svn commit: r535266 - in head/biology: . scrm scrm/files

[Yuri Victorovich]

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 at 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/