Re: [PATCH] Add vcflib.

[Roel Janssen <roel@gnu.org>]

Ricardo Wurmus writes:

> 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?

That's an oldie indeed.  These patches intended to add freebayes.  The
freebayes patch I submitted no longer works, so I'll need to work on
that.  Before doing so, not all license issues have been resolved
(yet?), so let's wait for that.

Do you think it's useful for these patches to be committed regardless of
whether freebayes will be added?  If so, then I'll take the time to
rebase and push them.

Kind regards,
Roel Janssen