diff options
| author | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
|---|---|---|
| committer | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
| commit | 4f2d7949f03e1c198bc888f2d05f421d35c57e21 (patch) | |
| tree | ba5f07bf3f9d22d82e54a462313f5d244036c768 /sci-biology/fasttree/files | |
reinit the tree, so we can have metadata
Diffstat (limited to 'sci-biology/fasttree/files')
3 files changed, 80 insertions, 0 deletions
diff --git a/sci-biology/fasttree/files/CMakeLists.txt b/sci-biology/fasttree/files/CMakeLists.txt new file mode 100644 index 000000000000..e7c53afdaf36 --- /dev/null +++ b/sci-biology/fasttree/files/CMakeLists.txt @@ -0,0 +1,30 @@ +cmake_minimum_required (VERSION 2.6) +project(fasttree C) + +option(USE_OPENMP "Use OpenMP to parallelize many of the steps in computing a tree" ON) +option(USE_DOUBLE "Use double precission" OFF) +option(HAS_SSE3 "Use SSE2/SSE3 instructions to speed up some inner loops" ON) + +if(USE_OPENMP) + SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DOPENMP -fopenmp" ) + SET( CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -DOPENMP -fopenmp" ) +endif(USE_OPENMP) + +if(USE_DOUBLE) + SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DUSE_DOUBLE" ) +endif(USE_DOUBLE) + +if(NOT HAS_SSE3) + SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DNO_SSE" ) +endif(NOT HAS_SSE3) + + +add_executable(FastTree FastTree-${VERSION}.c) +add_executable(FastTreeUPGMA FastTreeUPGMA-${VERSION}.c) + +target_link_libraries(FastTree m) +target_link_libraries(FastTreeUPGMA m) + +install (TARGETS FastTree FastTreeUPGMA DESTINATION bin) + +install(FILES MOTree.pm CompareTree.pl CompareToBootstrap.pl DESTINATION share/fasttree) diff --git a/sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch b/sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch new file mode 100644 index 000000000000..31dafdad46de --- /dev/null +++ b/sci-biology/fasttree/files/fasttree-2.1.7-format-security.patch @@ -0,0 +1,25 @@ + FastTreeUPGMA-2.1.7.c | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/FastTreeUPGMA-2.1.7.c b/FastTreeUPGMA-2.1.7.c +index af76cb1..4065f42 100644 +--- a/FastTreeUPGMA-2.1.7.c ++++ b/FastTreeUPGMA-2.1.7.c +@@ -535,7 +535,7 @@ int main(int argc, char **argv) { + break; + } + if(iArg < argc-1) { +- fprintf(stderr, usage); ++ fprintf(stderr, "%s", usage); + exit(1); + } + +@@ -953,7 +953,7 @@ void PrintUPGMA(FILE *fp, UPGMA_t *UPGMA, char **names, + assert(first >= 0); + /* Print the name, or the subtree of duplicate names */ + if (nameNext[first] == -1) { +- fprintf(fp, names[uniqueFirst[node]]); ++ fprintf(fp, "%s", names[uniqueFirst[node]]); + } else { + fprintf(fp,"(%s:0.0",names[first]); + int iName = nameNext[first]; diff --git a/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch b/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch new file mode 100644 index 000000000000..15f5c174ec40 --- /dev/null +++ b/sci-biology/fasttree/files/fasttree-2.1.8-format-security.patch @@ -0,0 +1,25 @@ + FastTreeUPGMA-2.1.8.c | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/FastTreeUPGMA-2.1.8.c b/FastTreeUPGMA-2.1.8.c +index af76cb1..4065f42 100644 +--- a/FastTreeUPGMA-2.1.8.c ++++ b/FastTreeUPGMA-2.1.8.c +@@ -535,7 +535,7 @@ int main(int argc, char **argv) { + break; + } + if(iArg < argc-1) { +- fprintf(stderr, usage); ++ fprintf(stderr, "%s", usage); + exit(1); + } + +@@ -953,7 +953,7 @@ void PrintUPGMA(FILE *fp, UPGMA_t *UPGMA, char **names, + assert(first >= 0); + /* Print the name, or the subtree of duplicate names */ + if (nameNext[first] == -1) { +- fprintf(fp, names[uniqueFirst[node]]); ++ fprintf(fp, "%s", names[uniqueFirst[node]]); + } else { + fprintf(fp,"(%s:0.0",names[first]); + int iName = nameNext[first]; |