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| author | Marius Bakke <mbakke@fastmail.com> | 2016-08-30 18:49:21 +0100 |
|---|---|---|
| committer | Leo Famulari <leo@famulari.name> | 2016-09-10 17:41:38 -0400 |
| commit | 84be3b9920120e7cc03095baca06d61b7f3fb741 (patch) | |
| tree | 6f249abd59a8913fb09cc274b6ca435990fdd0c2 | |
| parent | 0e790a7ce0410dc7f991bca4e566fb73004ddd39 (diff) | |
| download | patches-84be3b9920120e7cc03095baca06d61b7f3fb741.tar patches-84be3b9920120e7cc03095baca06d61b7f3fb741.tar.gz | |
gnu: Add mash.
* gnu/packages/bioinformatics.scm (mash): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 57 |
1 files changed, 57 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 74360832b0..2c28ac0a24 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 +3047,62 @@ 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 and htslib are statically embedded in the final + ;; application. Therefore we also list their licenses, below. + ("capnproto" ,capnproto) + ("htslib" ,htslib))) + (inputs + `(("gsl" ,gsl) + ("zlib" ,zlib))) + (supported-systems '("x86_64-linux")) + (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.") + (license (list license:bsd-3 ; Mash + license:expat ; HTSlib and capnproto + license:public-domain ; MurmurHash 3 + license:cpl1.0)))) ; Open Bloom Filter + (define-public metabat (package (name "metabat") |