I have several files called as follow:
dosulepin3D_CID_5284550.pdbqt
protriptyline3D_CID_4976.pdbqt
These are small molecules. Now I want to create a file in the Results folder for each one of these molecules, ignoring the 3D_CID_5284550.pdbqt they all have behind, and have folders called:
dosulepin
protriptyline
I want to do this with a for loop, since I'm also performing some functions with these files. This is what I have:
DIR="/home/roy/MolecularDocking/VirtualScreening/Dockings"
cd $DIR
for ligand in ligands/*; do
echo $ligand
mkdir "/home/roy/MolecularDocking/Results/$ligand"
done;
But this obviuosly creates folders with the full name.
Something like this.
DIR="/home/roy/MolecularDocking/VirtualScreening/Dockings"
cd "$DIR" || exit
for ligand in ligands/*.pdbqt; do
echo "$ligand"
echo mkdir -p "/home/roy/MolecularDocking/Results/${ligand%3D*}"
done
Remove the echo from the mkdir if you're satisfied with the output.
See Parameter Expansion for more details.
New to bash scripting, and I'm stuck. Within a static directory I'm trying to create a folder '001_scanned name' and within that directory create 6 more subfolders. I'm able to do it all brutishly with this code:
cd ~/deej/Test/Capture
mkdir "$1"
cd "$1"
mkdir "$1_1"
mkdir "$1_2"
mkdir "$1_3"
mkdir "$1_4"
mkdir "$1_5"
mkdir "$1_6"
Ugly, but works for now.
$1 is the scanned name and I was manually appending the prefix of the file names with "001, 002, etc.". Is there an easy way to do this within an Automator prompt since I'll be unable to keep the last variable stored in the code?
If you use the -p option with mkdir it will create intermediate directories as needed so you can do both commands at once. The seq function can create zero-padded integers:
for n in $(seq -f "%03g" 1 10);
do mkdir -p ${i}/${i}_${n};
done;
You can test using echo instead of mkdir -p. Below I had i set to 015...
015/015_001
015/015_002
015/015_003
015/015_004
015/015_005
015/015_006
015/015_007
015/015_008
015/015_009
015/015_010
I wrote this little shell script(test.sh) to create a basic folder structure:
#!/bin/bash
# Check if directory already exists,
# if it doesnt, create one.
if [ ! -d "~/.dir1" ]; then
mkdir ".dir1"
else
rm -rf ".dir1"
mkdir ".dir1"
fi
When I run
test.sh
in console, the hidden folder is created.
But:
When I run it again it tells me:
mkdir: .dir1: File exists
But it could exist because I removed it in my shell script before I created a new one!
So why does it display this message?
Thanks and greetings!
Replace
[ ! -d "~/.dir1" ]
by
[ ! -d "${HOME}/.dir1" ]
I would simply use -p.
mkdir -p "$HOME/dir1"
If you pass -p, mkdir wouldn't throw an error if the directory already exists, it would simply silently return in that case.
If you want to make sure folder is empty use this:
rm -rf "$HOME/dir1"
mkdir -p "$HOME/dir1"
and no if! The basic problem with the if is the fact that it is not immune against race conditions. When the script went off from CPU right after the if - and creates "dir1" - your script will fail when it enters the CPU again since it still thinks the directory does not exist.
What you are doing by "~/.dir1" is not right. It's just another string for a directory name literally "~/.dir1" i.e ~ is not being expanded to $HOME.
Use full path or ~/".dir1" or ~/.dir1 instead.
You can use $HOME too: $HOME/.dir1 or "$HOME/.dir1" or "$HOME"/".dir1" all of them will produce same result... but quoting variables is a good practice.
~ isn't expanded when you place it in quotes. You need to leave it unquoted.
if [ ! -d ~/.dir1 ]
Of note, you're checking for ~/.dir1 but you make .dir1. That's only the same directory if the current directory is ~. If it isn't, they're not the same.
Also, mkdir -p will do this for you, creating a directory only if it doesn't exist already. You could simplify your script to:
mkdir -p ~/.dir1
or
rm -rf ~/.dir1
mkdir ~/.dir1
I was learing basic terminal command these days.
I found that I can make parallel directories by add a space between them:
mkdir dir_a dir_b
But when I trying to make parallel directories under a mother-directory, this fails.
mkdir dir_a/dir_a_1 dir_a_2
# Failed, the dir_a_2 is on top level
Is there a way that I can make parallel sub-directories under a mother-directory without change to that mother-directory (without cd method) ?
Each argument to mkdir is rooted in the current directory. The behavior your are seeing is intentional. There's no special treatment of the first argument to mkdir.
However, there are several options available to achieve the result you are looking for.
You could use a loop:
for f in dir_a_1 dir_a_2; do mkdir -p "dir_a/$f"; done
You could use pushd:
mkdir dir_a; pushd dir_a; mkdir dir_a_1 dir_a_2; popd
You could use printf and command substitution:
mkdir -p $(printf 'dir_a/%s ' dir_a_1 dir_a_2)
You could use printf and xargs:
printf 'dir_a/%s ' dir_a_1 dir_a_2 | xargs mkdir -p
Any of these should work for you.
I am writing a shell script to run under the KornShell (ksh) on AIX. I would like to use the mkdir command to create a directory. But the directory may already exist, in which case I do not want to do anything. So I want to either test to see that the directory does not exist, or suppress the "File exists" error that mkdir throws when it tries to create an existing directory.
How can I best do this?
Try mkdir -p:
mkdir -p foo
Note that this will also create any intermediate directories that don't exist; for instance,
mkdir -p foo/bar/baz
will create directories foo, foo/bar, and foo/bar/baz if they don't exist.
Some implementation like GNU mkdir include mkdir --parents as a more readable alias, but this is not specified in POSIX/Single Unix Specification and not available on many common platforms like macOS, various BSDs, and various commercial Unixes, so it should be avoided.
If you want an error when parent directories don't exist, and want to create the directory if it doesn't exist, then you can test for the existence of the directory first:
[ -d foo ] || mkdir foo
This should work:
$ mkdir -p dir
or:
if [[ ! -e $dir ]]; then
mkdir $dir
elif [[ ! -d $dir ]]; then
echo "$dir already exists but is not a directory" 1>&2
fi
which will create the directory if it doesn't exist, but warn you if the name of the directory you're trying to create is already in use by something other than a directory.
Use the -p flag.
man mkdir
mkdir -p foo
Defining complex directory trees with one command
mkdir -p project/{lib/ext,bin,src,doc/{html,info,pdf},demo/stat/a}
If you don't want to show any error message:
[ -d newdir ] || mkdir newdir
If you want to show your own error message:
[ -d newdir ] && echo "Directory Exists" || mkdir newdir
mkdir foo works even if the directory exists.
To make it work only if the directory named "foo" does not exist, try using the -p flag.
Example:
mkdir -p foo
This will create the directory named "foo" only if it does not exist. :)
The old tried and true
mkdir /tmp/qq >/dev/null 2>&1
will do what you want with none of the race conditions many of the other solutions have.
Sometimes the simplest (and ugliest) solutions are the best.
Simple, silent and deadly:
mkdir -p /my/new/dir >/dev/null 2>&1
You can either use an if statement to check if the directory exists or not. If it does not exits, then create the directory.
dir=/home/dir_name
if [ ! -d $dir ]
then
mkdir $dir
else
echo "Directory exists"
fi
You can directory use mkdir with -p option to create a directory. It will check if the directory is not available it will.
mkdir -p $dir
mkdir -p also allows to create the tree structure of the directory. If you want to create the parent and child directories using same command, can opt mkdir -p
mkdir -p /home/parent_dir /home/parent_dir/child1 /home/parent_dir/child2
mkdir does not support -p switch anymore on Windows 8+ systems.
You can use this:
IF NOT EXIST dir_name MKDIR dir_name
directory_name = "foo"
if [ -d $directory_name ]
then
echo "Directory already exists"
else
mkdir $directory_name
fi
This is a simple function (Bash shell) which lets you create a directory if it doesn't exist.
#------------------------------------------#
# Create a directory if it does not exist. #
#------------------------------------------#
# Note the "-p" option in the mkdir #
# command which creates directories #
# recursively. #
#------------------------------------------#
createDirectory() {
mkdir -p -- "$1"
}
You can call the above function as:
createDirectory "$(mktemp -d dir-example.XXXXX)/fooDir/BarDir"
The above creates fooDir and BarDir if they don't exist. Note the "-p" option in the mkdir command which creates directories recursively.
Referring to man page man mkdir for option -p
-p, --parents
no error if existing, make parent directories as needed
which will create all directories in a given path, if exists throws no error otherwise it creates all directories from left to right in the given path. Try the below command. the directories newdir and anotherdir doesn't exists before issuing this command
Correct Usage
mkdir -p /tmp/newdir/anotherdir
After executing the command you can see newdir and anotherdir created under /tmp. You can issue this command as many times you want, the command always have exit(0). Due to this reason most people use this command in shell scripts before using those actual paths.
Or if you want to check for existence first:
if [[ ! -e /path/to/newdir ]]; then
mkdir /path/to/newdir
fi
-e is the exist test for KornShell.
You can also try googling a KornShell manual.
Improvement on the 'classic' solution (by Brian Campbell) - to handle the case of symlink to a directory.
[ -d foo/. ] || mkdir foo
mkdir -p sam
mkdir = Make Directory
-p = --parents
(no error if existing, make parent directories as needed)
if [ !-d $dirName ];then
if ! mkdir $dirName; then # Shorter version. Shell will complain if you put braces here though
echo "Can't make dir: $dirName"
fi
fi