src/geneFinder/Operon_LP.java | 17 0 + 17 - 0 !
src/geneFinder/OptimizeAmbis.java | 44 0 + 44 - 0 !
src/geneFinder/ReadInParameters_GeneFinder.java | 10 4 + 6 - 0 !
3 files changed, 4 insertions(+), 67 deletions(-)

 upstream makes use of cplex java library which is not
 free. Glpk can be used as an alternative.
 Update code to use glpk as only default option and remove cplex code
 to allow compilation

src/geneFinder/Giira.java | 2 1 + 1 - 0 !
src/geneFinder/ReadInParameters_GeneFinder.java | 2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-)

 hardcode path to python helper scripts
 The documentation says that you can set the path to the Python
 helper scripts via
    -script /usr/share/giira/scipts
 but this is wrong as the output looks like
 .
 Call: 
 java -Xmx894m -cp /usr/share/java/giira.jar:/usr/share/java/giira-0.0.20140210.jar geneFinder.GeneFinder -opti glpk -scripts /usr/share/giira/scripts -iG example/Scer_chr4.fasta -iR example/scer_example_reads.fastq -out GIIRA_example/ -iter 1 -scripts /usr/share/java/giira-0.0.201scripts/
 .
 which seems to magically force some wrong scriptPath.  This patch
 forces the correct installation path of the Debian package.