our command-line as source arguments to the move command mv. The target argument is the path to the new directory passed to mkdir referenced using $_ and output using echo.
Based on a comment in another answer, here's my shell function.
# mvp = move + create parents
function mvp () {
source="$1"
target="$2"
target_dir="$(dirname "$target")"
mkdir --parents $target_dir; mv $source $target
}
Include this in .bashrc or similar so you can use it everywhere.
Code:
if [[ -e $1 && ! -e $2 ]]; then
mkdir --parents --verbose -- "$(dirname -- "$2")"
fi
mv --verbose -- "$1" "$2"
Example:
arguments: "d1" "d2/sub"
mkdir: created directory 'd2'
renamed 'd1' -> 'd2/sub'
((cd src-path && tar --remove-files -cf - files-to-move) | ( cd dst-path && tar -xf -))
I frequently stumble upon this issue while bulk moving files to new subdirectories. Ideally, I want to do this:
mv * newdir/
Most of the answers in this thread propose to mkdir and then mv, but this results in:
mkdir newdir && mv * newdir
mv: cannot move 'newdir/' to a subdirectory of itself
The problem I face is slightly different in that I want to blanket move everything, and, if I create the new directory before moving then it also tries to move the new directory to itself. So, I work around this by using the parent directory:
mkdir ../newdir && mv * ../newdir && mv ../newdir .
Caveats: Does not work in the root folder (/).
My one string solution:
test -d "/home/newdir/" || mkdir -p "/home/newdir/" && mv /home/test.txt /home/newdir/
i accomplished this with the install command on linux:
root#logstash:# myfile=bash_history.log.2021-02-04.gz ; install -v -p -D $myfile /tmp/a/b/$myfile
bash_history.log.2021-02-04.gz -> /tmp/a/b/bash_history.log.2021-02-04.gz
the only downside being the file permissions are changed:
root#logstash:# ls -lh /tmp/a/b/
-rwxr-xr-x 1 root root 914 Fev 4 09:11 bash_history.log.2021-02-04.gz
if you dont mind resetting the permission, you can use:
-g, --group=GROUP set group ownership, instead of process' current group
-m, --mode=MODE set permission mode (as in chmod), instead of rwxr-xr-x
-o, --owner=OWNER set ownership (super-user only)
There's a lot of conflicting solutions around for this, here's what worked for us:
## ss_mv ##
function ss_mv {
mkdir -p $(dirname "$2") && mv -f "$#"
}
This assumes commands in the following syntax:
ss_mv /var/www/myfile /var/www/newdir/myfile
In this way the directory path /var/www/newdir is extracted from the 2nd part of the command, and that new directory is then created (it's critical that you use the dirname tag to avoid myfile being added to the new directory being created).
Then we go ahead and mv on the entire string again by using the "$#" tag.
You can even use brace extensions:
mkdir -p directory{1..3}/subdirectory{1..3}/subsubdirectory{1..2}
which creates 3 directories (directory1, directory2, directory3),
and in each one of them two subdirectories (subdirectory1, subdirectory2),
and in each of them two subsubdirectories (subsubdirectory1 and subsubdirectory2).
You have to use bash 3.0 or newer.
$what=/path/to/file;
$dest=/dest/path;
mkdir -p "$(dirname "$dest")";
mv "$what" "$dest"