specify temporary file location

[nick-youngblut]

It appears that the user cannot specify the temporary file location. This has created a problem for our research group, because panx.py when run with many threads will create many child processing running mafft, which in turn create child processes running awk. The many awk jobs slams our hard drives and slows down our file server greatly. We need to be able to specify where the temporary files are written in order to use a different set of hard drives so that all users of our server are not affected by the high I/O load caused by the awk jobs.

[nick-youngblut]

For anyone that also has this issue, @wdingx told me in an email:

PanX generates the tmp folders for alignment and tree building of gene clusters in the given species folder (specified by the -fn parameter). So, all the data should be generated under the given path