updated so user has control over where temp files are written, fixes #62
updated so stdout and stderr files are not written to /tmp
Merge pull request #65 from gregcaporaso/issue-62

improved output file names (ported fix from qiime's pycogent backports) and gives user control over temp file location
fixed bug - we don't actually want to change WorkingDir
Merge pull request #67 from gregcaporaso/issue-62

fixed bug - we don't actually want to change WorkingDir
Fixing default arguments for "params" parameter

Was set to {} in several cases, which can cause problems. Set to None instead,
then in the function set to {} if the value is None.
Merge pull request #68 from adamrp/fix_default_parameters

Fixing default arguments for "params" parameter