diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 56 | ||||
| -rw-r--r-- | plink-ng-Makefile-zlib.patch | 13 |
2 files changed, 69 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 3fbab19..f30266d 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -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 diff --git a/plink-ng-Makefile-zlib.patch b/plink-ng-Makefile-zlib.patch new file mode 100644 index 0000000..6c1f62e --- /dev/null +++ b/plink-ng-Makefile-zlib.patch @@ -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) |