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[PATCH] gnu: Add mash.
From: |
Marius Bakke |
Subject: |
[PATCH] gnu: Add mash. |
Date: |
Tue, 30 Aug 2016 18:54:49 +0100 |
>From 20974083333c8e94d10423d4a156caa5298d6dcb Mon Sep 17 00:00:00 2001
From: Marius Bakke <address@hidden>
Date: Tue, 30 Aug 2016 18:49:21 +0100
Subject: [PATCH 1/1] gnu: Add mash.
* gnu/packages/bioinformatics.scm (mash): New variable.
---
gnu/packages/bioinformatics.scm | 53 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 53 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ed20b56..9b96d37 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -76,6 +76,7 @@
#:use-module (gnu packages python)
#:use-module (gnu packages readline)
#:use-module (gnu packages ruby)
+ #:use-module (gnu packages serialization)
#:use-module (gnu packages statistics)
#:use-module (gnu packages tbb)
#:use-module (gnu packages tex)
@@ -3046,6 +3047,58 @@ sequences).")
"http://mafft.cbrc.jp/alignment/software/license.txt"
"BSD-3 with different formatting"))))
+(define-public mash
+ (package
+ (name "mash")
+ (version "1.1.1")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/marbl/mash/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "08znbvqq5xknfhmpp3wcj574zvi4p7i8zifi67c9qw9a6ikp42fj"))
+ (modules '((guix build utils)))
+ (snippet
+ ;; Delete bundled kseq.
+ ;; TODO: Also delete bundled murmurhash and open bloom filter.
+ '(delete-file "src/mash/kseq.h"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; No tests.
+ #:configure-flags
+ (list
+ (string-append "--with-capnp=" (assoc-ref %build-inputs "capnproto"))
+ (string-append "--with-gsl=" (assoc-ref %build-inputs "gsl")))
+ #:make-flags (list "CC=gcc")
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'fix-includes
+ (lambda _
+ (substitute* '("src/mash/Sketch.cpp" "src/mash/CommandFind.cpp")
+ (("^#include \"kseq\\.h\"")
+ "#include \"htslib/kseq.h\""))
+ #t))
+ (add-before 'configure 'autoconf
+ (lambda _ (zero? (system* "autoconf")))))))
+ (native-inputs
+ `(("autoconf" ,autoconf)
+ ("capnproto" ,capnproto)
+ ("htslib" ,htslib)))
+ (inputs
+ `(("gsl" ,gsl)
+ ("zlib" ,zlib)))
+ (home-page "https://mash.readthedocs.io")
+ (synopsis "Fast genome and metagenome distance estimation using MinHash")
+ (description "Mash is a fast sequence distance estimator that uses the
+MinHash algorithm and is designed to work with genomes and metagenomes in the
+form of assemblies or reads.")
+ ;; Mash is distributed under 3-clause BSD, but includes software covered
+ ;; by other licenses.
+ (license (list license:bsd-3 license:public-domain license:cpl1.0))))
+
(define-public metabat
(package
(name "metabat")
--
2.9.3
- [PATCH] gnu: Add mash.,
Marius Bakke <=