diff options
Diffstat (limited to 'gnu/packages')
-rw-r--r-- | gnu/packages/bioinformatics.scm | 77 |
1 files changed, 77 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 395e8ce509..63b391683c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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. |