SLURM_bioinformatics_scripts

SLURM_bioinformatics_scripts is perl libraray that helps to run a bioinformatics core facility.

INSTALL

As you most likely run the scripts on a server you are not admin of you might consider installing Perl local::lib.

In addition you need git:

You will need my base libs which you can get from my Stefans_Lib_Esentials repository. And my stefans_libs::BAMfile from the respective guthub page.

Clone this repository and use the perl Makefile.PL make make install combination.

USAGE

The package comes with a set of scripts. They report there usage on the command line and should be in your path after the install.

bowtie2_run_aurora.pl would return (at the time of writing the readme)

the cmd line switch -files is undefined! the cmd line switch -options is undefined! the cmd line switch -genome is undefined! . Usage: bowtie2_run_aurora.pl -files :a list of fastq or fastq.gz files
-options :additional options in the format key_1 value_1 key_2 value_2 ... key_n value_n -genome :the genome definition as used by bowtie2 -X -coverage :the genome coverage file to create bigwig tracks -paired :if you have paired data to map use this option and give me the pired files one after the other

       -bigwigTracks :If I have a coverage file I can create the 
                      bigwig tracks information and stoire it there

       -help      :print this help
       -debug     :verbose output

    required options:

    n   :number of cores to request from SLURM (rec. 10)
    N   :number of nodes to request from SLURM (rec. 1)
    mem :minimum memory from SLURM (rec. 4000M for e.g. human genome)
    t   :the time the job should get to finish - do not set too short
         rec 02:00:00 == 2h