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-rw-r--r--gn/packages/bioinformatics.scm65
1 files changed, 65 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 1aee0ef..bb5c0fd 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -417,3 +417,68 @@ association studies (GWAS).")
(synopsis "Full genenetwork services")
(description "Genenetwork installation sumo.")
(license license:agpl3+))))
+
+(define-public sambamba
+ (package
+ (name "sambamba")
+ (version "0.5.9")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/lomereiter/sambamba/archive/v"
+ version "tar.gz"))
+ (sha256
+ (base32 ""))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("ldc" ,ldc)
+ ;; These are currently included in "ldc".
+ ;;("druntime-ldc" ,druntime-ldc)
+ ;;("phobos2-ldc" ,phobos2-ldc)
+ ("lz4" ,lz4)))
+ (native-inputs
+ `(("ldc" ,ldc)
+ ;;("druntime-ldc" ,druntime-ldc)
+ ;;("phobos2-ldc" ,phobos2-ldc)
+ ("lz4" ,lz4)
+ ("gcc" ,gcc)
+ ("htslib-src"
+ (let ((version "0.2.0-rc10"))
+ ,(origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/lomereiter/htslib/archive/"
+ version ".tar.gz"))
+ (file-name (string-append "htslib-" version ".tar.gz"))
+ (sha256
+ (base32 "1k6dlf6m8yayhcp7b4yisgw1xqdy1xg2xyrllss6ld0wg00hfcbs")))))
+ ("biod-src"
+ ,(origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/biod/BioD.git")
+ (commit "7efdb8a2f7fdcd71c9ad9596be48d1262bb1bd5b")))
+ (sha256
+ (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf"))
+ (file-name "biod")))))
+ (arguments
+ `(#:make-flags "sambamba-ldmd2-64" ; This target is used for releases.
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-after 'unpack 'unpack-htslib-sources
+ (lambda* (#:key inputs #:allow-other-keys)
+ (with-directory-excursion "htslib"
+ (zero? (system* "tar" "xvf" (assoc-ref inputs "htslib-src")
+ "--strip-components=1")))))
+ (add-after 'unpack 'move-biod-sources
+ '()))) ; TODO: Figure out how to move or symlink the BioD sources to the right place.
+ (home-page "https://github.com/lomereiter/sambamba")
+ (synopsis "A tool for working with SAM and BAM files written in D.")
+ (description
+ "Sambamba is a high performance modern robust and fast tool (and
+library), written in the D programming language, for working with SAM
+and BAM files. Current parallelised functionality is an important
+subset of samtools functionality, including view, index, sort,
+markdup, and depth.")
+ (license license:gpl2+))))