From: Ben Woodcroft <b.woodcroft@uq.edu.au>
To: Mark H Weaver <mhw@netris.org>
Cc: guix-devel@gnu.org, Alex Kost <alezost@gmail.com>
Subject: Re: [PATCH] Add FastTree
Date: Sun, 21 Jun 2015 09:12:07 +1000 [thread overview]
Message-ID: <5585F347.5060004@uq.edu.au> (raw)
In-Reply-To: <87zj3u9u4r.fsf@netris.org>
[-- Attachment #1: Type: text/plain, Size: 1263 bytes --]
On 21/06/15 03:17, Mark H Weaver wrote:
> Hi Ben,
>
> Instead of using 'trivial-build-system' for this, it would be better to
> use 'gnu-build-system' and remove/replace the phases that aren't
> appropriate. So, you'll probably want to remove the 'configure' phase
> and replace the 'build' and 'install' phases.
>
> Even so, there are many important phases and implicit inputs in
> 'gnu-build-system', notably setting the environment variables before the
> build, and checking for missing rpaths in the installed binaries.
>
> As you have it now, since you used bare 'binutils' and not our
> 'ld-wrapper' package, and you didn't add explicit rpaths options to the
> linker, I guess that the produced executable won't be able to find the
> specific shared libraries it was linked against without more help.
I'm sure you are right, though I tried a few things and cannot get it to
fail. Is there a way to ensure there is nothing amiss?
Updated patch attached.
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.
[-- Attachment #2: 0001-gnu-Add-fasttree.patch --]
[-- Type: text/x-patch, Size: 3433 bytes --]
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
* 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"
+ ))
+ (sha256
+ (base32
+ "0dzqc9vr9iiiw21y159xfjl2z90vw0y7r4x6456pcaxiy5hd2wmi"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; no "check" target
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'unpack)
+ (delete 'configure)
+ (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")))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out")
+ "/bin")))
+ (mkdir-p bin)
+ (copy-file "FastTree"
+ (string-append bin "/FastTree"))
+ (copy-file "FastTreeMP"
+ (string-append bin "/FastTreeMP"))
+ #t))))))
+ (home-page "http://www.microbesonline.org/fasttree")
+ (synopsis "Infers approximately-maximum-likelihood phylogenetic trees")
+ (description
+ "FastTree can handle alignments with up to a million of sequences in a
+reasonable amount of time and memory. For large alignments, FastTree is
+100-1,000 times faster than PhyML 3.0 or RAxML 7.")
+ (license license:gpl2+)))
+
(define-public fastx-toolkit
(package
(name "fastx-toolkit")
--
2.1.4
next prev parent reply other threads:[~2015-06-20 23:12 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 [this message]
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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