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Re: [PATCH] Add vcflib.
From: |
Ricardo Wurmus |
Subject: |
Re: [PATCH] Add vcflib. |
Date: |
Mon, 16 Jan 2017 22:59:57 +0100 |
User-agent: |
mu4e 0.9.18; emacs 25.1.1 |
Roel Janssen <address@hidden> writes:
> From 5cc17f0ceca12998a658dcd3cfd7494b137274e1 Mon Sep 17 00:00:00 2001
> From: Roel Janssen <address@hidden>
> Date: Tue, 26 Apr 2016 19:28:54 +0200
> Subject: [PATCH] gnu: Add tabixpp.
>
> * gnu/packages/bioinformatics.scm (tabixpp): New variable.
> ---
> gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++++++++++++
> 1 file changed, 34 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 620439f..450d250 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -5102,3 +5102,37 @@ group or two ChIP groups run under different
> conditions.")
> (description "This program compares version strings. It intends to be
> a
> replacement for strverscmp.")
> (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)
> + (arguments
> + `(#:tests? #f ; There are no tests to run.
> + #:make-flags (let ((htslib-ref (assoc-ref %build-inputs "htslib")))
> + `("HTS_HEADERS=" ; Do not check for local htslib headers.
> + ,(string-append "HTS_LIB=" htslib-ref "/lib/libhts.a")
> + ,(string-append "LIBPATH=-L. -L" htslib-ref
> "/include")))
> + #:phases
> + (modify-phases %standard-phases
> + (delete 'configure) ; There is no configure phase.
> + (replace 'install
> + (lambda* (#:key outputs #:allow-other-keys)
> + (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
> + (install-file "tabix" bin)))))))
> + (inputs
> + `(("htslib" ,htslib)
> + ("zlib" ,zlib)))
> + (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)))
One more from the bottom of my inbox at work… (I haven’t even started
looking at my private inbox.)
Please add “#t” to the end of the “install” phase and adjust the
indentation of the make-flags. The rest looks good.
Thanks!
--
Ricardo