add numpy 1.8
Merge branch 'master' of https://github.com/bgruening/galaxytools
add GNU coreutils in version 8.22
Merge branch 'master' of https://github.com/bgruening/galaxytools
Remove left-out of standard_gatk_options macro.

This was causing the following error:

Traceback (most recent call last):
  File "/opt/shed_tools/central/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/f760c0de8e3a/gatk2/gatk2_wrapper.py", line 138, in <module>
    __main__()
  File "/opt/shed_tools/central/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/f760c0de8e3a/gatk2/gatk2_wrapper.py", line 96, in __main__
    gatk_filename = gatk_filename_from_galaxy( filename, galaxy_ext, target_dir = tmp_dir, prefix = prefix )
  File "/opt/shed_tools/central/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/f760c0de8e3a/gatk2/gatk2_wrapper.py", line 29, in gatk_filename_from_galaxy
    os.symlink( galaxy_filename, gatk_filename )
OSError: [Errno 17] File exists
upgrade to GNU coreutils 8.22 to fix a build bug on cluster environments
Merge branch 'master' of https://github.com/bgruening/galaxytools
remove parallelism tag
Merge branch 'master' of https://github.com/bgruening/galaxytools
update to the latest bugfix release https://github.com/bgruening/galaxytools/pull/57
Update README.rst
fix bug reported by Sebastian
Merge branch 'master' of https://github.com/bgruening/galaxytools
restructure EDeN wrappers
GATK2: Update upstream documentation links for 2 tools. Documentation for ReduceReads has been removed.
remove obsolete tools
add new bedtools wrappers
Merge branch 'master' of https://github.com/bgruening/galaxytools
add samtools sort
Merge branch 'master' of https://github.com/bgruening/galaxytools