New port: biology/rampler: Standalone module for sampling genomic sequences

svn path=/head/; revision=562039

biology/Makefile

@@ -148,6 +148,7 @@
     SUBDIR += pyfasta
     SUBDIR += python-nexus
     SUBDIR += rainbow
+    SUBDIR += rampler
     SUBDIR += recombine
     SUBDIR += ruby-bio
     SUBDIR += rubygem-bio

biology/rampler/Makefile

@@ -0,0 +1,26 @@
+# $FreeBSD$
+
+PORTNAME=	rampler
+DISTVERSION=	2.0.0
+CATEGORIES=	biology
+
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	Standalone module for sampling genomic sequences
+
+LICENSE=	MIT
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+BUILD_DEPENDS=	bioparser>0:biology/bioparser \
+		${LOCALBASE}/include/biosoup/nucleic_acid.hpp:biology/biosoup
+
+USES=		cmake localbase
+USE_LDCONFIG=	yes
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	rvaser
+
+LDFLAGS+=	-lz
+
+PLIST_FILES=	bin/${PORTNAME}
+
+.include <bsd.port.mk>

biology/rampler/distinfo

@@ -0,0 +1,3 @@
+TIMESTAMP = 1611049494
+SHA256 (rvaser-rampler-2.0.0_GH0.tar.gz) = 3a589b1ce1c2a0ac55a105cdd185b5698b4a5f6c9e015e59edee56fd64261eb8
+SIZE (rvaser-rampler-2.0.0_GH0.tar.gz) = 5190

biology/rampler/files/patch-CMakeLists.txt

@@ -0,0 +1,31 @@
+--- CMakeLists.txt.orig	2021-01-19 09:45:19 UTC
++++ CMakeLists.txt
+@@ -13,19 +13,20 @@ set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_BINARY_DI
+ set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
+ set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/bin)
+ 
+-if (NOT TARGET bioparser)
+-  add_subdirectory(vendor/bioparser EXCLUDE_FROM_ALL)
+-endif ()
+-if (NOT TARGET biosoup)
+-  add_subdirectory(vendor/bioparser/vendor/biosoup EXCLUDE_FROM_ALL)
+-endif ()
++#if (NOT TARGET bioparser)
++#  add_subdirectory(vendor/bioparser EXCLUDE_FROM_ALL)
++#endif ()
++#if (NOT TARGET biosoup)
++#  add_subdirectory(vendor/bioparser/vendor/biosoup EXCLUDE_FROM_ALL)
++#endif ()
+ 
+ add_executable(${PROJECT_NAME}
+   src/main.cpp
+   src/sampler.cpp)
+ target_link_libraries(${PROJECT_NAME}
+-  bioparser
+-  biosoup)
++  #bioparser
++  #biosoup
++)
+ target_compile_definitions(${PROJECT_NAME} PRIVATE
+   RAMPLER_VERSION="v${PROJECT_VERSION}")
+ 

biology/rampler/pkg-descr

@@ -0,0 +1,5 @@
+Rampler is a standalone module for sampling genomic sequences. It supports two
+modes, random subsampling of sequencing data to a desired depth (given the
+reference length) and file splitting to desired size in bytes.
+
+WWW: https://github.com/rvaser/rampler