Re: [PATCHES] Add vsearch.

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

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Updated patchset for vsearch 1.4.1 released today.

ben

On 29/09/15 22:24, Ben Woodcroft wrote:
> Excellent to see an open source competitor to usearch.
>
> Thanks in advance for review as usual. I'm not especially adept at 
> using gcc's flags so perhaps some attention is warranted in the second 
> patch's snippet.


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From e1789cbcfcf7dc6f1657f53bad04fca7180400cc Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Tue, 29 Sep 2015 22:10:33 +1000
Subject: [PATCH 1/2] gnu: Add cityhash.

* gnu/packages/textutils.scm (cityhash): New variable.
---
 gnu/packages/textutils.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index 95a8ad1..5204297 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015 Ben Woodcroft <donttrustben@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -153,3 +154,26 @@ encoding, supporting Unicode version 7.0.")
      "libgtextutils is a text utilities library used by the fastx toolkit from
 the Hannon Lab.")
     (license license:agpl3+)))
+
+(define-public cityhash
+  (let ((commit "8af9b8c")
+        (revision "1"))
+    (package
+      (name "cityhash")
+      (version (string-append "1.1." revision "." commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/google/cityhash.git")
+                      (commit commit)))
+                (file-name (string-append name "-" version ".tar.gz"))
+                (sha256
+                 (base32
+                  "0n6skf5dv8yfl1ckax8dqhvsbslkwc9158zf2ims0xqdvzsahbi6"))))
+    (build-system gnu-build-system)
+    (home-page "https://github.com/google/cityhash")
+    (synopsis "A family of functions for strings")
+    (description
+     "CityHash provides hash functions for strings.  The functions mix the
+input bits thoroughly but are not suitable for cryptography.")
+    (license license:expat))))
-- 
2.4.3


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From 5a403f43bafe129d8a22b1d0ea169c2e97d2fb5b Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Wed, 30 Sep 2015 18:35:32 +1000
Subject: [PATCH 2/2] gnu: Add vsearch.

* gnu/packages/bioinformatics.scm (vsearch): New variable.
---
 gnu/packages/bioinformatics.scm | 59 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 59 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8fc6142..25f65ae 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -33,6 +33,7 @@
   #:use-module (guix build-system ruby)
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)
+  #:use-module (gnu packages autotools)
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages base)
   #:use-module (gnu packages boost)
@@ -53,6 +54,7 @@
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages tbb)
   #:use-module (gnu packages textutils)
+  #:use-module (gnu packages tls)
   #:use-module (gnu packages vim)
   #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
@@ -2709,6 +2711,63 @@ data in the form of VCF files.")
     ;; at http://vcftools.sourceforge.net/license.html
     (license license:lgpl3)))
 
+(define-public vsearch
+  (package
+    (name "vsearch")
+    (version "1.4.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://github.com/torognes/vsearch/archive/v"
+             version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32
+         "0b1359wbzgb2cm04h7dq05v80vik88hnsv298xxd1q1f2q4ydni7"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           ;; Remove bundled cityhash
+           (substitute* "src/Makefile.am"
+             (((string-append "^AM_CXXFLAGS=-I\\$\\{srcdir\\}/cityhash"
+                              " -O3 -mtune=native -Wall -Wsign-compare"))
+              (string-append "AM_CXXFLAGS=-lcityhash"
+                             " -O3 -mtune=native -Wall -Wsign-compare"))
+             (("^__top_builddir__bin_vsearch_SOURCES = cityhash/city.h \\\\")
+              "__top_builddir__bin_vsearch_SOURCES = \\")
+             (("^cityhash/config.h \\\\") "\\")
+             (("^cityhash/city.cc \\\\") "\\"))
+           (substitute* "src/vsearch.h"
+             (("^\\#include \"cityhash/city.h\"")
+              "#include <city.h>"))
+           (delete-file-recursively "src/cityhash")
+           #t))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'configure 'autogen
+                     (lambda _ (zero? (system* "autoreconf" "-vif")))))))
+    (inputs
+     `(("zlib" ,zlib)
+       ("bzip2" ,bzip2)
+       ("cityhash" ,cityhash)))
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)))
+    (synopsis "Sequence search tools for metagenomics")
+    (description
+     "VSEARCH supports DNA sequence searching, clustering, chimera detection,
+dereplication, pairwise alignment, shuffling, subsampling, sorting and
+masking.  The tool takes advantage of parallelism in the form of SIMD
+vectorization as well as multiple threads to perform accurate alignments at
+high speed.  VSEARCH uses an optimal global aligner (full dynamic programming
+Needleman-Wunsch).")
+    (home-page "https://github.com/torognes/vsearch")
+    ;; dual licensed, plus some public domain source
+    (license (list license:gpl3 license:bsd-2 license:public-domain))))
+
 (define-public bio-locus
   (package
     (name "bio-locus")
-- 
2.4.3