Re: [PATCH] Add vcflib.

[Roel Janssen <roel@gnu.org>]

Ricardo Wurmus writes:

> Roel Janssen <roel@gnu.org> writes:
>> From 3ed14719121a952fca48a8ad3426588ebb58a130 Mon Sep 17 00:00:00 2001
>> From: Roel Janssen <roel@gnu.org>
>> Date: Tue, 22 Mar 2016 15:57:33 +0100
>> Subject: [PATCH 7/8] 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 9cbde46..5a0eb16 100644
>> --- a/gnu/packages/bioinformatics.scm
>> +++ b/gnu/packages/bioinformatics.scm
>> @@ -4985,3 +4985,35 @@ automatically handles index file generation and use.")
>>        ;; this program is a submodule, is licensed MIT, which is the same as
>>        ;; the Expat license.
>>        (license (list license:gpl2 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"))))
>
> The indentation looks wrong here.  Could you please double-check that
> you’re not using tabs?

I don't know what went wrong there, sorry.  Attached a new patch that
should be better.

>> +           (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))))
>
> The rest looks good to me.

Thanks a lot for reviewing my patches!

Kind regards,
Roel Janssen