>From 98ed1adae91aca2c118779f5333dc21446f1c720 Mon Sep 17 00:00:00 2001
From: Roel Janssen <r...@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")
--
2.7.4
This time, it is attached :).
Roel Janssen writes:
> Ricardo Wurmus writes:
>
>> Roel Janssen <r...@gnu.org> writes:
>>> From 3ed14719121a952fca48a8ad3426588ebb58a130 Mon Sep 17 00:00:00 2001
>>> From: Roel Janssen <r...@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
