calls to uclust should use temp_dir

[antgonza]

When pick_otus.py calls uclust it uses /tmp/ vs. using the temp_dir in the qiime configuration, an example: uclust --input /tmp/UclustExactMatchFilterlS4C2v.fasta --id 0.97 --tmpdir /tmp --rev --w 12 --stepwords 20 --usersort --maxaccepts 20 --stable_sort --maxrejects 500 --uc ucrss/step4_otus/failures_failures_clusters.uc

This is a problem on systems with limited /tmp/ and several jobs running on the same node.

[josenavas]

Depends on biocore/brokit#21

[antgonza]

Just saw, this mentioned in a Qiime1 forum post. A possible solution is: export TMPDIR=[your folder]