Dear all,

I have a Perl code that take some parameters. I would then run this code on few parameter sets on a Linux Cluster - comprising 40 CPUs. Finally, I would con-cat-enate the result into one single file.

Here is the general steps I would do:
1. Perl code is executed in this way individually.

 $ perl mycode.pl file1.txt param1 param2 > param_set1.out 
 $ perl mycode.pl file1.txt param3 param4 > param_set3.out
 $ perl mycode.pl file1.txt param4 param5 > param_set4.out

 $ cat param_set1.out param_set3.out param_set4.out  > final.out
[download]

Here we have param_set1 = (param1,param2), etc. There are many of these param sets. For each of this param set I would run on Linux Cluster via qsub command.

2. Before running qsub command I have this bash script required by qsub to do his job. Let's call this script "runcode.sh".

#!/usr/bin/bash

cd ~/some_dir
perl mycode.pl $1 $2 > ~/some_out_dir/param_set$1.out
[download]

3. Subsequently I would manually submit each param set to the cluster as in shown in step 1 as follows:

$ qsub runcode.sh param1 param2
$ qsub runcode.sh param3 param4
$ qsub runcode.sh param5 param6
[download]

My question is how can I write a Perl script that:

• Automatically submit all these parameter sets into Linux Cluster.
• Automatically concatenate each of the results into one single final file.
  Noting that all outputs of each param set must be completed first before concatenating them.

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