Re: [PATCH] Add vcflib.

[Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>]

Roel Janssen <roel@gnu.org> writes:

> From 5cc17f0ceca12998a658dcd3cfd7494b137274e1 Mon Sep 17 00:00:00 2001
> From: Roel Janssen <roel@gnu.org>
> 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