Added gatk to the resources of qcsummary.
Set quality flag properly for Tophat alignment.

Thanks to @mjafin.
Merge branch 'tophat-quality-fix'
Update Tophat fix.
Keep original compressed fastq files.
Save original compressed FASTQ files.

Also write uncompressed FASTQ files to the work directory so
they can be cleaned up easily.

Swapped the explant integration testing data to use gzipped files.
Also added another replicate, just because.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Use standard exist instead of checking file size when transferring directories to final location. Touch final copied directories to avoid multiple transfers with time preserving copytree. Fixes #198
Fixed transcriptome-index not being located correctly.

Thanks to @mjafin.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Added .ver to the end of the transcriptome_index files.
Tophat and FASTQ fixes.
Bumped version numbers on resources files so they get tagged as new.
Annotate NA12878 example datasets as females so variant calling will treat sex chromosomes correctly
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Document relocatability and medium term move to docker. Fixes #197
Avoid usage of pbgzip until can better debug and fix segfault issues
Avoid overwriting existing configuration file when creating from a template. Back up current files with .bak timestamp. Fixes #196
Correctly avoid setting ploidy to non-diploid when using GATK lite versions. Provide better error messages for GATK directories with multiple jars. Thanks to Severine Catreux
Fixed bug in complexity figure calculation.