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Difference between revisions of "Ada:GCATemplates"

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Revision as of 15:37, 7 April 2017

GCATemplates is a tool on Ada that allows you to copy a Bioinformatics job script template to your current working directory.

 module load GCATemplates

Run the following command then follow the menus to find a template script.

 gcatemplates


GCATemplates




















  • The final menu will allow you to copy the template file to your current working directory.
  • The template files have default settings for a tool.
  • You need to edit the input files and read the manual for available options to use other than defaults.
  • You will need to adjust the BSUB parameters as well as variables in the TODO section based on your project.


Below is an example of a template file.

#BSUB -L /bin/bash              # uses the bash login shell to initialize the job's execution environment.
#BSUB -J fastqc                 # job name
#BSUB -n 2                      # assigns 2 cores for execution
#BSUB -R "span[ptile=2]"        # assigns 2 cores per node
#BSUB -R "rusage[mem=2000]"     # reserves 2000MB memory per core
#BSUB -M 2000                   # sets to 2000MB process enforceable memory limit. (M * n)
#BSUB -W 1:00                   # sets to 1 hour the job's runtime wall-clock limit.
#BSUB -o stdout.%J              # directs the job's standard output to stdout.jobid
#BSUB -e stderr.%J              # directs the job's standard error to stderr.jobid

module load FastQC/0.11.5-Java-1.7.0_80

<<README
    - FASTQC homepage: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
    - FASTQC manual: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
README

################################################################################
# TODO Edit these variables as needed:
threads=2                       # make sure this is <= your BSUB -n value

pe1_1='/scratch/datasets/GCATemplates/data/sra/m_tuberculosis/ERR551981_pe_1.fastq.gz'
pe1_2='/scratch/datasets/GCATemplates/data/sra/m_tuberculosis/ERR551981_pe_2.fastq.gz'

################################################################################
# use -o <directory> to save results to <directory> instead of directory where reads are located
#   <directory> must already exist before using -o <directory> option
# --nogroup will calculate average at each base instead of bins after the first 50 bp
# fastqc runs one thread per file; using 20 threads for 2 files does not speed up the processing

fastqc -t $threads -o ./ $pe1_1 $pe1_2

<<CITATION
    - Acknowledge TAMU HPRC: https://hprc.tamu.edu/wiki/index.php/HPRC:AckUs

    - FastQC: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
CITATION