[med-svn] [giira] 01/01: remove cplex code with patch and force use of glpk instead of cplex
Olivier Sallou
osallou at debian.org
Sat Feb 8 08:23:02 UTC 2014
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osallou pushed a commit to branch master
in repository giira.
commit b56cd9a841999d8720a2818fc0a1c99db1c0aa9e
Author: Olivier Sallou <olivier.sallou at debian.org>
Date: Sat Feb 8 09:22:59 2014 +0100
remove cplex code with patch and force use of glpk instead of cplex
---
debian/changelog | 3 +-
debian/control | 2 +-
debian/patches/remove_cplex_code | 136 +++++++++++++++++++++++++++++++++++++++
debian/patches/series | 1 +
4 files changed, 140 insertions(+), 2 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 7245ac5..0cbb461 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -7,6 +7,7 @@ giira (0.0.20131015-1) UNRELEASED; urgency=low
Olivier Sallou Remarks:
- Software needs Cplex to compile. Gonna test to remove references in code to use only glpk.
+ Software needs Cplex to compile. removed references in code to use only glpk.
+ Created a ticket upstream (https://sourceforge.net/p/giira/tickets/1/) to know where CigarParser comes from. It is used but I could not found any local class nor library providing it.
-- Andreas Tille <tille at debian.org> Fri, 07 Feb 2014 11:38:38 +0100
diff --git a/debian/control b/debian/control
index 6d57998..7d9a19e 100644
--- a/debian/control
+++ b/debian/control
@@ -17,7 +17,7 @@ Package: giira
Architecture: any
Depends: ${misc:Depends},
${java:Depends},
- glpk,
+ glpk-utils,
libglpk-java
Description: RNA-Seq driven gene finding incorporating ambiguous reads
GIIRA is a gene prediction method that identifies potential coding
diff --git a/debian/patches/remove_cplex_code b/debian/patches/remove_cplex_code
new file mode 100644
index 0000000..d68b61d
--- /dev/null
+++ b/debian/patches/remove_cplex_code
@@ -0,0 +1,136 @@
+Subject: remove Cplex code
+Description: 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
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2014-02-08
+Forwarded: no
+--- a/src/geneFinder/OptimizeAmbis.java
++++ b/src/geneFinder/OptimizeAmbis.java
+@@ -1,7 +1,5 @@
+ package geneFinder;
+
+-import ilog.concert.IloException;
+-import ilog.cplex.IloCplex;
+
+ import java.io.*;
+ import java.util.HashMap;
+@@ -376,48 +374,7 @@
+ */
+
+ public static void solveMaxFlowWithCPLEX(int numMulti){
+-
+- try {
+- System.out.println("Start cplex solve...");
+- IloCplex cplex = new IloCplex();
+-
+- cplex.importModel(GeneFinder.pathOut+"resultsRun/input_it" + GeneFinder.iteration + ".lp");
+-
+- cplex.setParam(IloCplex.IntParam.RootAlg,IloCplex.Algorithm.Network);
+- cplex.setParam(IloCplex.DoubleParam.EpGap,0.01);
+- cplex.setParam(IloCplex.IntParam.Threads,GeneFinder.numberThreads);
+-
+- if(numMulti >= 10000000){
+-
+- if(GeneFinder.memForCplex != -1){
+- cplex.setParam(IloCplex.DoubleParam.WorkMem,GeneFinder.memForCplex);
+- }
+-
+- cplex.setParam(IloCplex.StringParam.WorkDir,GeneFinder.pathOut+"resultsRun/");
+- System.out.println("Directory: " + cplex.getParam(IloCplex.StringParam.WorkDir));
+-
+- cplex.setParam(IloCplex.DoubleParam.PolishTime,1000.0);
+- System.out.println("polish time: " + cplex.getParam(IloCplex.DoubleParam.PolishTime));
+-
+- cplex.setParam(IloCplex.IntParam.HeurFreq,-1);
+-
+- cplex.setParam(IloCplex.IntParam.NodeFileInd,3);
+- System.out.println(cplex.getParam(IloCplex.IntParam.NodeFileInd));
+-
+- cplex.setParam(IloCplex.BooleanParam.MemoryEmphasis,true);
+- System.out.println(cplex.getParam(IloCplex.BooleanParam.MemoryEmphasis));
+-
+- }
+-
+- cplex.solve();
+-
+- cplex.writeSolution(GeneFinder.pathOut+"resultsRun/solutionCPLEX_it" + GeneFinder.iteration + ".sol");
+-
+-
+- } catch (IloException e2) {
+- e2.printStackTrace();
+- }
+-
++ System.err.println("CPLEX implementation not available");
+ }
+
+ /*
+--- a/src/geneFinder/Operon_LP.java
++++ b/src/geneFinder/Operon_LP.java
+@@ -9,8 +9,6 @@
+ *
+ */
+
+-import ilog.concert.IloException;
+-import ilog.cplex.IloCplex;
+
+ import java.io.*;
+ import java.util.Vector;
+@@ -256,22 +254,7 @@
+ */
+
+ public static void solveOperonLPWithCPLEX(){
+-
+- try {
+- IloCplex cplex = new IloCplex();
+- cplex.setOut(null);
+- cplex.importModel(GeneFinder.pathOut+"resultsRun/input_operonLP.lp");
+- cplex.setParam(IloCplex.IntParam.Threads,GeneFinder.numberThreads);
+-
+- cplex.solve();
+-
+- cplex.writeSolution(GeneFinder.pathOut+"resultsRun/solution_operonLP.sol");
+-
+-
+- } catch (IloException e2) {
+- e2.printStackTrace();
+- }
+-
++ System.err.println("CPLEX implementation not available");
+ }
+
+ /*
+--- a/src/geneFinder/ReadInParameters_GeneFinder.java
++++ b/src/geneFinder/ReadInParameters_GeneFinder.java
+@@ -242,9 +242,8 @@
+ GeneFinder.useGLPK = true;
+ inputText += "Using glpk for ambiguous read optimization.\n";
+ } else{
+- GeneFinder.useCPLEX = true;
+- GeneFinder.useGLPK = false;
+- inputText += "Using cplex for ambiguous read optimization.\n";
++ System.err.println("CPLEX implementation not available");
++ return;
+ }
+ } else if(arg.equals("-mem")){
+ GeneFinder.memForCplex = Integer.parseInt(args[i+1]);
+@@ -376,7 +375,8 @@
+ GeneFinder.noAmbiOpti = false;
+ }
+ if(!foundOptiMethod){
+- GeneFinder.useCPLEX = true;
++ GeneFinder.useCPLEX = false;
++ GeneFinder.useGLPK = true;
+ }
+ if(!foundSolveOn){
+ GeneFinder.optiSolve = true;
+@@ -458,8 +458,6 @@
+ " \n -haveSam [samfileName]: if a sam file already exists, provide the name, else a mapping is performed. NOTE: the sam file has to be sorted according to read names! \n" +
+ " \n -nT [numberThreads] : specify the maximal number of threads that are allowed to be used, DEFAULT: 1 \n" +
+ " \n -mT [tophat/bwa/bwasw] : specify desired tool for the read mapping, DEFAULT: tophat \n" +
+- " \n -opti [cplex/glpk] : specify the desired optimization method, either using CPLEX optimizer (cplex, DEFAULT) or glpk solver (glpk) \n" +
+- " \n -libPath [PATH] : if cplex is the desired optimizer, specify the absolute path to the cplex library Djava.library.path \n" +
+ " \n -cp [PATH] : if cplex is the desired optimizer, specify the absolute path to the cplex jar file cplex.jar\n" +
+ //" \n -splitRunAndOpti [y/n] : indicates if the optimization and giira shall be run separately, to reduce the memory consumption (y), DEFAULT: n" +
+ " \n -mem [int] : specify the amount of memory that cplex is allowed to use \n" +
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..eb35575
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+remove_cplex_code
--
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