>From dfc9b373bbce0f36882407cec47440a0a44c78d1 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Tue, 22 Mar 2016 14:59:05 +0100 Subject: [PATCH 1/8] gnu: Add tabixpp. * gnu/packages/bioinformatics.scm (tabixpp): New variable. --- gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 281bd1f..6792be9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4791,3 +4791,42 @@ negative binomial distribution to model the read counts among the samples in the same group, and look for consistent differences between ChIP and control group or two ChIP groups run under different conditions.") (license license:gpl3+))) + +(define-public tabixpp + (package + (name "tabixpp") + (version "1.0.0") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/ekg/tabixpp/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1s0lgks7qlvlhvcjhi2wm18nnza1bwcnic44ij7z8wfg88h4ivwn")))) + (build-system gnu-build-system) + (inputs + `(("htslib" ,htslib) + ("zlib" ,zlib))) + (arguments + `(#:tests? #f ; There are no tests to run. + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + ;; Modify the build phase to use the separately packaged htslib. + (replace 'build + (lambda* (#:key inputs #:allow-other-keys) + (let ((htslib-ref (assoc-ref inputs "htslib"))) + (zero? + (system* "make" + (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a") + "HTS_HEADERS=" ; Do not check for local htslib headers. + (string-append "LIBPATH=-L. -L" htslib-ref "/include")))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "tabix++" bin))))))) + (home-page "https://github.com/ekg/tabixpp") + (synopsis "C++ wrapper around tabix project") + (description "This is a C++ wrapper around the Tabix project which abstracts +some of the details of opening and jumping in tabix-indexed files.") + (license license:expat))) -- 2.5.5