From: Alex Kost <alezost@gmail.com>
To: Ben Woodcroft <b.woodcroft@uq.edu.au>
Cc: "guix-devel@gnu.org" <guix-devel@gnu.org>
Subject: Re: [PATCH] Add FastTree
Date: Fri, 19 Jun 2015 13:13:08 +0300 [thread overview]
Message-ID: <87oakcqa4r.fsf@gmail.com> (raw)
In-Reply-To: <5583C3A2.1080906@uq.edu.au> (Ben Woodcroft's message of "Fri, 19 Jun 2015 17:24:18 +1000")
Ben Woodcroft (2015-06-19 10:24 +0300) wrote:
> Hi,
Hi, I didn't try your patch, so I don't have real comments, just some
general cosmetic notes, if you don't mind.
[...]
> + (source (origin
> + (method url-fetch)
> + (uri (string-append
> + "http://www.microbesonline.org/fasttree/FastTree-"
> + version
> + ".c"
> + ))
Please put it on one line:
version ".c"))
> + (sha256
> + (base32
> + "0dzqc9vr9iiiw21y159xfjl2z90vw0y7r4x6456pcaxiy5hd2wmi"))))
> + (build-system trivial-build-system)
> + (arguments
> + '(#:modules ((guix build utils))
> + #:builder
> + (begin
> + (use-modules (guix build utils) (system base compile))
> + (let ((source (assoc-ref %build-inputs "source"))
> + (gcc (assoc-ref %build-inputs "gcc"))
> + (glibc (assoc-ref %build-inputs "glibc"))
> + (binutils (assoc-ref %build-inputs "binutils"))
> + (out (assoc-ref %outputs "out")))
Please remove trailing spaces ^^^^^^^^^^
And it would be more readable to align this 'let':
(let ((source (assoc-ref %build-inputs "source"))
(gcc (assoc-ref %build-inputs "gcc"))
(glibc (assoc-ref %build-inputs "glibc"))
(binutils (assoc-ref %build-inputs "binutils"))
(out (assoc-ref %outputs "out")))
> + (setenv "PATH" (string-append binutils "/bin:" gcc "/bin"))
> + (setenv "LIBRARY_PATH" (string-append glibc "/lib"))
> + (let ((bin (string-append out "/bin")))
> + (mkdir-p bin)
> + (system* "gcc"
> + "-O3"
> + "-finline-functions"
> + "-funroll-loops"
> + "-Wall"
> + "-o"
> + (string-append bin "/FastTree")
> + source
> + "-lm")
> + (system* "gcc"
> + "-DOPENMP"
> + "-fopenmp"
> + "-O3"
> + "-finline-functions"
> + "-funroll-loops"
> + "-Wall"
> + "-o"
> + (string-append bin "/FastTreeMP")
> + source
> + "-lm"))))))
> + (native-inputs
> + `(("gcc", gcc-5.1)
> + ("binutils" ,binutils)
> + ("glibc" ,glibc)))
> + (home-page "http://www.microbesonline.org/fasttree")
> + (synopsis "FastTree infers approximately-maximum-likelihood
> +phylogenetic trees from alignments of nucleotide or protein sequences")
Synopsis is too long; it should be a one-liner. You may use "guix lint
fasttree" to perform some common checks.
--
Alex
next prev parent reply other threads:[~2015-06-19 10:13 UTC|newest]
Thread overview: 9+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-06-19 7:24 [PATCH] Add FastTree Ben Woodcroft
2015-06-19 10:13 ` Alex Kost [this message]
2015-06-19 22:30 ` Ben Woodcroft
2015-06-20 5:32 ` Ben Woodcroft
2015-06-20 17:17 ` Mark H Weaver
2015-06-20 23:12 ` Ben Woodcroft
2015-06-21 4:41 ` Mark H Weaver
2015-06-21 6:52 ` Ben Woodcroft
2015-06-21 7:32 ` Mark H Weaver
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