Support GATK-compatible VCF output format.

There are 2 errors which can happen when running GATK Variant Annotator
with a SnpEff result file as input:
- in GATK2: "The version of SnpEff used to generate the SnpEff input
file (3.x) is not currently supported by the GATK, and was not run in
GATK compatibility mode. Supported versions are: [2.0.5], as well as
later versions when run with the option -o gatk": this is fixed just by
selecting the "GATK-compatible VCF" output type;
- in GATK1: "The version of SnpEff used to generate the SnpEff input
file (x.x) is not currently supported by the GATK. Supported versions
are: [2.0.5]": this is fixed by selecting the GATK-compatible VCF output
type and also the "Compatible with GATK 1.x" checkbox.
upgrades bismark to 0.10
no longer sorts bam by defaults (methylation extractor can't take that)
methylation extractor can now handle bam files directly
bismark takes an argument -p, which it passed
directly to bowtie2 for *each* bowtie2 process
it runs.

This is bad on a shared cluster since it uses
double the cpus compared to the number of slots requested.

This changes the meaning of -p from 
"number of threads used by each bowtie2 process"
to 
"number of total threads used by bismark"

(if a --non_directional flag is ever added, we'll need to divide by 4 instead of 2)
bam_path is just a plain variable, not a member of args
Merge pull request #42 from bwlang/bismark_0.10

upgrades bismark to 0.10
update tool version number
adjust the effective genome size
add CFLAGS and CPPFLAGS to adjust to clang errors
remove unuesed requirement
Merge branch 'master' of https://github.com/bgruening/galaxytools