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| author | Yuri Victorovich <yuri@FreeBSD.org> | 2020-05-15 04:58:27 +0000 |
|---|---|---|
| committer | Yuri Victorovich <yuri@FreeBSD.org> | 2020-05-15 04:58:27 +0000 |
| commit | 04c132a637463e0556a8b7089fad7a44a04648d1 (patch) | |
| tree | f867ae2e1f798fdb824c89298dc08c60cc82097a /biology/scrm | |
| parent | 053cbfdcb94539e1a624cabba39044643d81942e (diff) | |
| download | ports-04c132a637463e0556a8b7089fad7a44a04648d1.tar.gz ports-04c132a637463e0556a8b7089fad7a44a04648d1.zip | |
New port: biology/scrm: Coalescent simulator for biological sequences
Notes
Notes:
svn path=/head/; revision=535266
Diffstat (limited to 'biology/scrm')
| -rw-r--r-- | biology/scrm/Makefile | 22 | ||||
| -rw-r--r-- | biology/scrm/distinfo | 3 | ||||
| -rw-r--r-- | biology/scrm/files/patch-src_random_fastfunc.h | 11 | ||||
| -rw-r--r-- | biology/scrm/pkg-descr | 8 |
4 files changed, 44 insertions, 0 deletions
diff --git a/biology/scrm/Makefile b/biology/scrm/Makefile new file mode 100644 index 000000000000..afcf57f23b3a --- /dev/null +++ b/biology/scrm/Makefile @@ -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> diff --git a/biology/scrm/distinfo b/biology/scrm/distinfo new file mode 100644 index 000000000000..26a9894b9b44 --- /dev/null +++ b/biology/scrm/distinfo @@ -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 diff --git a/biology/scrm/files/patch-src_random_fastfunc.h b/biology/scrm/files/patch-src_random_fastfunc.h new file mode 100644 index 000000000000..018a0d8464ba --- /dev/null +++ b/biology/scrm/files/patch-src_random_fastfunc.h @@ -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 + diff --git a/biology/scrm/pkg-descr b/biology/scrm/pkg-descr new file mode 100644 index 000000000000..99d784f7fdf9 --- /dev/null +++ b/biology/scrm/pkg-descr @@ -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/ |