svn commit: r562039 - in head/biology: . rampler rampler/files
Yuri Victorovich
yuri at FreeBSD.org
Tue Jan 19 09:49:55 UTC 2021
Author: yuri
Date: Tue Jan 19 09:49:53 2021
New Revision: 562039
URL: https://svnweb.freebsd.org/changeset/ports/562039
Log:
New port: biology/rampler: Standalone module for sampling genomic sequences
Added:
head/biology/rampler/
head/biology/rampler/Makefile (contents, props changed)
head/biology/rampler/distinfo (contents, props changed)
head/biology/rampler/files/
head/biology/rampler/files/patch-CMakeLists.txt (contents, props changed)
head/biology/rampler/pkg-descr (contents, props changed)
Modified:
head/biology/Makefile
Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile Tue Jan 19 09:41:54 2021 (r562038)
+++ head/biology/Makefile Tue Jan 19 09:49:53 2021 (r562039)
@@ -148,6 +148,7 @@
SUBDIR += pyfasta
SUBDIR += python-nexus
SUBDIR += rainbow
+ SUBDIR += rampler
SUBDIR += recombine
SUBDIR += ruby-bio
SUBDIR += rubygem-bio
Added: head/biology/rampler/Makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/rampler/Makefile Tue Jan 19 09:49:53 2021 (r562039)
@@ -0,0 +1,26 @@
+# $FreeBSD$
+
+PORTNAME= rampler
+DISTVERSION= 2.0.0
+CATEGORIES= biology
+
+MAINTAINER= yuri at 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>
Added: head/biology/rampler/distinfo
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/rampler/distinfo Tue Jan 19 09:49:53 2021 (r562039)
@@ -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
Added: head/biology/rampler/files/patch-CMakeLists.txt
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/rampler/files/patch-CMakeLists.txt Tue Jan 19 09:49:53 2021 (r562039)
@@ -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}")
+
Added: head/biology/rampler/pkg-descr
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/rampler/pkg-descr Tue Jan 19 09:49:53 2021 (r562039)
@@ -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
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