Merge pull request #64 from roryk/master

Tophat2 support, vcf splitter by chromosome, some utilities.
Move splitting VCF functionality into split namespace
Provide support for configuring with debian/ubuntu's picard-tools package or a Picard download of jar files. Thanks to @guillermo-carrasco.
Provide distributed task for re-writing recalibrated BAM files. Provides parallel speed up when recalibrating on whole genome BAMs
Provide general mechanism to group together samples for concurrent processing. Use this to implement multi-sample GATK calling. Handles calling plus split and recombine into final single sample VCFs
Write documentation for distributed phylogenetic BLAST. Provide ability to process local pre-downloads FASTA dbs. Handle errors with no descriptions of recent blast+ versions
Improve naming for grouped variant calling: batches instead of families
Support variant calling with mpileup and VarScan, which uses a heuristic/statistic calling approach
Merge pull request #65 from roryk/master

Generic options support
Convert VarScan indel format into VCF compatible representation. Use local temporary directories by default for GATK runs
Avoid additional filtering for VarScan calls since calls are filtered as part of calling process
Increase input counts for recalibration on whole genomes to include additional data and keep recal/re-write times in sync
Include multiple batching target in ipython tasks
Refactor @memoize_outfile to not also transform the filename.
Changed decorator signatures to more closely match the originals.
Memoize returns the output from the function it decorates if the function runs.
Added unit tests for the updated decorators.
Inclusive varscan p-value that still includes calculation of p-values
Refactor of memoize output to take either ext or stem as an argument and do the right thing.
Added a fastq groomer to play with the updated memoization.