Preventing .pyc files from being tracked
removing igv.log from repository
new modules:
- fastqc : run 'FastQC' for .fastq files
- annotate_mutscan_batch : annotate output from mutscan using VEP
- annotate_join_cosmic_batch : filter 'confirmed somatic mutation' using cosmic
- annotate_join_cosmic : subroutine for annotate_join_cosmic_batch (for each sample)
- new symbolic link to '/pipeline': /var/www/html/pipeline2
- Change apachBase to new symbolic link to '/pipeine' so that everying under project folder can be directly linked from web report file
- rsq2expr, rsq2mut, xsq2mut is modified to include new modules: fastqc, annotatate_mutscan (VEP), annotate_join_cosmic
temporarily add mygenome.pyc
Merge branch 'master' of https://github.com/SMC1/JK1

Conflicts:
	modules/mygenome.pyc
	modules/mygp.pyc
	modules/mygsnap.pyc