This file is part of PumpKin (see http://www.pumpkin-tool.org).
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Before installing PumpKin, the user should have installed the GLPK package. For this we recommend tools like MacPorts (www.macports.org) or Fink (www.finkproject.org) for Mac OS X and package management systems for GNU/Linux distributions. The windows user can get installation instructions at (winglpk.sourceforge.net).
The full source code of PumpKin is available at:
After the download user should do:
1. Copy the pumpkin distribution file to a working directory.
2. Unpack the distribution file with the following command:
$ gzip -d pumpkin-X.Y.tar.gz
After unpacking the distribution file is automatically renamed to ‘pumpkin- X.Y.tar’.
3. Unarchive the distribution file with the following command:
$ tar -x < pumpkin-X.Y.tar
It automatically creates the subdirectory ‘pumpkin-X.Y’ containing the pumpkin distribution.
The PumpKin package contains the folling files:
Copyright_and_License README User manual.pdf src/ Makefile PumpKin.cpp pk_Array.h pk_IO.cpp pk_Pathways.cpp pk_Print.cpp pk_Array.cpp pk_DataTypes.h pk_IO.h pk_Pathways.h pk_Print.h Examples/ ZDPlasKin/ Input_10/ input.txt qt_conditions_list.txt qt_matrix.txt qt_reactions_list.txt qt_conditions.txt qt_densities.txt qt_rates.txt qt_species_list.txt Input_20/ input.txt qt_conditions_list.txt qt_matrix.txt qt_reactions_list.txt qt_conditions.txt qt_densities.txt qt_rates.txt qt_species_list.txt Global_Kin/
The package consists of the following C++ files:
PumpKin.cpp pk_DataTypes.h pk_Array.h, pk_Array.cpp pk_IO.h, pk_IO.cpp pk_Print.h, pk_Print.cpp pk_Pathways.h, pk_Pathways.cpp
a. PumpKin.cpp -- is the user defined file to run PumpKin and make output. b. pk_DataTypes.h -- contains all the abstract structures which store the data like rates etc. c. pk_Array.h(.cpp) -- multidimensional dynamic array structures d. pk_IO.h(.cpp) -- contains all the input routines to read input data e. pk_Print.h(.cpp) -- contains all the printing (output) routines g. pk_Pathways.h(.cpp) -- performs all operations over pathways. The core of algorithm is implemented in these files.
The simplest way to build this package is:
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`cd' to the directory containing the package's source code: $ cd pumpkin-X.Y/src
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Type make to buid it: $ make
To run simple examples provided with package type: $ ./pumpkin Examples/ZDPlasKin/Input_10 $ ./pumpkin Examples/ZDPlasKin/Input_20 or $ ./pumpkin Examples/Global_Kin
- On fedora 32, 64bit arch, i5 10th Gen Dell Inspiron: The original Makefile (when downloading the package from Aram's website) has the following on line 23:
$(LINK) $(LFLAGS) -std=gnu++0x $(OBJ) -o $@ $(LIBS)where$(LFLAGS) = -stdlib=libc++.
This line gives me an error. I found the solution here: https://stackoverflow.com/questions/34654682/unrecognized-command-line-option-stdlib-libc-gcc-homebrew-gcc-5-3-0-5-3-0
- I had to install glpk (GNU Linear Programming Kit). Earlier I installed the ix86 version. This gave me an error saying that my libglpk.so is incompatible. I found the solution in: https://stackoverflow.com/questions/53668578/skipping-incompatible-directory-gcc . Basically, reinstalling the x86_64 version of ligglpk.so using the dnf dragrora software manager fixed the problem.