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-rw-r--r--gn/packages/bioinformatics.scm93
-rw-r--r--gn/packages/sambamba.scm111
2 files changed, 111 insertions, 93 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index d6fd7d3..6be95dc 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -921,99 +921,6 @@ mixed model and some of its close relatives for genome-wide
association studies (GWAS).")
(license license:gpl3))))
-(define-public sambamba
- (let ((commit "6ae174bcb50d3a8f1b6dd10de9c68bbc4770e56a"))
- (package
- (name "sambamba")
- (version (string-append "0.6.6-pre3-" (string-take commit 7)))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/pjotrp/sambamba.git")
- (commit commit)))
- (file-name (string-append name "-" version "-checkout"))
- (sha256
- (base32
- "1m26i8icllclynqia4yi2mp7zfs2zajllva6bzxn188fhlyjwzqr"))))
- (build-system gnu-build-system)
- (outputs '("out"
- "debug"))
- (native-inputs
- `(("ldc" ,ldc)
- ("lz4" ,lz4)
- ("shunit2" ,shunit2)
- ("zlib" ,zlib)
- ("coreutils" ,coreutils) ; for env
- ("perl" ,perl) ; Needed for htslib
- ("ruby" ,ruby) ; Needed for htslib
- ("python" ,python-2) ; Needed for htslib
- ("gcc" ,gcc)
- ("which" ,which)
- ("htslib-src"
- ,(origin
- (method url-fetch)
- (uri "https://github.com/lomereiter/htslib/archive/2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5.tar.gz")
- ;;(uri "https://github.com/samtools/htslib/archive/1.3.tar.gz")
- (file-name "htslib-0.2.0-rc10-271-g2f3c3ea-dirty.tar.gz")
- (sha256
- (base32 "0bl6w856afnbgdsw8bybsxpqsyf2ba3f12rqh47hhpxvv866g08w"))))
- ;;(base32 "1bqkif7yrqmiqak5yb74kgpb2lsdlg7y344qa1xkdg7k1l4m86i9"))
- ;;(patches (list (search-patch "htslib-add-cram_to_bam.patch")))))
- ("biod-src"
- ,(origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/pjotrp/BioD.git")
- (commit "b7f1db860d212ee5fb6f9adfb36c6e783aaeb6f5")))
- (file-name (string-append "biod-src-" (string-take commit 7) "-checkout"))
- (sha256
- (base32 "01xkdjdn9lb2b4b5ykzhnrk2rjikagav8b3fyac3zafcfq600cr4"))))
- ("dlang-undeaD-src"
- ,(origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/dlang/undeaD.git")
- (commit "610234f159132f91046d4fb893889fb8ee14cd2f")))
- (file-name (string-append "dlang-undeaD-src-" (string-take commit 7) "-checkout"))
- (sha256
- (base32 "12zxsgvka4a82ghp2gaviph6kz13jzjb5pbc8v6i3rmcnifzpbrl"))))))
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (delete 'configure)
- (delete 'check)
- (add-after 'unpack 'unpack-htslib-sources
- (lambda* (#:key inputs #:allow-other-keys)
- ;; The current build compiles htslib statically into the
- ;; executable. On top of that, we need to patch the latest
- ;; version of htslib to have it working with Sambamba.
- (and (with-directory-excursion "htslib"
- (zero? (system* "tar" "xvf" (assoc-ref inputs "htslib-src")
- "--strip-components=1")))
- (copy-recursively (assoc-ref inputs "dlang-undeaD-src") "undeaD")
- (copy-recursively (assoc-ref inputs "biod-src") "BioD"))))
- (replace
- 'build
- (lambda* (#:key inputs make-flags #:allow-other-keys)
- (zero? (system* "make" "-f" "Makefile.guix" "guix-debug"
- (string-append "LDC_LIB_PATH="
- (assoc-ref inputs "ldc")
- "/lib")))))
- (replace
- 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
- (install-file "build/sambamba" bin)))))))
- (home-page "https://github.com/lomereiter/sambamba")
- (synopsis "Fast tool for working with SAM, BAM and CRAM 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, BAM and CRAM files. Current parallelised functionality is
-an important subset of samtools functionality, including view, index,
-sort, markdup, and depth.")
- (license license:gpl2+))))
-
(define-public vcflib
(let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb"))
(package
diff --git a/gn/packages/sambamba.scm b/gn/packages/sambamba.scm
new file mode 100644
index 0000000..46cf0e7
--- /dev/null
+++ b/gn/packages/sambamba.scm
@@ -0,0 +1,111 @@
+;; Sambamba
+
+(define-module (gn packages sambamba)
+ #:use-module ((guix licenses) #:prefix license:)
+ #:use-module (guix packages)
+ #:use-module (guix utils)
+ #:use-module (guix download)
+ #:use-module (guix git-download)
+ #:use-module (guix build-system gnu)
+ #:use-module (gnu packages base)
+ #:use-module (gnu packages compression)
+ #:use-module (gnu packages gcc)
+ #:use-module (gnu packages perl)
+ #:use-module (gnu packages python)
+ #:use-module (gnu packages ruby)
+ #:use-module (gn packages ldc)
+ #:use-module (gn packages shell)
+ #:use-module (srfi srfi-1))
+
+(define-public sambamba
+ (let ((commit "6ae174bcb50d3a8f1b6dd10de9c68bbc4770e56a"))
+ (package
+ (name "sambamba")
+ (version (string-append "0.6.6-pre3-" (string-take commit 7)))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/pjotrp/sambamba.git")
+ (commit commit)))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32
+ "1m26i8icllclynqia4yi2mp7zfs2zajllva6bzxn188fhlyjwzqr"))))
+ (build-system gnu-build-system)
+ (outputs '("out"
+ "debug"))
+ (native-inputs
+ `(("ldc" ,ldc)
+ ("lz4" ,lz4)
+ ("shunit2" ,shunit2)
+ ("zlib" ,zlib)
+ ("coreutils" ,coreutils) ; for env
+ ("perl" ,perl) ; Needed for htslib
+ ("ruby" ,ruby) ; Needed for htslib
+ ("python" ,python-2) ; Needed for htslib
+ ("gcc" ,gcc)
+ ("which" ,which)
+ ("htslib-src"
+ ,(origin
+ (method url-fetch)
+ (uri "https://github.com/lomereiter/htslib/archive/2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5.tar.gz")
+ ;;(uri "https://github.com/samtools/htslib/archive/1.3.tar.gz")
+ (file-name "htslib-0.2.0-rc10-271-g2f3c3ea-dirty.tar.gz")
+ (sha256
+ (base32 "0bl6w856afnbgdsw8bybsxpqsyf2ba3f12rqh47hhpxvv866g08w"))))
+ ;;(base32 "1bqkif7yrqmiqak5yb74kgpb2lsdlg7y344qa1xkdg7k1l4m86i9"))
+ ;;(patches (list (search-patch "htslib-add-cram_to_bam.patch")))))
+ ("biod-src"
+ ,(origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/pjotrp/BioD.git")
+ (commit "b7f1db860d212ee5fb6f9adfb36c6e783aaeb6f5")))
+ (file-name (string-append "biod-src-" (string-take commit 7) "-checkout"))
+ (sha256
+ (base32 "01xkdjdn9lb2b4b5ykzhnrk2rjikagav8b3fyac3zafcfq600cr4"))))
+ ("dlang-undeaD-src"
+ ,(origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/dlang/undeaD.git")
+ (commit "610234f159132f91046d4fb893889fb8ee14cd2f")))
+ (file-name (string-append "dlang-undeaD-src-" (string-take commit 7) "-checkout"))
+ (sha256
+ (base32 "12zxsgvka4a82ghp2gaviph6kz13jzjb5pbc8v6i3rmcnifzpbrl"))))))
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (delete 'check)
+ (add-after 'unpack 'unpack-htslib-sources
+ (lambda* (#:key inputs #:allow-other-keys)
+ ;; The current build compiles htslib statically into the
+ ;; executable. On top of that, we need to patch the latest
+ ;; version of htslib to have it working with Sambamba.
+ (and (with-directory-excursion "htslib"
+ (zero? (system* "tar" "xvf" (assoc-ref inputs "htslib-src")
+ "--strip-components=1")))
+ (copy-recursively (assoc-ref inputs "dlang-undeaD-src") "undeaD")
+ (copy-recursively (assoc-ref inputs "biod-src") "BioD"))))
+ (replace
+ 'build
+ (lambda* (#:key inputs make-flags #:allow-other-keys)
+ (zero? (system* "make" "-f" "Makefile.guix" "guix-debug"
+ (string-append "LDC_LIB_PATH="
+ (assoc-ref inputs "ldc")
+ "/lib")))))
+ (replace
+ 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "build/sambamba" bin)))))))
+ (home-page "https://github.com/lomereiter/sambamba")
+ (synopsis "Fast tool for working with SAM, BAM and CRAM 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, BAM and CRAM files. Current parallelised functionality is
+an important subset of samtools functionality, including view, index,
+sort, markdup, and depth.")
+ (license license:gpl2+))))