uclust.py should accept a temporary directory as an argument

[ebolyen]

Instead of using from tempfile import gettempdir.
related to biocore/qiime#1319

[walterst]

The functions can accept a tmp_dir parameter, they just currently aren't being passed one.
We'd have to track down each time these functions are called from QIIME and pass the temp_dir from the qiime_config when they are called rather then letting them default to the gettempdir value:
uclust_cluster_from_sorted_fasta_filepath
uclust_search_and_align_from_fasta_filepath
uclust_fasta_sort_from_filepath

[gregcaporaso]

A work-around until we have this in place will be to set the one of the three environment variables that python looks at when trying to determine the value for tempfile.tempdir (see here). These are:

• TMPDIR
• TEMP
• TMP

Note that you may need to set this variable in ~/.bashrc (not ~/.bash_profile!) if the shell that will execute these jobs is not a login shell. This is likely the case if you're using QIIME's parallel wrappers. So, you'd want to do something like this:

echo "export TMPDIR=$HOME/temp" >> ~/.bashrc