[med-svn] [giira] 01/03: update patches to latest upstream code
Olivier Sallou
osallou at debian.org
Mon Feb 10 10:03:26 UTC 2014
This is an automated email from the git hooks/post-receive script.
osallou pushed a commit to branch master
in repository giira.
commit e3e537204675559d3c5ebaa8c519e4065b6045e4
Author: Olivier Sallou <olivier.sallou at debian.org>
Date: Mon Feb 10 11:02:00 2014 +0100
update patches to latest upstream code
---
debian/get-orig-source | 2 +-
debian/patches/remove_cplex_code | 93 +++++++++++++++++++---------------------
2 files changed, 46 insertions(+), 49 deletions(-)
diff --git a/debian/get-orig-source b/debian/get-orig-source
index 4c733f1..13cc183 100755
--- a/debian/get-orig-source
+++ b/debian/get-orig-source
@@ -17,7 +17,7 @@ wget http://sourceforge.net/projects/${NAME}/files/GIIRA.zip
unzip GIIRA.zip
mv GIIRA $TARDIR
mkdir -p $EXAMPLEDIR
-mv $TARDIR/example $EXAMPLEDIR
+#mv $TARDIR/example $EXAMPLEDIR
cd $TARDIR
rm -f *.jar
# fetch source from SVN
diff --git a/debian/patches/remove_cplex_code b/debian/patches/remove_cplex_code
index d68b61d..2fce17d 100644
--- a/debian/patches/remove_cplex_code
+++ b/debian/patches/remove_cplex_code
@@ -6,26 +6,59 @@ Description: upstream makes use of Cplex Java library which is not
Author: Olivier Sallou <osallou at debian.org>
Last-Updated: 2014-02-08
Forwarded: no
+--- 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" +
--- a/src/geneFinder/OptimizeAmbis.java
+++ b/src/geneFinder/OptimizeAmbis.java
-@@ -1,7 +1,5 @@
+@@ -1,8 +1,5 @@
package geneFinder;
-import ilog.concert.IloException;
-import ilog.cplex.IloCplex;
-
+-
import java.io.*;
import java.util.HashMap;
-@@ -376,48 +374,7 @@
- */
+ import java.util.Map;
+@@ -377,47 +374,6 @@
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.importModel(GeneFinder.pathOut+"input_it" + GeneFinder.iteration + ".lp");
-
- cplex.setParam(IloCplex.IntParam.RootAlg,IloCplex.Algorithm.Network);
- cplex.setParam(IloCplex.DoubleParam.EpGap,0.01);
@@ -37,7 +70,7 @@ Forwarded: no
- cplex.setParam(IloCplex.DoubleParam.WorkMem,GeneFinder.memForCplex);
- }
-
-- cplex.setParam(IloCplex.StringParam.WorkDir,GeneFinder.pathOut+"resultsRun/");
+- cplex.setParam(IloCplex.StringParam.WorkDir,GeneFinder.pathOut);
- System.out.println("Directory: " + cplex.getParam(IloCplex.StringParam.WorkDir));
-
- cplex.setParam(IloCplex.DoubleParam.PolishTime,1000.0);
@@ -55,14 +88,13 @@ Forwarded: no
-
- cplex.solve();
-
-- cplex.writeSolution(GeneFinder.pathOut+"resultsRun/solutionCPLEX_it" + GeneFinder.iteration + ".sol");
+- cplex.writeSolution(GeneFinder.pathOut+"solutionCPLEX_it" + GeneFinder.iteration + ".sol");
-
-
- } catch (IloException e2) {
- e2.printStackTrace();
- }
-
-+ System.err.println("CPLEX implementation not available");
}
/*
@@ -77,60 +109,25 @@ Forwarded: no
import java.io.*;
import java.util.Vector;
-@@ -256,22 +254,7 @@
- */
+@@ -257,21 +255,6 @@
public static void solveOperonLPWithCPLEX(){
--
+
- try {
- IloCplex cplex = new IloCplex();
- cplex.setOut(null);
-- cplex.importModel(GeneFinder.pathOut+"resultsRun/input_operonLP.lp");
+- cplex.importModel(GeneFinder.pathOut+"input_operonLP.lp");
- cplex.setParam(IloCplex.IntParam.Threads,GeneFinder.numberThreads);
-
- cplex.solve();
-
-- cplex.writeSolution(GeneFinder.pathOut+"resultsRun/solution_operonLP.sol");
+- cplex.writeSolution(GeneFinder.pathOut+"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" +
--
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