Hi,
I was a bit confused the best way to package FastTree as it is so simple
- the install instructions just give how to run gcc and I couldn't find
anything similar (enough for me) in other .scm files.
I'm also not clear which version of gcc should be chosen - I chose 5.1
as it was new, but it also compiles with other versions.
During development of this patch I noticed badly specified system* does
not throw an error - is there a way to do this so?
And more generally, there's no equivalent of make check here, should one
be manually specified?
Thanks,
ben
>From b89cd0e855adc05e0f8ef6e2d6cdf6132af076e9 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrust...@gmail.com>
Date: Fri, 19 Jun 2015 17:01:56 +1000
Subject: [PATCH] gnu: Add fasttree
* gnu/packages/bioinformatics.scm (fasttree): New variable.
---
gnu/packages/bioinformatics.scm | 63 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 63 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 12c9175..311635b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -34,6 +34,7 @@
#:use-module (gnu packages boost)
#:use-module (gnu packages compression)
#:use-module (gnu packages file)
+ #:use-module (gnu packages gcc)
#:use-module (gnu packages java)
#:use-module (gnu packages linux)
#:use-module (gnu packages machine-learning)
@@ -780,6 +781,68 @@ 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 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")))
+ (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")
+ (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
