commiting fixes for pull request #1
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Thanks for the great tool!
I've made a few changes I hope you will incorporate into the main repo.
Mostly, I want to change filepaths being hardcoded in the script. All necessary executables should be available in the PATH environmental variable.
For instance, when running quake.py, I should already have
baseapp/quake/bin/quake.py,correct,count-qmers in the PATH var.
By the same token I already have jellyfish in my path. There is no need to create an additional install step where jellyfish and the libraries need to have a symbolic link to the quake bin.