added stacks code
fixed up several packages in regard to compiler types
added load of scipy module to biopython
added load of intel module
made default compiler icc
made default compiler intel (mistake last commit)
added load of intel module for edena
added PKGROOT as mount point
added load of scipy and intel modules
add install directory to PYTHONPATH
new tophat version (doesnt need external samtools anymore)
removed some more references to samtools from tophat
added intel module load for miso Makefile
added scipy, and intel modules to bx-python and pysam
Merge pull request #1 in APS/biotools-roll from feature/APS-21-add-stacks-to-biotools to master

* commit '76c40f1ebb0473d61fca373e2d81c5e45eadb69f':
  added scipy, and intel modules to bx-python and pysam
  added intel module load for miso Makefile
  removed some more references to samtools from tophat
  new tophat version (doesnt need external samtools anymore)
  add install directory to PYTHONPATH
  added load of scipy and intel modules
  added PKGROOT as mount point
  added load of intel module for edena
  made default compiler intel (mistake last commit)
  made default compiler icc
  added load of intel module
  added load of scipy module to biopython
  fixed up several packages in regard to compiler types
  added stacks code