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authorEfraim Flashner2021-09-29 16:40:33 +0300
committerEfraim Flashner2021-09-29 16:41:24 +0300
commit8e59af5447699a26518427e0a761437e2e5cc9fa (patch)
tree90bc500f9d0431e9111250b6881d8b5b2a712bae /gn
parent75e92b9503280ac11195a58af157f3edccce3695 (diff)
downloadguix-bioinformatics-8e59af5447699a26518427e0a761437e2e5cc9fa.tar.gz
gn: Add minia.
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/bioinformatics.scm40
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+)))