I am trying to make a bash script to create directories with the same name as each file in a given directory, then move said files to their respective directories, and then rename the files.
Basically - a quantum chemistry program that I use requires that the input files be named "ZMAT". So, if I have multiple jobs, I currently need to manually create directories, and then move the ZMAT files into them (can only run one job per folder).
When I run my code, I get "binary operator expected". I am not sure what this means. Some help please.
Here is what I have so far:
#!/bin/bash
if [ -e *.ZMAT ];
then
echo "CFOUR Job Detected"
for INPFILE in *.ZMAT; do
BASENAME=$(basename $INPFILE )
INPFILE=$BASENAME.ZMAT
OUTFILE=$BASENAME.out
XYZFILE=$BASENAME.xyz
ERRORFILE=$BASENAME.slu
if [ ! -e $ERRORFILE ];
then
# Create folder in scratch directory with the basename
mkdir /scratch/CFOUR/$BASENAME
# Move the file to its directory
mv -f $INPFILE /scratch/CFOUR/$BASENAME
# cd to the new directory
cd /scratch/CFOUR/$BASENAME
# Change the file name to just ZMAT
mv -f $INPFILE ZMAT
echo "Submitting CFOUR Job"
# Submit to scheduler
#RUN_COMMAND="sbatch -J $BASENAME _CFOUR_MRCC_SLURM.SUB"
#eval $RUN_COMMAND
else
echo "Error File Detected - Not Submitting Job"
fi
done
fi
An alternative would be to create symlinks to the original files.
As you said before, each ZMAT symlink would need to be in its own directory.
The upside is that the original data doesn't move, so less risk of breaking it, but the tool you want to use should read the symlinks as if they are the files it is looking for.
This one-liner creates an out directory in the current folder that you could subsequently move wherever you want it. You could easily create it where you do want it by replacing "out" with whatever absolute path you wanted
for i in *.ZMAT; do mkdir -p out/$i ; ln -s $PWD/$i out/$i/ZMAT ; done
I believe I have solved my problem. Here is the new script, which appears to be working fine. Any input is welcome though!
#!/bin/bash
SUBDIR=$(pwd)
for i in *.ZMAT; do
BASENAME=$(basename $i .ZMAT)
INPFILE=$BASENAME.ZMAT
OUTFILE=$BASENAME.out
XYZFILE=$BASENAME.xyz
ERRORFILE=$BASENAME.slu
if [ ! -e $ERRORFILE ];
then
mkdir /scratch/CFOUR/$BASENAME # Create Scratch Folder
cp $INPFILE /scratch/cdc/CFOUR/$BASENAME # Move Input to Scratch
cd /scratch/CFOUR/$BASENAME #cd to Scratch Folder
mv -f $INPFILE ZMAT # Change Input Name
echo "Submitting CFOUR Job"
# Submit to scheduler
#RUN_COMMAND="sbatch -J $BASENAME _CFOUR_MRCC_SLURM.SUB"
#eval $RUN_COMMAND
cd $SUBDIR #Go back to SUBDIR
else
echo "Error File Already Exists"
fi
done
Related
I am not able to find a way to make bash create a file with the same name as the file the user dragged into the terminal.
read -p 'file: ' file
if [ "$file" -eq "" ]; then
cd desktop
mkdir
fi
I am trying to make this part of the script take the name of the file they dragged in so for example /Users/admin/Desktop/test.app cd into it copy the "contents" file make another folder with the same name so test.app for this example and then paste the contents file into that folder and delete the old file.
From your .app example, I assume you are using MacOS. Therefore you will need to test this script yourself since I don't have MacOS, but I think it should be doing what you want. Execute it as bash script.sh and it will give you your desired directory test.app/contents in the current working directory.
#! /bin/bash
read -rp 'file: ' file
if [ -e "$file" ]; then
if [ -e "$file"/contents ]; then
base=$(basename "$file")
mkdir "$base"
cp -R "$file"/contents "$base"
rm -rf "$file"
else
echo "The specified file $file has no directory 'contents'."
fi
else
echo "The specified file $file does not exist."
fi
for d in dirlist;
do
cd $d
echo $PWD "primul"
for p in *.HEIC;
do
echo $PWD "din al doilea"
if [ -e "COPY ${p%.*}.jpg" ]; then
echo "COPY ${p%.*}.jpg exists"
else
convert $p "COPY ${p%.*}.jpg"
echo "COPY ${p%.*}.jpg created"
fi
done
done
I have written a script to convert all files that are .HEIC to .jpg. Now I have a structure of folders that is
/main/2019/01
/main/2019/03
/main/2018/12
/main/2018/11
/main/2018/10
/main/2018/09
And I want to run the second for in each directory.
What I get when I run the commands below is only a list of directories and a mention that there are no files to convert.
How do I change the directory using the first for and run the second for in that directory?
cd - changes to the previous directory. That one solution to put it after the first done (second for cycle).
pushd and popd using stack to handle directory changes
check out: https://www.gnu.org/software/bash/manual/html_node/Directory-Stack-Builtins.html
I have this snippet:
#!/bin/bash
parent=/parent
newfolder=/newfolder
mkdir "$newfolder"
for folder in "$parent"/*; do
if [[ -d $folder ]]; then
foldername="${folder##*/}"
for file in "$parent"/"$foldername"/*; do
filename="${file##*/}"
newfilename="$foldername"_"$filename"
cp "$file" "$newfolder"/"$newfilename"
done
fi
done
I do need to turn it around in a way that the copied files would be named after the folder they are being moved to (e.g. moving to the /root/Case22 files would be renamed to case22_1.jpg, case22_2.docx, case22_3.JPG etc). The files would be copied from USB and both destination and source directries would be entered by the user. I have written everything else and it works apart from actual renaming and thought I could adapt this snippet.
thanks
p.s. the snippet is written by Jahid and found on stackoverflow
you can try something like this;
#!/bin/bash
parent=/root
a=1
for file in $parent/Case22*; do
filename="${file%.*}"
extension="${file##*.}"
newfilename=$(printf "$filename"_"$a"."$extension")
mv -- "$file" "$newfilename"
let a=a+1
done
Thanks for the help. I have found the solution and thought I might post it here in case someone else will be looking at this.
As the title suggests I needed a Linux shell script to copy and rename multiple files keeping original directory tree (the file source and archive locations would be specified by the user of the script). Here is the code that I came up with after few days research of different sources (it includes a trap so only one instance of script would be running at a time):
lockdir=/var/tmp/mylock #directory for lock file creation
pidfile=/var/tmp/mylock/pid #directory to get the process ID number
if ( mkdir ${lockdir} ) 2> /dev/null; then #main argument to create lock file
echo $$ > $pidfile #if successful script will proceed, otherwise it will skip to the else part of the statement at the end of the script
trap 'rm -rf "$lockdir"; exit $?' INT TERM EXIT #trap to capture reasons of script termination and removal of the lock file so it could be launched again
#start of the main script body, part of successful "if" statement
# read entry_for_testing_only #request for user entry to keep script running and try to run another script instance
findir="$2/$(basename "$1")" #variable that defines final directory to which files from USB will be copied
if [ ! -d "$1" ]; then #testing if first directory entry is a valid directory’’
echo "$1" "is not a directory"
echo ""
exit
else
if [ ! -d "$2" ]; then #testing if second entry is a valid directory
echo "archive directory non existant"
exit
else
if [ -d "$findir" ] && [ "$(ls -A "$findir")" ]; then #testing if second entry directory contains the same name folders and if the folders are empty - to avoid file overwriting
echo "such folder already there and it's not empty"
exit
else
if [ ! -d "$findir" ] ; then #last archive directory argument to create final archive directory
mkdir "$findir"
else true
fi
fi
fi
fi
rsync -a "$1"/ "$findir" #command to copy all files from the source to the archive retaining the directory tree
moved_files="$(find "$findir" -type f)" #variable that finds all files that have been copied to the archive directory
for file in $moved_files; do #start of the loop that renames copied files
counter="$((counter+1))" #incrementation variable
source_name="$(basename "$1")" #variable that captures the name of the source directory
new_name="$source_name"_"$counter" #variable that puts start of the file name and incrementation element together
if echo "$file" | grep "\." #argument that captures the extension of the file
then
extension="$(echo "$file" | cut -f2 -d. )"
else
extension=
fi
full_name="$new_name"."$extension" #variable that defines the final new name of the file
dir="$(dirname "${file}")" #variable that captures the directorry address of currently looped file
mv "$file" "$dir/$full_name" #move command to rename currently looped file with the final new name
done
#end of the main script body, unsuccessful "if" statement continues here
else
echo "Another instance of this script is already running. PID: $(cat $pidfile)"
fi
I have a file that contains some keywords and I intend to create subdirectories into the same directory of the same keyword using a bash script. Here is the code I am using but it doesn't seem to be working.
I don't know where I have gone wrong. Help me out
for i in `cat file.txt`
do
# if [[ ! -e $path/$i ]]; then
echo "creating" $i "directory"
mkdir $path/$i
# fi
grep $i file >> $path/$i/output.txt
done
echo "created the files in "$path/$TEMP/output.txt
You've gone wrong here, and you've gone wrong here.
while read i
do
echo "Creating $i directory"
mkdir "$path/$i"
grep "$i" file >> "$path/$i"/output.txt
done < file.txt
echo "created the files in $path/$TEMP/output.txt"
78mkdir will refuse to create a directory, if parts of it do not exist.
e.g. if there is no /foo/bar directory, then mkdir /foo/bar/baz will fail.
you can relax this a bit by using the -p flag, which will create parent directories if necessary (in the example, it might create /foo and /foo/bar).
you should also use quotes, in case your paths contain blanks.
mkdir -p "${path}/${i}"
finally, make sure that you are actually allowed to create directories in $path
I am having trouble with a simple grading script I am writing. I have a directory called HW5 containing a folder for each student in the class. From my current directory, which contains the HW5 folder, I would like to copy all files starting with the word mondial, to each of the students' folders. My script runs but does not copy any of the files over. Any suggestions?
#!/bin/bash
for file in ./HW5; do
if [ -d $file ]; then
cp ./mondial.* ./$file;
fi
done
Thanks,
The first loop was executing only once, with file equal ./HW5. Add the star to actually select the files or directories inside it.
#!/bin/bash
for file in ./HW5/*; do
if [ -d "$file" ]; then
cp ./mondial.* ./"$file"
fi
done
As suggested by Mark Reed, this can be simplified:
for file in ./HW5/*/; do
cp ./mondial.* ./"$file"
done