Re: [PATCH] Add vcflib.

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

Roel Janssen <roel@gnu.org> writes:
> From dfc9b373bbce0f36882407cec47440a0a44c78d1 Mon Sep 17 00:00:00 2001
> From: Roel Janssen <roel@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