From 6c2c0499e817badf1cc41822dfdf813e065a34a3 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Tue, 23 Feb 2016 10:38:55 +0100 Subject: Using my own fork of the Sambamba repository. --- gn/packages/bioinformatics.scm | 155 ++++++++++++++++++++++------------------- 1 file changed, 85 insertions(+), 70 deletions(-) (limited to 'gn') diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 098411e..cfc5dae 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -310,82 +310,97 @@ and freshness without requiring additional information from the user.") (license license:boost1.0)))) (define-public sambamba - (let ((commit "2ca5a2dba")) - (package - (name "sambamba") - (version (string-append "0.5.9-" commit)) - (source (origin + (let ((commit "8fe1bda92423c7c97a52ef81c6871fd6569fd1da")) + ;;(let ((commit "2ca5a2dbac5ab90c3b4c588519edc3edcb71df84")) + (package + (name "sambamba") + (version (string-append "0.5.9-" commit)) + (source (origin + (method git-fetch) + (uri (git-reference + ;; https://github.com/pjotrp/sambamba.git + (url "https://github.com/roelj/sambamba.git") + (commit commit))) + (file-name (string-append name "-" (string-take commit 7))) + (sha256 + (base32 + ;;"1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5" + "14gx0hhn039xhgkf5hbvffn9d0ld4zn9ka2zvvdi16k441sc8wjh")))) + (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) + ("rdmd" ,rdmd) + ("zlib" ,zlib) + ("gcc" ,gcc) + ("lz4-src" + ,(origin + (method url-fetch) + (uri (string-append + "https://github.com/Cyan4973/lz4/archive/r131.tar.gz")) + (file-name "lz4-131.tar.gz") + (sha256 + (base32 "1vfg305zvj50hwscad24wan9jar6nqj14gdk2hqyr7bb9mhh0kcx")))) + ("htslib-src" + ,(origin + (method url-fetch) + (uri (string-append + "https://github.com/lomereiter/htslib/archive/0.2.0-rc10.tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1k6dlf6m8yayhcp7b4yisgw1xqdy1xg2xyrllss6ld0wg00hfcbs")))) + ("biod-src" + ,(origin (method git-fetch) - (uri (git-reference - ;; https://github.com/pjotrp/sambamba.git - (url "https://github.com/pjotrp/sambamba.git") - (commit commit))) - (file-name (string-append name "-" commit)) + (uri (git-reference + (url "https://github.com/biod/BioD.git") + (commit "7efdb8a2f7fdcd71c9ad9596be48d1262bb1bd5b"))) (sha256 - (base32 - "1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5")))) - (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) - ("rdmd" ,rdmd) - ("htslib-src" - ,(origin - (method url-fetch) - (uri (string-append - "https://github.com/lomereiter/htslib/archive/0.2.0-rc10.tar.gz")) - (file-name (string-append "htslib-0.2.0-rc10.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 - '(#:phases - (modify-phases %standard-phases - (delete 'configure) - (add-after 'unpack 'unpack-htslib-sources - (lambda* (#:key inputs #:allow-other-keys) - ;; Unfortunately, the current build compiles htslib statically - ;; into the executable. Instead of patching the build files - ;; for Guix, this should be resolved on Sambamba upstream. For - ;; now, just extract the source code to the desired directory. - (and (with-directory-excursion "htslib" - (zero? (system* "tar" "xvf" (assoc-ref inputs "htslib-src") - "--strip-components=1"))) - (zero? (system* "cp" "-R" (assoc-ref inputs "biod-src") "BioD")) - ))) - ;; Building a production-quality executable is done with a - ;; non-default make target. Adding it with #:make-flags breaks - ;; building tests. Therefore, the default make got replaced by this. - (replace - 'build - (lambda* (#:key (make-flags '()) #:allow-other-keys) - (zero? (system* "make" "-f" "Makefile.guix" make-flags))))))) - (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 + (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf")) + (file-name "biod-src"))))) + (arguments + `(#:tests? #f + #:make-flags (list "CC=gcc" "D_COMPILER=ldc2") + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-after 'unpack 'unpack-htslib-sources + (lambda* (#:key inputs #:allow-other-keys) + ;; Unfortunately, the current build compiles htslib statically + ;; into the executable. Instead of patching the build files + ;; for Guix, this should be resolved on Sambamba upstream. For + ;; now, just extract the source code to the desired directory. + (and (with-directory-excursion "htslib" + (zero? (system* "tar" "xvf" (assoc-ref inputs "htslib-src") + "--strip-components=1"))) + (with-directory-excursion "lz4" + (zero? (system* "tar" "xvf" (assoc-ref inputs "lz4-src") + "--strip-components=1"))) + (zero? (system* "ln" "--symbolic" (assoc-ref inputs "biod-src") "BioD"))))) + ;; Building a production-quality executable is done with a + ;; non-default make target. Adding it with #:make-flags breaks + ;; building tests. Therefore, the default make got replaced by this. + (replace + 'build + (lambda* (#:key inputs #:allow-other-keys) + (zero? (system* "make" "sambamba-ldmd2-64"))))))) + (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+)))) + (license license:gpl2+)))) (define-public picard (package -- cgit v1.2.3