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gnu: Add qtltools.

* gnu/packages/bioinformatics.scm (qtltools): New variable.
master
Ricardo Wurmus 2021-10-22 21:28:34 +00:00
parent 41492639e0
commit 4a0cd6297a
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1 changed files with 77 additions and 0 deletions

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@ -1361,6 +1361,83 @@ relying on a complex dependency tree.")
long-read sequencing data.")
(license license:expat)))
(define-public qtltools
(package
(name "qtltools")
(version "1.3.1")
(source (origin
(method url-fetch/tarbomb)
(uri (string-append "https://qtltools.github.io/qtltools/"
"binaries/QTLtools_" version
"_source.tar.gz"))
(sha256
(base32
"13gdry5l43abn3464fmk8qzrxgxnxah2612r66p9dzhhl92j30cd"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no tests included
#:make-flags
(list (string-append "BOOST_INC="
(assoc-ref %build-inputs "boost") "/include")
(string-append "BOOST_LIB="
(assoc-ref %build-inputs "boost") "/lib")
(string-append "HTSLD_INC="
(assoc-ref %build-inputs "htslib") "/include")
(string-append "HTSLD_LIB="
(assoc-ref %build-inputs "htslib") "/lib")
(string-append "RMATH_INC="
(assoc-ref %build-inputs "rmath-standalone")
"/include")
(string-append "RMATH_LIB="
(assoc-ref %build-inputs "rmath-standalone")
"/lib"))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-linkage
(lambda _
(substitute* "qtltools/Makefile"
(("libboost_iostreams.a")
"libboost_iostreams.so")
(("libboost_program_options.a")
"libboost_program_options.so")
(("-lblas") "-lopenblas"))))
(add-before 'build 'chdir
(lambda _ (chdir "qtltools")))
(replace 'configure
(lambda _
(substitute* "qtltools/Makefile"
(("LIB_FLAGS=-lz")
"LIB_FLAGS=-lz -lcrypto -lssl")
(("LIB_FILES=\\$\\(RMATH_LIB\\)/libRmath.a \
\\$\\(HTSLD_LIB\\)/libhts.a \
\\$\\(BOOST_LIB\\)/libboost_iostreams.a \
\\$\\(BOOST_LIB\\)/libboost_program_options.a")
"LIB_FILES=$(RMATH_LIB)/libRmath.so \
$(HTSLD_LIB)/libhts.so \
$(BOOST_LIB)/libboost_iostreams.so \
$(BOOST_LIB)/libboost_program_options.so"))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(mkdir-p bin)
(install-file "bin/QTLtools" bin)))))))
(inputs
`(("curl" ,curl)
("gsl" ,gsl)
("boost" ,boost)
("rmath-standalone" ,rmath-standalone)
("htslib" ,htslib-1.3)
("openssl" ,openssl)
("openblas" ,openblas)
("zlib" ,zlib)))
(home-page "https://qtltools.github.io/qtltools/")
(synopsis "Tool set for molecular QTL discovery and analysis")
(description "QTLtools is a tool set for molecular QTL discovery
and analysis. It allows to go from the raw genetic sequence data to
collection of molecular @dfn{Quantitative Trait Loci} (QTLs) in few
easy-to-perform steps.")
(license license:gpl3+)))
(define-public bpp-core
;; The last release was in 2014 and the recommended way to install from source
;; is to clone the git repository, so we do this.