Re: [PATCH] Add FastTree

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

[-- 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