How to create a bash script to make directories and specific files inside each directory - bash

Question

I wrote a bash script trying to generate one directory named after each file inside the directory from which I run the script.
Original directory= /home/agalvez/data//sims/phylip_format
sim1.phylip
sim2.phylip
Directories to create = sim1 sim2
The contents of these new directories should be a copy of the original file that names the new directory and an extra file called "input". This file should contain the name of the .phylip file as well as the following:
"Name of original file"
U
5
Y
/home/agalvez/data/sims/trees/tree_nodenames.txt
After that I want to run the following command (sequentially) in all these new directories:
phylip dollop < input > screenout
My approach is the following one but it is not working:
!/bin/bash
for f in *.phylip;
mkdir /home/agalvez/data/sims/dollop/$f;
cp $f /home/agalvez/data/sims/dollop/$f;
cd /home/agalvez/data/sims/dollop/$f;
echo "$f" | cat > input;
echo "U" | cat >> input;
echo "5" | cat >> input;
echo "Y" | cat >> input;
echo "/home/agalvez/data/sims/trees/tree_nodenames.txt" | cat >> input;
phylip dollop < input > screenout;
;done
Edit: The error messge looks like this:
line 4: syntax error near unexpected token `mkdir'
line 4: ` mkdir /home/agalvez/data/sims/dollop/$f;'
FINAL SOLUTION:
#!/bin/bash
for f in *.phylip;
do
mkdir /home/agalvez/data/sims/dollop/$f;
cp /home/agalvez/data/sims/phylip_format/$f /home/agalvez/data/sims/dollop/$f;
cd /home/agalvez/data/sims/dollop/$f;
echo "$f" | cat > input;
echo "U" | cat >> input;
echo "5" | cat >> input;
echo "Y" | cat >> input;
echo "/home/agalvez/data/sims/trees/tree_nodenames.txt" | cat >> input;
phylip dollop < input > screenout;
done

Answer 1

The immediate problem is that you are lacking a do at the beginning of the loop body; but you'll want to refactor this code to avoid hardcoding the directory structure etc.
The first line needs to start with literally the two characters # and ! in order to be a valid shebang.
Notice also When to wrap quotes around a shell variable?
The printf could be replaced with a here document; I like the compactness of printf here.
#!/bin/bash
for f in *.phylip; do
mkdir -p dollop/"$f"
cp "$f" dollop/"$f"
cd dollop/"$f"
printf "%s\n" "$f" "U" "5" "Y" \
"/home/agalvez/data/sims/trees/tree_nodenames.txt" |
phylip dollop > screenout
done
Going forward, try http://shellcheck.net/ for diagnosing many common beginner problems in shell scripts.

Answer 2

Assuming you have a directory named pingping in your ${HOME} folder with files 1.txt, 2.txt, 3.txt. You can accomplish that like this. Modify this code to suit your needs.
#! /bin/bash
working_directory="${HOME}/pingping/"
cd $working_directory
for f in *.txt
do
mkdir "${f%%.*}"
if [ -f "${f%%.*}.txt" ]
then
if [ -d "${f%%.*}" ]
then
cp ${f%%.*}.txt ${f%%.*}
echo "Done copying"
#phylip dollop < input > screenout
#echo "Succesfully ran the command
fi
else
echo "not found"
fi
done