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directory and you're having a problem remember that Cygwin's path syntax
may not be the correct one. Cygwin understands `/home/jacky` or
`/cygdrive/e/cygwin/home/jacky` (when referring to the E: drive) but the
external resource may want `E:/cygwin/home/jacky`. So your `*rc` files may end
up with paths written in these different syntaxes, depending.

For example, here's how to set the environmental variable TMPDIR, programs
like BLAST and clustalw need a place to create temporary files:

```
setenv TMPDIR e:/cygwin/tmp    # csh, tcsh
export TMPDIR=e:/cygwin/tmp    # sh, bash
```