Date: Fri, 15 May 2020 04:58:27 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r535266 - in head/biology: . scrm scrm/files Message-ID: <202005150458.04F4wRkD092128@repo.freebsd.org>
next in thread | raw e-mail | index | archive | help
Author: yuri Date: Fri May 15 04:58:27 2020 New Revision: 535266 URL: https://svnweb.freebsd.org/changeset/ports/535266 Log: New port: biology/scrm: Coalescent simulator for biological sequences Added: head/biology/scrm/ head/biology/scrm/Makefile (contents, props changed) head/biology/scrm/distinfo (contents, props changed) head/biology/scrm/files/ head/biology/scrm/files/patch-src_random_fastfunc.h (contents, props changed) head/biology/scrm/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Fri May 15 04:25:56 2020 (r535265) +++ head/biology/Makefile Fri May 15 04:58:27 2020 (r535266) @@ -143,6 +143,7 @@ SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools + SUBDIR += scrm SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps Added: head/biology/scrm/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/scrm/Makefile Fri May 15 04:58:27 2020 (r535266) @@ -0,0 +1,22 @@ +# $FreeBSD$ + +PORTNAME= scrm +DISTVERSIONPREFIX= v +DISTVERSION= 1.7.4 +CATEGORIES= biology + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Coalescent simulator for biological sequences + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/COPYING + +USES= autoreconf gmake +USE_GITHUB= yes + +GNU_CONFIGURE= yes + +PLIST_FILES= bin/scrm \ + man/man1/scrm.1.gz + +.include <bsd.port.mk> Added: head/biology/scrm/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/scrm/distinfo Fri May 15 04:58:27 2020 (r535266) @@ -0,0 +1,3 @@ +TIMESTAMP = 1589518122 +SHA256 (scrm-scrm-v1.7.4_GH0.tar.gz) = 13f4b0febabcdf6a2b478693febd2fb9d3f47532fb39ffaa4f01fe816f69ceb7 +SIZE (scrm-scrm-v1.7.4_GH0.tar.gz) = 341612 Added: head/biology/scrm/files/patch-src_random_fastfunc.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/scrm/files/patch-src_random_fastfunc.h Fri May 15 04:58:27 2020 (r535266) @@ -0,0 +1,11 @@ +--- src/random/fastfunc.h.orig 2020-05-15 04:49:19 UTC ++++ src/random/fastfunc.h +@@ -27,7 +27,7 @@ + #include <cmath> + #include <vector> + +-#if !defined(__APPLE__) ++#if !defined(__APPLE__) && !defined(__FreeBSD__) + #include <malloc.h> + #endif + Added: head/biology/scrm/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/scrm/pkg-descr Fri May 15 04:58:27 2020 (r535266) @@ -0,0 +1,8 @@ +scrm simulates the evolution of genetic sequences. It takes a neutral +evolutionary model as input, and generates random sequences that evolved under +the model. As coalescent simulator, it traces the ancestry of the sampled +sequences backwards in time and is therefore extremely efficient. Compared to +other coalescent simulators, it can simulate chromosome-scale sequences without +a measureable reduction of genetic linkage between different sites. + +WWW: https://scrm.github.io/
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?202005150458.04F4wRkD092128>