From 482959ffa4601eff181688ec0e7ecaf68fe799a0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 6 Apr 2018 17:07:44 +0200
Subject: gnu: sambamba: Update to 0.6.7-10-g223fa20.

* gnu/packages/bioinformatics.scm (sambamba)[source]: Fetch from git.
[arguments]: Disable parallel build; rename build phase "place-biod" to
"place-biod-and-undead"; add build phase "fix-ldc-version"; adjust phase
"unbundle-prerequisites".
[native-inputs]: Add python2-minimal; update biod sources; add undead sources.
---
 gnu/packages/bioinformatics.scm | 51 +++++++++++++++++++++++++++++------------
 1 file changed, 36 insertions(+), 15 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 88aa48cd9e..0e9e6b13fd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10999,34 +10999,41 @@ droplet sequencing.  It has been particularly tailored for Drop-seq.")
 (define-public sambamba
   (package
     (name "sambamba")
-    (version "0.6.5")
+    (version "0.6.7-10-g223fa20")
     (source
      (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/lomereiter/sambamba/"
-                           "archive/v" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/lomereiter/sambamba.git")
+             (commit (string-append "v" version))))
+       (file-name (string-append name "-" version "-checkout"))
        (sha256
         (base32
-         "17076gijd65a3f07zns2gvbgahiz5lriwsa6dq353ss3jl85d8vy"))))
+         "1zb9hrxglxqh13ava9wwri30cvf85hjnbn8ccnr8l60a3k5avczn"))))
     (build-system gnu-build-system)
     (arguments
-     `(#:tests? #f ; there is no test target
-       #:make-flags
-       '("D_COMPILER=ldc2"
-         ;; Override "--compiler" flag only.
-         "D_FLAGS=--compiler=ldc2 -IBioD -g -d"
-         "sambamba-ldmd2-64")
+     `(#:tests? #f                      ; there is no test target
+       #:parallel-build? #f             ; not supported
        #:phases
        (modify-phases %standard-phases
          (delete 'configure)
-         (add-after 'unpack 'place-biod
+         (add-after 'unpack 'fix-ldc-version
+           (lambda _
+             (substitute* "gen_ldc_version_info.py"
+               (("/usr/bin/env.*") (which "python")))
+             (substitute* "Makefile"
+               (("\\$\\(shell which ldmd2\\)") (which "ldmd2")))
+             #t))
+         (add-after 'unpack 'place-biod-and-undead
            (lambda* (#:key inputs #:allow-other-keys)
              (copy-recursively (assoc-ref inputs "biod") "BioD")
+             (copy-recursively (assoc-ref inputs "undead") "undeaD")
              #t))
          (add-after 'unpack 'unbundle-prerequisites
            (lambda _
              (substitute* "Makefile"
+               (("htslib/libhts.a lz4/lib/liblz4.a")
+                "-L-lhts -L-llz4")
                ((" htslib-static lz4-static") ""))
              #t))
          (replace 'install
@@ -11039,8 +11046,9 @@ droplet sequencing.  It has been particularly tailored for Drop-seq.")
     (native-inputs
      `(("ldc" ,ldc)
        ("rdmd" ,rdmd)
+       ("python" ,python2-minimal)
        ("biod"
-        ,(let ((commit "1248586b54af4bd4dfb28ebfebfc6bf012e7a587"))
+        ,(let ((commit "c778e4f2d8bacea7499283ce39f5577b232732c6"))
            (origin
              (method git-fetch)
              (uri (git-reference
@@ -11051,7 +11059,20 @@ droplet sequencing.  It has been particularly tailored for Drop-seq.")
                                        "-checkout"))
              (sha256
               (base32
-               "1m8hi1n7x0ri4l6s9i0x6jg4z4v94xrfdzp7mbizdipfag0m17g3")))))))
+               "1z90562hg47i63gx042wb3ak2vqjg5z7hwgn9bp2pdxfg3nxrw37")))))
+       ("undead"
+        ,(let ((commit "92803d25c88657e945511f0976a0c79d8da46e89"))
+           (origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/dlang/undeaD.git")
+                   (commit commit)))
+             (file-name (string-append "undead-"
+                                       (string-take commit 9)
+                                       "-checkout"))
+             (sha256
+              (base32
+               "0vq6n81vzqvgphjw54lz2isc1j8lcxwjdbrhqz1h5gwrvw9w5138")))))))
     (inputs
      `(("lz4" ,lz4)
        ("htslib" ,htslib-for-sambamba)))
-- 
cgit 1.4.1