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Re: [PATCH] Add vcflib.
From: |
Ricardo Wurmus |
Subject: |
Re: [PATCH] Add vcflib. |
Date: |
Wed, 20 Apr 2016 14:46:21 +0200 |
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.
> + (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”?
> + (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”?
Could you please send an updated patch?
~~ Ricardo
Re: [PATCH] Add vcflib., Ricardo Wurmus, 2016/04/20