Make a config.txt file:
This file is used to specify what type of analysis is done on the data from each lane.
#This line points to the directory containing the genomes that the sequence reads will be aligned to
GENOME_DIR /data/pipeline/GENOMES
#This line stated the type of analysis that should be done. Lines that are not preceeded by any numbers indicate that this parameter applies to all lanes of the flowcell.
ANALYSIS eland_extended
#This line indicates that all bases should be used in the analysis
USE_BASES all
#This line indicates that the reads from lane 1 should be aligned to the P_furiosus genome
1:ELAND_GENOME /data/pipeline/GENOMES/P_furiosus/
#This line indicates that the reads from lane 2 should be aligned to the S_tokodaii genome
2:ELAND_GENOME /data/pipeline/GENOMES/S_tokodaii/
#This line indicates that the reads from lanes 3 and 5 should be aligned to the S_solfataricus genome
35:ELAND_GENOME /data/pipeline/GENOMES/S_solfataricus/
#This line indicates that the samples from lanes 4 and 7 should be aligned to the phi genome
47:ELAND_GENOME /data/pipeline/GENOMES/phi/
#This line indicates that the samples in lanes 6 and 8 should be aligned to the D_melanogaster genome
68:ELAND_GENOME /data/pipeline/GENOMES/D_melanogaster/
#This line indicates that the data should be output in "scarf" format
SEQUENCE_FORMAT --scarf
#This line indicates that the quality scores for the data should be displayed numerically
QUALITY_FORMAT --numeric
root# /illumina/pipeline/GAPipeline-0.3.0/Goat/goat_pipeline.py --GERALD=/data/pipeline/080606_HWI-EAS299_0003/config.txt /data/pipeline/080606_HWI-EAS299_0003
root# /illumina/pipeline/GAPipeline-0.3.0/Goat/goat_pipeline.py --GERALD=/data/pipeline/080606_HWI-EAS299_0003/config.txt --make /data/pipeline/080606_HWI-EAS299_0003
root# nohup make recursive -j 8 &