prepSamples.sh now expects VarScan in the CLASSPATH environment variable.
HPC support. Use all cpu cores by default.  Show defaults with create_snp_matrix.py --help.
Add the visio drawing source file beacuse it is going to change.
Split the bowtie align from prepSamples -- moved into alignSampleToReference.  The alignSampleToReference script gives better control of the HPC computing resources.  The prepSamples script now takes a sample directory argument instead of two fastq files.  Changed the test_from_scratch scripts to handle a mix of paired and unpaired samples.  Changed the docs to mention alignSampleToReference and to give instructions for feeding the pipeline with a mix of paired and unpaired samples.
Merge branch 'master' of /home/steven.davis/mnt/biob/svn/Biostats/rand/repo/snppipeline
Update pipeline drawing with alignSampleToReference.sh
Merge branch 'master' of b:/svn/Biostats/rand/repo/snppipeline
Update the installation instructions to recommend pip --user install.
Bug Fix: The snp list, snp matrix, and referenceSNP files were incorrectly sorted by position alphabetically, not numerically.
Add the --reorder option to bowtie alignment for reproducible pileup results.
Modify drawing to include the samtools faidx step as part of prepReference.
Parallel prepSamples with Xargs -P option.  Commit all intermediate result files to test reproducible results.
Log the executed commands with all options to stdout.
Fix snplist file path with os.path.join
Tested on Red Hat.
Bash syntax highlighting.