Fix for missing .fai and .dict when using reference file from the history.

When selecting the FASTA reference file from the history, GATK 2.8 and
later (and maybe earlier versions too) does not create '.fai' and '.dict'
anymore:

ERROR MESSAGE: Fasta index file /opt/galaxy/tmp/tmp-gatk-Obym0N/gatk_input.fasta.fai for reference /opt/galaxy/tmp/tmp-gatk-Obym0N/gatk_input.fasta does not exist. Please see http://gatkforums.broadinstitute.org/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference for help creating it.

Similar error if only the .fai, but not the .dict is created:

ERROR MESSAGE: Fasta dict file /opt/galaxy/tmp/tmp-gatk-vlrnAe/gatk_input.dict for reference /opt/galaxy/tmp/tmp-gatk-vlrnAe/gatk_input.fasta does not exist. Please see http://gatkforums.broadinstitute.org/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference for help creating it.
Suppress picard logging info on sys.stderr .
Merge pull request #37 from nsoranzo/gatk2

Fix for missing .fai and .dict when using reference file from the history
fix for a wrong specified *.loc file
add min=1 to the repeat tag, at least one needs to be specified
add validator no_option to the annotation column, at least one needs to be specified
Merge branch 'master' of https://github.com/bgruening/galaxytools
Annotation DepthOfCoverage is no longer available in the GATK; it has been deprecated since version 2.4 (renamed to Coverage)
See http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_MVLikelihoodRatio.html
Add HaplotypeCaller as additional valid_tool filter
remove MappingQualityZeroFraction
remove options that are not available anymore
add ncurses as samtools dependency #39, @bwlang: can you test  http://testtoolshed.g2.bx.psu.edu/view/iuc/package_samtools_0_1_19 if its working for you?
adopt VariantRecalibrator to new standard settings
add GATK2 R dependencies
adopting to new GATK 2.8 version
Add package_bwa_0_7_7 .
update to latest R version
export more ENV variables
export more ENV variables