From: Mark H Weaver <mhw@netris.org>
To: Ben Woodcroft <b.woodcroft@uq.edu.au>
Cc: guix-devel@gnu.org, Alex Kost <alezost@gmail.com>
Subject: Re: [PATCH] Add FastTree
Date: Sun, 21 Jun 2015 00:41:00 -0400 [thread overview]
Message-ID: <878ubdad2b.fsf@netris.org> (raw)
In-Reply-To: <5585F347.5060004@uq.edu.au> (Ben Woodcroft's message of "Sun, 21 Jun 2015 09:12:07 +1000")
Ben Woodcroft <b.woodcroft@uq.edu.au> writes:
> Updated patch attached.
Much better, thanks!
> In answer to my own question
>> During development of this patch I noticed badly specified system*
> does not throw an error - is there a way to do this so?
>
> One way is to replace system* with (zero? (system* with that being the
> return value of the lambda - there's an example in the attached patch.
Yes, that's a good option.
Please see below for more comments.
> From d18f50e17547fa741569be109b31ef13c79b3d97 Mon Sep 17 00:00:00 2001
> From: Ben Woodcroft <donttrustben@gmail.com>
> Date: Sun, 21 Jun 2015 09:02:26 +1000
> Subject: [PATCH] gnu: Add fasttree
Nitpick: we prefer to add a period "." to the end of the summary line
above.
>
> * gnu/packages/bioinformatics.scm (fasttree): New variable.
> ---
> gnu/packages/bioinformatics.scm | 60 +++++++++++++++++++++++++++++++++++++++++
> 1 file changed, 60 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 12c9175..0aacce7 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -780,6 +780,66 @@ analysis (from RNA-Seq), transcription factor binding quantification in
> ChIP-Seq, and analysis of metagenomic data.")
> (license license:artistic2.0)))
>
> +(define-public fasttree
> + (package
> + (name "fasttree")
> + (version "2.1.8")
> + (source (origin
> + (method url-fetch)
> + (uri (string-append
> + "http://www.microbesonline.org/fasttree/FastTree-"
> + version ".c"
> + ))
In the Scheme world, it is considered bad form to leave close
parentheses on their own line. Please move these to the previous line,
like this:
version ".c"))
> + (replace 'build
> + (lambda* (#:key source #:allow-other-keys)
> + (and (zero? (system* "gcc"
> + "-O3"
> + "-finline-functions"
> + "-funroll-loops"
> + "-Wall"
> + "-o"
> + "FastTree"
> + source
> + "-lm"))
> + (zero? (system* "gcc"
> + "-DOPENMP"
> + "-fopenmp"
> + "-O3"
> + "-finline-functions"
> + "-funroll-loops"
> + "-Wall"
> + "-o"
> + "FastTreeMP"
> + source
> + "-lm")))))
Is there any reason to build the single-threaded version? Maybe it
would be better to omit it, and call the multi-threaded version
FastTree. What do you think?
Thanks,
Mark
next prev parent reply other threads:[~2015-06-21 4:41 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
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 [this message]
2015-06-21 6:52 ` Ben Woodcroft
2015-06-21 7:32 ` Mark H Weaver
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