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Re: [PATCH] Add vcflib.
From: |
Ricardo Wurmus |
Subject: |
Re: [PATCH] Add vcflib. |
Date: |
Tue, 26 Apr 2016 16:47:09 +0200 |
Roel Janssen <address@hidden> writes:
> Hello Ricardo,
>
> Thank you for your review.
>
> Ricardo Wurmus writes:
>
>> Roel Janssen <address@hidden> writes:
>>> From dfc9b373bbce0f36882407cec47440a0a44c78d1 Mon Sep 17 00:00:00 2001
>>> From: Roel Janssen <address@hidden>
>>> Date: Tue, 22 Mar 2016 14:59:05 +0100
>>> Subject: [PATCH 1/8] gnu: Add tabixpp.
>>
>>> * gnu/packages/bioinformatics.scm (tabixpp): New variable.
>>> ---
>>> gnu/packages/bioinformatics.scm | 39
>>> +++++++++++++++++++++++++++++++++++++++
>>> 1 file changed, 39 insertions(+)
>>
>>> diff --git a/gnu/packages/bioinformatics.scm
>>> b/gnu/packages/bioinformatics.scm
>>> index 281bd1f..6792be9 100644
>>> --- a/gnu/packages/bioinformatics.scm
>>> +++ b/gnu/packages/bioinformatics.scm
>>> @@ -4791,3 +4791,42 @@ negative binomial distribution to model the read
>>> counts among the samples in
>>> the same group, and look for consistent differences between ChIP and
>>> control
>>> group or two ChIP groups run under different conditions.")
>>> (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)
>>> + (inputs
>>> + `(("htslib" ,htslib)
>>> + ("zlib" ,zlib)))
>>> + (arguments
>>> + `(#:tests? #f ; There are no tests to run.
>>> + #:phases
>>> + (modify-phases %standard-phases
>>> + (delete 'configure) ; There is no configure phase.
>>> + ;; Modify the build phase to use the separately packaged htslib.
>>> + (replace 'build
>>> + (lambda* (#:key inputs #:allow-other-keys)
>>> + (let ((htslib-ref (assoc-ref inputs "htslib")))
>>> + (zero?
>>> + (system* "make"
>>> + (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a")
>>> + "HTS_HEADERS=" ; Do not check for local htslib headers.
>>> + (string-append "LIBPATH=-L. -L" htslib-ref
>>> "/include"))))))
>>
>> Is this really necessary or could you use make-flags instead? That
>> would be the preferred way of doing this rather than replacing the build
>> phase.
>
> So I had tried, but my Scheme skills failed there.
> In the new patch I used make-flags instead. I hope the (let ...) is
> appropriate there. I like it because it allows me to stay within 80
> columns, and avoid repetitive (assoc-ref %build-inputs "htslib").
>
>>> + (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?
~~ Ricardo
Re: [PATCH] Add vcflib., Ricardo Wurmus, 2016/04/20
Re: [PATCH] Add vcflib., Ricardo Wurmus, 2016/04/20