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| -rw-r--r-- | gn/packages/bioinformatics.scm | 40 |
1 files changed, 40 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 91901a6..458eb28 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -2407,3 +2407,43 @@ To run the bundled rtg-tools software you will also need java. The @code{icedtea:jdk} output should work nicely.") (license (list license:expat ; bundled jsoncpp, klib license:bsd-2)))) + +;; TODO: +;; Unbundle gatb-core. +(define-public minia + (package + (name "minia") + (version "3.2.6") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/GATB/minia/releases" + "/download/v" version + "/minia-v" version "-Source.tar.gz")) + (sha256 + (base32 "03zg1jh0yjw7546kax8xs0zwiqhaiqz044409jc3ss6nj968ay70")))) + (build-system cmake-build-system) + (arguments + `(#:tests? #f ; Tests are expected to be run manually. + #:configure-flags '("-DNO_SSE=ON") ; Can be removed after unbundling gatb-core. + #:phases + (modify-phases %standard-phases + (add-after 'install 'remove-cruft + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (with-directory-excursion out + (delete-file-recursively "lib") + (delete-file-recursively "test") + (delete-file "bin/h5cc") + (delete-file "LICENSE") + (delete-file "README.md") + #t))))))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://gatb.inria.fr/software/minia") + (synopsis "Short-read assembler based on a de Bruijn graph") + (description "Minia is a short-read assembler based on a de Bruijn graph, +capable of assembling a human genome on a desktop computer in a day. The output +of Minia is a set of contigs. Back when it was released, Minia produced results +of similar contiguity and accuracy to other de Bruijn assemblers (e.g. Velvet).") + (license license:agpl3+))) |