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Adding plink

gn-stable
pjotrp pirms 4 gadiem
vecāks
revīzija
949a3b4062
2 mainītis faili ar 69 papildinājumiem un 0 dzēšanām
  1. +56
    -0
      gn/packages/bioinformatics.scm
  2. +13
    -0
      plink-ng-Makefile-zlib.patch

+ 56
- 0
gn/packages/bioinformatics.scm Parādīt failu

@@ -157,6 +157,62 @@ precision. It also performs bootstrap resampling to estimate the
confidence region for the location of a putative QTL.")
(license license:gpl2)))

(define-public plink2
(package
(name "plink2")
(version "1.90b3")
(source
(origin
(method url-fetch)
;; https://github.com/chrchang/plink-ng/archive/v1.90b3.tar.gz
(uri (string-append
"https://github.com/chrchang/plink-ng/archive/v"
version ".tar.gz"))
(sha256
(base32 "03fzib1al5qkr9vxv63wxmv6y2pfb1rmir0h8jpi72r87hczqjig"))
(patches (list (search-patch "plink-ng-Makefile-zlib.patch")))))
(build-system gnu-build-system)
(arguments
'(#:tests? #t ;no "check" target
#:make-flags (list (string-append "LIB_LAPACK="
(assoc-ref %build-inputs "lapack")
"/lib/liblapack.so")
"WITH_LAPACK=1"
"FORCE_DYNAMIC=1"
;; disable phoning home
"WITH_WEBCHECK=")
#:phases
(modify-phases %standard-phases
(delete 'configure)
(replace 'build
(lambda _
(system* "make" "-f" "Makefile.std")
))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out")
"/bin/")))
(install-file "plink" bin)
#t))))))
(inputs
`(("zlib" ,zlib)
("lapack" ,lapack)))
(native-inputs
`(("unzip" ,unzip)))
(home-page "https://www.cog-genomics.org/plink2")
(synopsis "Whole genome association analysis toolset")
(description
"PLINK is a whole genome association analysis toolset, designed to
perform a range of basic, large-scale analyses in a computationally efficient
manner. The focus of PLINK is purely on analysis of genotype/phenotype data,
so there is no support for steps prior to this (e.g. study design and
planning, generating genotype or CNV calls from raw data). Through
integration with gPLINK and Haploview, there is some support for the
subsequent visualization, annotation and storage of results.")
;; Code is released under GPLv2, except for fisher.h, which is under
;; LGPLv2.1+
(license (list license:gpl2 license:lgpl2.1+))))

(define-public gemma
(let ((commit "2de4bfab3"))
(package


+ 13
- 0
plink-ng-Makefile-zlib.patch Parādīt failu

@@ -0,0 +1,13 @@
diff --git a/Makefile.std b/Makefile.std
index 95b0940..630188a 100644
--- a/Makefile.std
+++ b/Makefile.std
@@ -22,7 +22,7 @@ endif
CFLAGS=-Wall -O2
BLASFLAGS=-L/usr/lib64/atlas -llapack -lcblas -latlas
LINKFLAGS=-lm -lpthread
-ZLIB=zlib-1.2.8/libz.so.1.2.8
+ZLIB=-lz
ifeq ($(SYS), MAC)
GCC_GTEQ_43 := $(shell expr `g++ -dumpversion | sed -e 's/\.\([0-9][0-9]\)/\1/g' -e 's/\.\([0-9]\)/0\1/g' -e 's/^[0-9]\{3,4\}$$/&00/'` \>= 40300)

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