Roel Janssen <r...@gnu.org> writes: > From dfc9b373bbce0f36882407cec47440a0a44c78d1 Mon Sep 17 00:00:00 2001 > From: Roel Janssen <r...@gnu.org> > 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")))))) Is this really necessary or could you use make-flags instead? That would be the preferred way of doing this rather than replacing the build phase. > + (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") “tabix” or “Tabix”? > + (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))) “tabix” or “Tabix”? Could you please send an updated patch? ~~ Ricardo
