mirror of
https://git.FreeBSD.org/ports.git
synced 2024-11-22 00:35:15 +00:00
Add new ports biology/plink [1] and biology/plinkseq [2]:
PLINK is a free, open-source whole genome association analysis toolset. PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. PR: ports/171918 [1] PR: ports/171922 [2] Submitted by: Jason Bacon <jwbacon at tds.net>
This commit is contained in:
Max Brazhnikov
parent
47ad784422
commit
ecd280d820
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=304954
@ -72,6 +72,8 @@
|
||||
SUBDIR += phylip
|
||||
SUBDIR += phyml
|
||||
SUBDIR += platon
|
||||
SUBDIR += plink
|
||||
SUBDIR += plinkseq
|
||||
SUBDIR += povchem
|
||||
SUBDIR += primer3
|
||||
SUBDIR += protomol
|
||||
|
||||
27
biology/plink/Makefile
Normal file
27
biology/plink/Makefile
Normal file
@ -0,0 +1,27 @@
|
||||
# Created by: Jason Bacon <jwbacon@tds.net>
|
||||
# $FreeBSD$
|
||||
|
||||
PORTNAME= plink
|
||||
PORTVERSION= 1.07
|
||||
CATEGORIES= biology science
|
||||
MASTER_SITES= http://pngu.mgh.harvard.edu/~purcell/plink/dist/
|
||||
DISTNAME= ${PORTNAME}-${PORTVERSION}-src
|
||||
|
||||
MAINTAINER= jwbacon@tds.net
|
||||
COMMENT= Whole genome association analysis toolset
|
||||
|
||||
LICENSE= GPLv2
|
||||
|
||||
LIB_DEPENDS= lapack:${PORTSDIR}/math/lapack
|
||||
|
||||
USE_ZIP= yes
|
||||
USE_GMAKE= yes
|
||||
USE_FORTRAN= yes # Make it use the same compiler as lapack
|
||||
|
||||
PLIST_FILES= bin/plink
|
||||
|
||||
do-install:
|
||||
${MKDIR} ${PREFIX}/bin
|
||||
${INSTALL_PROGRAM} ${WRKSRC}/plink ${PREFIX}/bin
|
||||
|
||||
.include <bsd.port.mk>
|
||||
2
biology/plink/distinfo
Normal file
2
biology/plink/distinfo
Normal file
@ -0,0 +1,2 @@
|
||||
SHA256 (plink-1.07-src.zip) = 4af56348443d0c6a1db64950a071b1fcb49cc74154875a7b43cccb4b6a7f482b
|
||||
SIZE (plink-1.07-src.zip) = 2257297
|
||||
52
biology/plink/files/patch-Makefile
Normal file
52
biology/plink/files/patch-Makefile
Normal file
@ -0,0 +1,52 @@
|
||||
--- Makefile.orig 2009-10-10 11:00:20.000000000 -0500
|
||||
+++ Makefile 2012-09-07 08:24:26.000000000 -0500
|
||||
@@ -26,7 +26,7 @@
|
||||
WITH_WEBCHECK = 1
|
||||
FORCE_32BIT =
|
||||
WITH_ZLIB = 1
|
||||
-WITH_LAPACK =
|
||||
+WITH_LAPACK = 1
|
||||
FORCE_DYNAMIC =
|
||||
|
||||
# Put C++ compiler here; Windows has it's own specific version
|
||||
@@ -34,17 +34,17 @@
|
||||
CXX_WIN = c:\bin\mingw\bin\mingw32-g++.exe
|
||||
|
||||
# Any other compiler flags here ( -Wall, -g, etc)
|
||||
-CXXFLAGS =
|
||||
+# CXXFLAGS =
|
||||
|
||||
# Misc
|
||||
-LIB_LAPACK = /usr/lib/liblapack.so.3
|
||||
+LIB_LAPACK = -L${LOCALBASE}/lib -llapack -lblas -lgfortran
|
||||
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
# Do not edit below this line
|
||||
# --------------------------------------------------------------------
|
||||
|
||||
-CXXFLAGS += -O3 -I.
|
||||
+CXXFLAGS += -I.
|
||||
OUTPUT = plink
|
||||
|
||||
# Some system specific flags
|
||||
@@ -58,8 +58,8 @@
|
||||
endif
|
||||
|
||||
ifeq ($(SYS),UNIX)
|
||||
- CXXFLAGS += -DUNIX
|
||||
- CXX = $(CXX_UNIX)
|
||||
+ CXXFLAGS += -DUNIX -Dfopen64=fopen
|
||||
+ CXX ?= $(CXX_UNIX)
|
||||
ifndef FORCE_DYNAMIC
|
||||
CXXFLAGS += -static
|
||||
endif
|
||||
@@ -128,7 +128,7 @@
|
||||
LIB += -ldl
|
||||
endif
|
||||
ifeq ($(SYS),UNIX)
|
||||
-LIB += -ldl -lcrypt
|
||||
+LIB += -lcrypt
|
||||
endif
|
||||
endif
|
||||
|
||||
5
biology/plink/pkg-descr
Normal file
5
biology/plink/pkg-descr
Normal file
@ -0,0 +1,5 @@
|
||||
PLINK is a free, open-source whole genome association analysis toolset,
|
||||
designed to perform a range of basic, large-scale analyses in a
|
||||
computationally efficient manner.
|
||||
|
||||
WWW: http://pngu.mgh.harvard.edu/~purcell/plink/
|
||||
28
biology/plinkseq/Makefile
Normal file
28
biology/plinkseq/Makefile
Normal file
@ -0,0 +1,28 @@
|
||||
# Created by: Jason Bacon <jwbacon@tds.net>
|
||||
# $FreeBSD$
|
||||
|
||||
PORTNAME= plinkseq
|
||||
PORTVERSION= 0.08
|
||||
CATEGORIES= biology science
|
||||
MASTER_SITES= http://atgu.mgh.harvard.edu/${PORTNAME}/dist/version-${PORTVERSION}/
|
||||
|
||||
MAINTAINER= jwbacon@tds.net
|
||||
COMMENT= Toolset for working with human genetic variation data
|
||||
|
||||
LICENSE= GPLv2
|
||||
|
||||
LIB_DEPENDS= protobuf:${PORTSDIR}/devel/protobuf
|
||||
|
||||
USE_DOS2UNIX= yes
|
||||
USE_LDCONFIG= yes
|
||||
GNU_CONFIGURE= yes
|
||||
CONFIGURE_ARGS+=--with-protobuf=${LOCALBASE}
|
||||
|
||||
post-patch:
|
||||
${REINPLACE_CMD} -e 's|PF_INET|AF_INET|g' ${WRKSRC}/browser/mongoose.c
|
||||
${REINPLACE_CMD} -e 's|-ldl||g' \
|
||||
${WRKSRC}/browser/Makefile.in \
|
||||
${WRKSRC}/client/Makefile.in \
|
||||
${WRKSRC}/index/Makefile.in
|
||||
|
||||
.include <bsd.port.mk>
|
||||
2
biology/plinkseq/distinfo
Normal file
2
biology/plinkseq/distinfo
Normal file
@ -0,0 +1,2 @@
|
||||
SHA256 (plinkseq-0.08.tar.gz) = 6bde88925a82a79c6fa2401a197865cf6d659163fd5f11c5fb426701b54bb24f
|
||||
SIZE (plinkseq-0.08.tar.gz) = 2991871
|
||||
8
biology/plinkseq/pkg-descr
Normal file
8
biology/plinkseq/pkg-descr
Normal file
@ -0,0 +1,8 @@
|
||||
PLINK/SEQ is an open-source C/C++ library for working with human
|
||||
genetic variation data. The specific focus is to provide a platform
|
||||
for analytic tool development for variation data from large-scale
|
||||
resequencing and genotyping projects, particularly whole-exome and
|
||||
whole-genome studies. It is independent of (but designed to be
|
||||
complementary to) the existing PLINK package.
|
||||
|
||||
WWW: http://atgu.mgh.harvard.edu/plinkseq/
|
||||
12
biology/plinkseq/pkg-plist
Normal file
12
biology/plinkseq/pkg-plist
Normal file
@ -0,0 +1,12 @@
|
||||
bin/behead
|
||||
bin/gcol
|
||||
bin/index
|
||||
bin/index.cgi
|
||||
bin/mongoose
|
||||
bin/pbrowse
|
||||
bin/pbrowse.cgi
|
||||
bin/pseq
|
||||
bin/tab2vcf
|
||||
lib/libplinkseq.la
|
||||
lib/libplinkseq.so
|
||||
lib/libplinkseq.so.0
|
||||
Loading…
Reference in New Issue
Block a user