sambamba: moved into its own module

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+))))