From 60a90630fce9249b76be6674bd98e1a36dcd319c Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Mon, 15 Feb 2016 21:37:09 +0100 Subject: Added a work-in-progress version of Sambamba. --- gn/packages/bioinformatics.scm | 65 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 65 insertions(+) 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+)))) -- cgit v1.2.3