gnu: Add mash.
* gnu/packages/bioinformatics.scm (mash): New variable. Signed-off-by: Leo Famulari <leo@famulari.name>
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@ -76,6 +76,7 @@
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#:use-module (gnu packages python)
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#:use-module (gnu packages readline)
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#:use-module (gnu packages ruby)
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#:use-module (gnu packages serialization)
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#:use-module (gnu packages statistics)
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#:use-module (gnu packages tbb)
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#:use-module (gnu packages tex)
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@ -3046,6 +3047,62 @@ sequences).")
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"http://mafft.cbrc.jp/alignment/software/license.txt"
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"BSD-3 with different formatting"))))
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(define-public mash
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(package
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(name "mash")
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(version "1.1.1")
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(source (origin
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(method url-fetch)
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(uri (string-append
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"https://github.com/marbl/mash/archive/v"
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version ".tar.gz"))
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(file-name (string-append name "-" version ".tar.gz"))
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(sha256
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(base32
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"08znbvqq5xknfhmpp3wcj574zvi4p7i8zifi67c9qw9a6ikp42fj"))
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(modules '((guix build utils)))
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(snippet
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;; Delete bundled kseq.
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;; TODO: Also delete bundled murmurhash and open bloom filter.
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'(delete-file "src/mash/kseq.h"))))
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(build-system gnu-build-system)
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(arguments
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`(#:tests? #f ; No tests.
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#:configure-flags
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(list
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(string-append "--with-capnp=" (assoc-ref %build-inputs "capnproto"))
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(string-append "--with-gsl=" (assoc-ref %build-inputs "gsl")))
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#:make-flags (list "CC=gcc")
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'fix-includes
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(lambda _
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(substitute* '("src/mash/Sketch.cpp" "src/mash/CommandFind.cpp")
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(("^#include \"kseq\\.h\"")
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"#include \"htslib/kseq.h\""))
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#t))
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(add-before 'configure 'autoconf
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(lambda _ (zero? (system* "autoconf")))))))
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(native-inputs
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`(("autoconf" ,autoconf)
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;; Capnproto and htslib are statically embedded in the final
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;; application. Therefore we also list their licenses, below.
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("capnproto" ,capnproto)
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("htslib" ,htslib)))
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(inputs
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`(("gsl" ,gsl)
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("zlib" ,zlib)))
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(supported-systems '("x86_64-linux"))
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(home-page "https://mash.readthedocs.io")
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(synopsis "Fast genome and metagenome distance estimation using MinHash")
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(description "Mash is a fast sequence distance estimator that uses the
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MinHash algorithm and is designed to work with genomes and metagenomes in the
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form of assemblies or reads.")
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(license (list license:bsd-3 ; Mash
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license:expat ; HTSlib and capnproto
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license:public-domain ; MurmurHash 3
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license:cpl1.0)))) ; Open Bloom Filter
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(define-public metabat
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(package
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(name "metabat")
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