Corona Lite without Job Scheduling

[doxologist]

I'm trying to implement Corona Lite on a linux box running Fedora Core 8.
I don't have PBS on the machine.
So, I'm trying just to run without job scheduling.

This is what ABI suggests:
>To execute the jobs without a scheduling system, locally execute each of >the scripts in JOB_LIST.txt as follows:
>% cut -f2 JOB_LIST.txt > cmd
>% sh cmd

However, it still calls a Perl module called PBSJob.pm.

two questions:
1) Is it easy to put PBS on the box? (from http://www.openpbs.org) it doesn't seem trivial.

2) Where can I find PBSjob.pm or prevent the script from needing this?

Thanks.

[Mr Mutundes]

This works for me as described with 'matching' (although haven't tried 'pairing' or 'SNPs')

Does your 'cmds' file have a list of filenames (it should of course)? What is in e.g. the first one of these? Which perl program gave the error about requiring the PBS module?

[lgoff]

I have gotten this to work without the error or PBS using the method described. Perhaps if you post more information about the error we can be of more help? Which script?

PBSJob.pm is located in the following location...

$INSTALL_DIR/corona_lite_v0.32/lib/perl/PBSJob.pm

It is possible that you do not have your perl path setup correctly to include the CORONALITE lib?

Just a thought.

-Loyal

[doxologist]

thanks for all the help.

I was trying to run
matching_large_genomes_cmap_save_script.pl

yes, the error was setting the wrong paths. silly me.

thanks