>From 5cc17f0ceca12998a658dcd3cfd7494b137274e1 Mon Sep 17 00:00:00 2001
From: Roel Janssen <r...@gnu.org>
Date: Tue, 26 Apr 2016 19:28:54 +0200
Subject: [PATCH] gnu: Add tabixpp.
* gnu/packages/bioinformatics.scm (tabixpp): New variable.
---
gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++++++++++++
1 file changed, 34 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 620439f..450d250 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5102,3 +5102,37 @@ group or two ChIP groups run under different conditions.")
(description "This program compares version strings. It intends to be a
replacement for strverscmp.")
(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)
+ (arguments
+ `(#:tests? #f ; There are no tests to run.
+ #:make-flags (let ((htslib-ref (assoc-ref %build-inputs "htslib")))
+ `("HTS_HEADERS=" ; Do not check for local htslib headers.
+ ,(string-append "HTS_LIB=" htslib-ref "/lib/libhts.a")
+ ,(string-append "LIBPATH=-L. -L" htslib-ref "/include")))
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; There is no configure phase.
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "tabix" bin)))))))
+ (inputs
+ `(("htslib" ,htslib)
+ ("zlib" ,zlib)))
+ (home-page "https://github.com/ekg/tabixpp";)
+ (synopsis "C++ wrapper around Tabix project")
+ (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)))
--
2.7.4
Ricardo Wurmus writes:
> Roel Janssen <r...@gnu.org> writes:
>
>> Hello Ricardo,
>>
>> Thank you for your review.
>>
>> Ricardo Wurmus writes:
>>>> + (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”?
>>
>> Tabix I suppose.
>>
>>>> + (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”?
>>
>> Right. I changed both occurrences to “Tabix”.
>>
>>> Could you please send an updated patch?
>>
>> Here it is.
>
> Thanks, looks good, except for having the inputs before the arguments.
> I tried to apply the patch to master but it failed. Could you please
> rebase it onto master and resend?
Attached a new patch with the inputs after arguments.
Thanks!
Kind regards,
Roel Janssen
