Merge pull request #16 from nsoranzo/master

package_bowtie_1_0_0 plus a small fix.
add ruby 1.9 tool dependency
add ruby 2.0 tool dependency
add bioruby 1.4 with ruby2 tool dependency
remove --debug flag and enhance documentation
nothing
Merge branch 'master' of https://github.com/bgruening/galaxytools
use new EDeN output options, integrate fasta2shrep_gspan, use macros more aggressivly
add proper output selection to KNN search
add definition for RNAshapes
refactor the sequence to gspan wrapper and use separate repository
move molecule to gspan to a separate repository
migrate molecule2gspan to a new repository and add dependencies
remove unused softlink
add repository dependency to sequence2gspan
update EDeN wrapper
migrate to new autoconf feature
migrate to new autoconf feature
remove lapack dependency for know
add multiprocessing to sequence2gspan