reinit the tree, so we can have metadata

2 files changed, 145 insertions, 0 deletions

diff --git a/sci-biology/mothur/files/mothur-1.27.0-makefile.patch b/sci-biology/mothur/files/mothur-1.27.0-makefile.patch
new file mode 100644
index 000000000000..52a02585df14
--- /dev/null
+++ b/sci-biology/mothur/files/mothur-1.27.0-makefile.patch
@@ -0,0 +1,52 @@
+ makefile |   14 ++++++--------
+ 1 files changed, 6 insertions(+), 8 deletions(-)
+
+diff --git a/makefile b/makefile
+index db7c904..109488f 100644
+--- a/makefile
++++ b/makefile
+@@ -10,18 +10,18 @@
+ #
+ 
+ USEMPI ?= no
+-64BIT_VERSION ?= yes
++64BIT_VERSION ?= no
+ USEREADLINE ?= yes
+ CYGWIN_BUILD ?= no
+ USECOMPRESSION ?= no
+ MOTHUR_FILES="\"Enter_your_default_path_here\""
+ RELEASE_DATE = "\"8/8/2012\""
+ VERSION = "\"1.27.0\""
+-FORTAN_COMPILER = gfortran
+-FORTRAN_FLAGS = 
++FORTAN_COMPILER = ${FC}
++FORTRAN_FLAGS = ${FCFLAGS}
+ 
+ # Optimize to level 3:
+-CXXFLAGS += -O3 
++#CXXFLAGS += -O3
+ 
+ ifeq  ($(strip $(64BIT_VERSION)),yes)
+ 	#if you are using centos uncomment the following lines
+@@ -69,7 +69,7 @@ endif
+ 
+ 
+ ifeq  ($(strip $(USEMPI)),yes)
+-    CXX = mpic++
++#    CXX = mpic++
+     CXXFLAGS += -DUSE_MPI
+ endif
+ 
+@@ -95,11 +95,9 @@ OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
+ OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
+ OBJECTS+=$(patsubst %.f,%.o,$(wildcard *.f))
+ 
+-mothur : fortranSource $(OBJECTS) uchime
++mothur : fortranSource $(OBJECTS)
+ 	$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
+ 	
+-	strip mothur
+- 
+ uchime:
+ 	cd uchime_src && ./mk && mv uchime .. && cd ..
+ 	
diff --git a/sci-biology/mothur/files/mothur-1.27.0-overflows.patch b/sci-biology/mothur/files/mothur-1.27.0-overflows.patch
new file mode 100644
index 000000000000..0b612cf7b529
--- /dev/null
+++ b/sci-biology/mothur/files/mothur-1.27.0-overflows.patch
@@ -0,0 +1,93 @@
+ chimerauchimecommand.cpp |    2 +-
+ clearcutcommand.cpp      |   32 ++++++++++++++++----------------
+ 2 files changed, 17 insertions(+), 17 deletions(-)
+
+diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
+index bd31c19..2070840 100644
+--- a/chimerauchimecommand.cpp
++++ b/chimerauchimecommand.cpp
+@@ -1264,7 +1264,7 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
+ 		}
+ 		
+ 		if (ucl) {
+-			char* tempucl = new char[5]; 
++			char* tempucl = new char[6]; 
+ 			strcpy(tempucl, "--ucl"); 
+ 			cPara.push_back(tempucl);
+ 		}
+diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
+index 6a0eb25..2e8164e 100644
+--- a/clearcutcommand.cpp
++++ b/clearcutcommand.cpp
+@@ -269,35 +269,35 @@ int ClearcutCommand::execute() {
+ 		
+ 		vector<char*> cPara;
+ 		
+-		char* tempClearcut = new char[8];  
++		char* tempClearcut = new char[16];  
+ 		strcpy(tempClearcut, "clearcut"); 
+ 		cPara.push_back(tempClearcut);
+ 				
+ 		//you gave us a distance matrix
+-		if (phylipfile != "") {  char* temp = new char[10];  strcpy(temp, "--distance");  cPara.push_back(temp);	}
++		if (phylipfile != "") {  char* temp = new char[16];  strcpy(temp, "--distance");  cPara.push_back(temp);	}
+ 		
+ 		//you gave us a fastafile
+-		if (fastafile != "") { char* temp = new char[11];  strcpy(temp, "--alignment");  cPara.push_back(temp); 	}
++		if (fastafile != "") { char* temp = new char[16];  strcpy(temp, "--alignment");  cPara.push_back(temp); 	}
+ 		
+-		if (version)			{  char* temp = new char[9];  strcpy(temp, "--version");  cPara.push_back(temp);	}
+-		if (verbose)			{  char* temp = new char[9];  strcpy(temp, "--verbose");  cPara.push_back(temp);	}
+-		if (quiet)				{  char* temp = new char[7];  strcpy(temp, "--quiet");  cPara.push_back(temp);	}
++		if (version)			{  char* temp = new char[16];  strcpy(temp, "--version");  cPara.push_back(temp);	}
++		if (verbose)			{  char* temp = new char[16];  strcpy(temp, "--verbose");  cPara.push_back(temp);	}
++		if (quiet)				{  char* temp = new char[16];  strcpy(temp, "--quiet");  cPara.push_back(temp);	}
+ 		if (seed != "*")		{  
+ 			string tempSeed = "--seed=" + seed;
+ 			char* temp = new char[tempSeed.length()];
+ 			strcpy(temp, tempSeed.c_str());
+ 			cPara.push_back(temp);
+ 		}
+-		if (norandom)			{  char* temp = new char[10];  strcpy(temp, "--norandom");  cPara.push_back(temp);	}
+-		if (shuffle)			{  char* temp = new char[9];  strcpy(temp, "--shuffle");  cPara.push_back(temp);	}
+-		if (neighbor)			{  char* temp = new char[10];  strcpy(temp, "--neighbor");  cPara.push_back(temp);	}
++		if (norandom)			{  char* temp = new char[16];  strcpy(temp, "--norandom");  cPara.push_back(temp);	}
++		if (shuffle)			{  char* temp = new char[16];  strcpy(temp, "--shuffle");  cPara.push_back(temp);	}
++		if (neighbor)			{  char* temp = new char[16];  strcpy(temp, "--neighbor");  cPara.push_back(temp);	}
+ 		
+ 		string tempIn = "--in=" + inputFile;  
+ 		char* tempI = new char[tempIn.length()];
+ 		strcpy(tempI, tempIn.c_str());
+ 		cPara.push_back(tempI);
+ 		
+-		if (stdoutWanted)		{  char* temp = new char[8];  strcpy(temp, "--stdout");  cPara.push_back(temp);	}
++		if (stdoutWanted)		{  char* temp = new char[16];  strcpy(temp, "--stdout");  cPara.push_back(temp);	}
+ 		else{  
+ 			string tempOut = "--out=" + outputName;  
+ 			
+@@ -306,10 +306,10 @@ int ClearcutCommand::execute() {
+ 			cPara.push_back(temp);
+ 		}
+ 			
+-		if (DNA)				{  char* temp = new char[5];  strcpy(temp, "--DNA");  cPara.push_back(temp);		}
+-		if (protein)			{  char* temp = new char[9];  strcpy(temp, "--protein");  cPara.push_back(temp);	}
+-		if (jukes)				{  char* temp = new char[7];  strcpy(temp, "--jukes");  cPara.push_back(temp);		}
+-		if (kimura)				{ char* temp = new char[8];  strcpy(temp, "--kimura");  cPara.push_back(temp);		}
++		if (DNA)				{  char* temp = new char[16];  strcpy(temp, "--DNA");  cPara.push_back(temp);		}
++		if (protein)			{  char* temp = new char[16];  strcpy(temp, "--protein");  cPara.push_back(temp);	}
++		if (jukes)				{  char* temp = new char[16];  strcpy(temp, "--jukes");  cPara.push_back(temp);		}
++		if (kimura)				{ char* temp = new char[16];  strcpy(temp, "--kimura");  cPara.push_back(temp);		}
+ 		if (matrixout != "")	{  
+ 			string tempMatrix =  "--matrixout=" + outputDir + matrixout; 
+ 			char* temp = new char[tempMatrix.length()];
+@@ -326,8 +326,8 @@ int ClearcutCommand::execute() {
+ 			cPara.push_back(temp);
+ 		}
+ 
+-		if (expblen)			{ char* temp = new char[9];  strcpy(temp, "--expblen");  cPara.push_back(temp); 	}
+-		if (expdist)			{ char* temp = new char[9];  strcpy(temp, "--expdist");  cPara.push_back(temp);	}
++		if (expblen)			{ char* temp = new char[16];  strcpy(temp, "--expblen");  cPara.push_back(temp); 	}
++		if (expdist)			{ char* temp = new char[16];  strcpy(temp, "--expdist");  cPara.push_back(temp);	}
+ 		
+ 		char** clearcutParameters;
+ 		clearcutParameters = new char*[cPara.size()];