Re: [PATCH] Add FastTree

[Ben Woodcroft <b.woodcroft@uq.edu.au>]

[-- Attachment #1: Type: text/plain, Size: 355 bytes --]



On 20/06/15 08:30, Ben Woodcroft wrote:
> On 19/06/15 20:13, Alex Kost wrote:
>> 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.
> Thanks, all help appreciated. Updated patch attached.
Sorry now without the extraneous files.

[-- Attachment #2: 0001-gnu-Add-fasttree.patch --]
[-- Type: text/x-patch, Size: 3387 bytes --]

From af17052d0f613ba53c7bc14fb99e143a60f97713 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Sat, 20 Jun 2015 15:30:42 +1000
Subject: [PATCH] gnu: Add fasttree

* gnu/packages/bioinformatics.scm (fasttree): New variable.
---
 gnu/packages/bioinformatics.scm | 61 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 61 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 12c9175..fb701f9 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 +781,66 @@ 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 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 "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