Re: [PATCH] Add vcflib.

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

Roel Janssen <roel@gnu.org> writes:

> From 98ed1adae91aca2c118779f5333dc21446f1c720 Mon Sep 17 00:00:00 2001
> From: Roel Janssen <roel@gnu.org>
> Date: Tue, 26 Apr 2016 19:48:31 +0200
> Subject: [PATCH] gnu: Add intervaltree.
>
> * gnu/packages/bioinformatics.scm (intervaltree): New variable.
> ---
>  gnu/packages/bioinformatics.scm | 32 ++++++++++++++++++++++++++++++++
>  1 file changed, 32 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 620439f..9ad6c38 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -885,6 +885,38 @@ well as many of the command line options.")
>  multiple sequence alignments.")
>      (license license:expat)))
>  
> +(define-public intervaltree
> +  (let ((commit "dbb4c513d1ad3baac516fc1484c995daf9b42838"))
> +    (package
> +      (name "intervaltree")
> +      (version (string-append "0-1." (string-take commit 7)))
> +      (source (origin
> +        (method url-fetch)
> +        (uri (string-append "https://github.com/ekg/intervaltree/archive/"
> +                            commit ".tar.gz"))
> +        (file-name (string-append name "-" version ".tar.gz"))
> +        (sha256
> +         (base32 "19prwpn2wxsrijp5svfqvfcxl5nj7zdhm3jycd5kqhl9nifpmcks"))))
> +      (build-system gnu-build-system)
> +      (arguments
> +       `(#:phases
> +         (modify-phases %standard-phases
> +           (delete 'configure) ; There is no configure phase.
> +           (replace 'check
> +             (lambda _
> +               (zero? (system* "./interval_tree_test"))))
> +           (replace 'install
> +             (lambda* (#:key outputs #:allow-other-keys)
> +               (let ((include (string-append (assoc-ref outputs "out")
> +                                             "/include/intervaltree")))
> +                 (install-file "IntervalTree.h" include)))))))
> +      (home-page "https://github.com/ekg/intervaltree/")
> +      (synopsis "Minimal C++ interval tree implementation")
> +      (description "This library provides a basic implementation of an interval
> +tree using C++ templates, allowing the insertion of arbitrary types into the
> +tree.")
> +      (license license:expat))))
> +
>  (define-public python-pysam
>    (package
>      (name "python-pysam")

That’s a nice patch that doesn’t seem to be in Guix yet.  It was part of
your vcflib series, but it never made it upstream.  Would you like to
rebase and push it?

-- 
Ricardo