Installation

First, download FlexFlux executable version here.

Unzip FlexFlux_1.0_executable.zip in the folder of your choice.

To use FlexFlux you need Java to be installed. It can be downloaded from http://www.oracle.com/technetwork/java/javase/downloads/index.html.

FlexFlux runs on Java 7 or higher.

Linux

For FlexFlux to work, you must have already installed a solver. At this point, FlexFlux supports CPLEX and GLPK.

To install glpk for java on Ubuntu and Debian you can type this in a terminal :

sudo apt-get install libglpk-java

Open a terminal and go into the directory where you put FlexFlux/
make Flexflux.sh and GraphicalFlexflux.sh executables by typing the commands :
```
chmod +x Flexflux.sh
```
```
chmod +x GraphicalFlexflux.sh
```
Test your solvers and run the unit tests by typing :
```
./Flexflux.sh Test
```
If a solver is OK, you are all set ! Skip step 4, you can use FlexFlux. If no solver is OK, go to step 4.

Open the configuration file : config

which looks like that :

#IF YOU ARE USING CPLEX YOU MUST SET THE RIGHT VALUE FOR THOSE TWO VARIABLES
#link to the CPLEX shared library (directory containing libcplex124.so)
CPLEX_shared_library=/usr/local/ILOG/CPLEX_Studio124/cplex/bin/x86-64_sles10_4.1/
#link to CPLEX.jar
CPLEX_JAR=/usr/local/ILOG/CPLEX_Studio124/cplex/lib/cplex.jar


#IF YOU ARE USING GLPK YOU MUST SET THE RIGHT VALUE FOR THOSE TWO VARIABLES
#link to the GLPK shared library (directory containing libglpk_java.so)
GLPK_shared_library=/usr/local/lib/jni:/usr/lib/jni/
GLPK_JAR=lib/glpk-java-linux.jar

Set the right value(s) for your solver, ignore the others. Try the ./Flexflux.sh Test again.

Use the graphical version of Flexflux by executing the file "GraphicalFlexflux.sh"

OR

Launch the analysis you want by typing :
```
./Flexflux.sh your_analysis your_parameters
```
Example :
```
./Flexflux.sh FBA -s network.xml -cond conditions.txt -plot
```
See the documentation for details on all possible analyses.

You can test each function by running the examples provided in the "examples" folder.

make them executables by typing the command :
```
chmod +x examples/*.sh
```
Run an example for instance :
```
./examples/FBA_example.sh
```

Windows

The solver GLPK is already included in FlexFlux so if you want to use it you have nothing to do.

If you want to use another solver, you must install it.

Open the folder Flexflux/
Test your solvers by running the windows command file "GraphicalFlexflux"
If a solver is OK, you are all set ! Skip step 3), you can use FlexFlux. If no solver is OK, go to step 3).

Open the configuration file : config.windows.bat

which looks like that :

@echo off

::IF YOU ARE USING CPLEX YOU MUST SET THE RIGHT VALUE FOR THOSE TWO VARIABLES
::link to the CPLEX shared library (directory containing libcplex124.so)
set CPLEX_shared_library=
::link to CPLEX.jar
set CPLEX_JAR=


::IF YOU ARE USING GLPK YOU MUST SET THE RIGHT VALUE FOR THOSE TWO VARIABLES
::link to the GLPK shared library (directory containing glpk_4_50_java.dll)

if %PROCESSOR_ARCHITECTURE%==x86 (
  set GLPK_shared_library=lib\glpk-4.50\w32
) else (
  set GLPK_shared_library=lib\glpk-4.50\w64
)

::link to glpk jar
set GLPK_JAR=lib\glpk-java-win.jar

Set the right value(s) for your solver, ignore the others. Try the Flexflux.bat Test again.

Use the graphical version of Flexflux by running the windows command file "GraphicalFlexflux"

OR

Launch the analysis you want by typing in the command line :
```
Flexflux.bat your_analysis your_parameters
```
Example :
```
Flexflux.bat FBA -s network.xml -cond conditions.txt -plot
```
See the documentation for details on all possible analyses.

You can test each function by running the examples provided in the "examples" folder.
You can run any of the examples by double clicking on it (the windows files have a ".bat" extension)

FlexFlux installation

Linux

Windows