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Need a Bash file to run a perl script.

This is the Perl file. 

#!/usr/bin/perl -w
use strict;


system "fastacmd -s $Q -d $NewQuery -o ./gifiles/$Q.$NewQuery.txt";

I have left alot out to avoid complications when understanding this script. Before using a bash command, the script did work with the variables defined.

Here is the Bash script

#!/bin/bash

#$ -o $HOME/xREPLaunch_$JOB_ID.out

#$ -e $HOME/xREPLaunch_$JOB_ID.err

cd $HOME/Labwork/Dbfiles/results

#$ -cwd

perl xREPredoTop.pl

For some reason I keep getting this error 

Can't exec "fastacmd": No such file or directory at xREPredoTop.pl line 78, <IN> line 1.

Really confused to why this is not working.

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3  
That's the perl script indicating that it cannot find "fastacmd". The output of the shell command which fastacmd might be handy, or to inspect what $ENV{PATH} contains in the perl script, to see what directories it is looking for things in. –  thrig Aug 20 at 19:37
    
Post the output of echo "$PATH" and of ls -l /path/to/fastacmd (with the right path to the script). –  Gilles Aug 20 at 21:48

1 Answer 1

up vote 3 down vote

Two possibilities I can think of:

The usual one is that you are running the bash script from something like cron, where your user profile script hasn't run and set up $PATH. In this case you can specify

system "/path/to/fastacmd ...

within the perl script so that it doesn't depend on the path, or you can set the

$ENV{PATH}= "/my/custom/paths:$ENV{PATH}";

inside the perl script, or you can fix the path in the bash script by loading your profile scripts:

source /etc/profile;
source ~/.profile;
source ~/.bash_profile;

But the other possibility is that #!/usr/bin/perl declared in your script is not the same perl as in your PATH. You can check this by saying

which perl

For example, if you say ./xREPredoTop.pl it becomes

/usr/bin/perl -w ./xREPredoTop.pl

but if you say perl ./xREPredoTop.pl it could become

/usr/local/bin/perl ./xREPredoTop.pl

and that one could be configured differently in some way that it changes the path.

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