From owner-svn-ports-all@freebsd.org Tue Jan 19 09:49:55 2021 Return-Path: Delivered-To: svn-ports-all@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 4CB724EE1BD; Tue, 19 Jan 2021 09:49:55 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4DKkQq1jK6z4vfc; Tue, 19 Jan 2021 09:49:55 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 2D7A92474B; Tue, 19 Jan 2021 09:49:55 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id 10J9ntq7072701; Tue, 19 Jan 2021 09:49:55 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id 10J9nsb3072696; Tue, 19 Jan 2021 09:49:54 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <202101190949.10J9nsb3072696@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Tue, 19 Jan 2021 09:49:54 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r562039 - in head/biology: . rampler rampler/files X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: in head/biology: . rampler rampler/files X-SVN-Commit-Revision: 562039 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Tue, 19 Jan 2021 09:49:55 -0000 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@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 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