Problems with my automation script

[Boggy667]

Hi, i wonder if someone could help me. I'm new to shell scripts and i've tried to write this script, the aim of it is to check if the $4, $5 etc variables are empty to avoid annoying errors when the program it calls tries to process an non existant file with no name
I'm running fedora core 4 if that makes any difference.

I have two main problems

ONE

++++++++++++++++++
the #!/bin/bash line as causes this error:

: bad interpreter: No such file or directory

the script (in an earlier simpler form) ran fine without it so i left it out for the time being

TWO

In it's new form the script keeps exiting with:

subst.codon: line 42: syntax error: unexpected end of file

     1  if ["$4" -ne ""]
     2  then
     3          subst -n $1 -p 1 -i "$4" $3 > ../output/$2/subst.codon/$4.1.txt;
     4          subst -n $1 -p 2 -i "$4" $3 > ../output/$2/subst.codon/$4.2.txt;
     5          subst -n $1 -p 3 -i "$4" $3 > ../output/$2/subst.codon/$4.3.txt;
     6  elseif ["$5" -ne ""]
     7  then
     8          subst -n $1 -p 1 -i "$5" $3 > ../output/$2/subst.codon/$5.1.txt;
     9          subst -n $1 -p 2 -i "$5" $3 > ../output/$2/subst.codon/$5.2.txt;
    10          subst -n $1 -p 3 -i "$5" $3 > ../output/$2/subst.codon/$5.3.txt;
    11  elseif ["$6" -ne ""]
    12  then
    13          subst -n $1 -p 1 -i "$6" $3 > ../output/$2/subst.codon/$6.1.txt;
    14          subst -n $1 -p 2 -i "$6" $3 > ../output/$2/subst.codon/$6.2.txt;
    15          subst -n $1 -p 3 -i "$6" $3 > ../output/$2/subst.codon/$6.3.txt;
    16  elseif ["$7" -ne ""]
    17  then
    18          subst -n $1 -p 1 -i "$7" $3 > ../output/$2/subst.codon/$7.1.txt;
    19          subst -n $1 -p 2 -i "$7" $3 > ../output/$2/subst.codon/$7.2.txt;
    20          subst -n $1 -p 3 -i "$7" $3 > ../output/$2/subst.codon/$7.3.txt;
    21  elseif
    22  if ["$8" -ne ""]
    23  then
    24          subst -n $1 -p 1 -i "$8" $3 > ../output/$2/subst.codon/$8.1.txt;
    25          subst -n $1 -p 2 -i "$8" $3 > ../output/$2/subst.codon/$8.2.txt;
    26          subst -n $1 -p 3 -i "$8" $3 > ../output/$2/subst.codon/$8.3.txt;
    27  elseif ["$9" -ne ""]
    28  then
    29          subst -n $1 -p 1 -i "$9" $3 > ../output/$2/subst.codon/$9.1.txt;
    30          subst -n $1 -p 2 -i "$9" $3 > ../output/$2/subst.codon/$9.2.txt;
    31          subst -n $1 -p 3 -i "$9" $3 > ../output/$2/subst.codon/$9.3.txt;
    32  elseif ["$10" -ne ""]
    33  then
    34          subst -n $1 -p 1 -i "$10" $3 > ../output/$2/subst.codon/$10.1.txt;
    35          subst -n $1 -p 2 -i "$10" $3 > ../output/$2/subst.codon/$10.2.txt;
    36          subst -n $1 -p 3 -i "$10" $3 > ../output/$2/subst.codon/$10.3.txt;
    37  else
    38          exit;
    39  endif
    40  echo "All Done!";
    41  exit 0;

I've tried it with and without exit 0 at the end and that made no difference

Thanks for any help

Kev

[lakerdonald]

1. Try changing it to:

#!/usr/bin/bash

2. Please post the entire script inside [code] tags

[Boggy667]

Thanks for the speedy reply

Anywho i've tried changing the first line as you suggested and that had no effect. I still get the same error message even with

#!/usr/bin/bash

however the script will run without that line so i'm not too bothered by it my main issue is the rest of my script and the unexpected end of file problem.

Unless of course the issue with the first line is a symptom of a bigger problem as it happens with my perl scripts as well even when the path is correct.

[burnit]

The very first line indicates wich program can handle the following script... so if you specify #!/bin/bash, /bin/bash must exists and must executable. I suggest to put /bin/sh, wich should be a soft link to the default sheel of the system.

About your error... you should numer all lines (cat can do it for you! ).

[Boggy667]

Thanks burnit but, I've tried all versions of the first line and bash is def in my /bin folder and executable. even #!/bin/sh doesn't work

Any ideas why #! line isn't working in any of my scripts (including perl)

Also i've modified my first post to include line numbers, hopefully that helps.

[lakerdonald]

Please remove the line numbers, it is very hard to read.

[Boggy667]

burnit recommended adding the line numbers, which i tend to agree with as it makes it easier to identify which lines the errors are referring to.

It should be fairly easy to read the code with the line numbers, as they're fairly well separated.

[eerok]

First, confirm that your bash is where it should be, which, if it's your default shell is /bin/bash

which bash

then be sure to invoke your script with an explicit pathname if it's not in a directory covered by your normal path (ie, use "./" if it's in your current directory)

./scriptname

As for the rest, well, it doesn't look like a bash script to me. What are you using for a reference?

For example, I'd expect to see if/elif/fi rather than if/elseif/endif and no semicolons as line terminators in a bash script.

[Boggy667]

my bash is definately where it should be, /bin/bash

so i'm not sure why it's having issues, if i add a switch to the line eg

#!/bin/bash --debug

then it recognises bash as the interpreter but gives

:invalid option

and then the bash switch list

i'm running the script from /bin

I can't remember the website is used for reference. I removed all the semicolons and switched everything to if/elif/fi and it gave the following error:

/bin/subst2.codon: line 6: syntax error near unexpected token `elif'
'bin/subst2.codon: line 6: `elif ["$5" -ne ""]

I also tried changing the endif to fi and elseif to elsif, which fixes the above problem but that still makes no difference to the 'unexpected end of file' error.

[scm]

You need whitspace after the [ of the if conditions:

if [ "$4" -ne "" ]

The [ must be whitespace separated because it's a synonym for the "test" command, and the trailing ] must be seen as an argument in its own right - tagging onto the "" will hide it from the shell, resulting in your unexpected end of file error.