Breaks on linking in the final stages.

1 files changed, 20 insertions, 16 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index cfc5dae..3363ea2 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -35,6 +35,7 @@
   #:use-module (gnu packages popt)
   #:use-module (gnu packages protobuf)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages ruby)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages tbb)
   #:use-module (gnu packages textutils)
@@ -310,22 +311,19 @@ and freshness without requiring additional information from the user.")
       (license license:boost1.0))))
 
 (define-public sambamba
-  (let ((commit "8fe1bda92423c7c97a52ef81c6871fd6569fd1da"))
-  ;;(let ((commit "2ca5a2dbac5ab90c3b4c588519edc3edcb71df84"))
+  (let ((commit "2ca5a2dbac5ab90c3b4c588519edc3edcb71df84"))
     (package
       (name "sambamba")
-      (version (string-append "0.5.9-" commit))
+      (version (string-append "0.5.9-1." (string-take commit 7)))
       (source (origin
         (method git-fetch)
         (uri (git-reference                
-              ;; https://github.com/pjotrp/sambamba.git
-              (url "https://github.com/roelj/sambamba.git")
+              (url "https://github.com/pjotrp/sambamba.git")
               (commit commit)))
-        (file-name (string-append name "-" (string-take commit 7)))
+        (file-name (string-append name "-" version "-checkout"))
         (sha256
          (base32
-          ;;"1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5"
-          "14gx0hhn039xhgkf5hbvffn9d0ld4zn9ka2zvvdi16k441sc8wjh"))))
+          "1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5"))))
       (build-system gnu-build-system)
       ;; (inputs
       ;;  `(("ldc" ,ldc)
@@ -340,13 +338,16 @@ and freshness without requiring additional information from the user.")
          ("lz4" ,lz4)
          ("rdmd" ,rdmd)
          ("zlib" ,zlib)
+         ("perl" ,perl) ; Needed for htslib
+         ("ruby" ,ruby) ; Needed for htslib
+         ("python" ,python) ; Needed for htslib
          ("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")
+             (file-name "lz4-r131.tar.gz")
              (sha256
               (base32 "1vfg305zvj50hwscad24wan9jar6nqj14gdk2hqyr7bb9mhh0kcx"))))
          ("htslib-src"
@@ -354,7 +355,7 @@ and freshness without requiring additional information from the user.")
              (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"))
+             (file-name "htslib-0.2.0-rc10.tar.gz")
              (sha256
               (base32 "1k6dlf6m8yayhcp7b4yisgw1xqdy1xg2xyrllss6ld0wg00hfcbs"))))
          ("biod-src"
@@ -363,15 +364,16 @@ and freshness without requiring additional information from the user.")
              (uri (git-reference
                    (url "https://github.com/biod/BioD.git")
                    (commit "7efdb8a2f7fdcd71c9ad9596be48d1262bb1bd5b")))
+             (file-name "biod-src")
              (sha256
-              (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf"))
-             (file-name "biod-src")))))
+              (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf"))))))
       (arguments
        `(#:tests? #f
-         #:make-flags (list "CC=gcc" "D_COMPILER=ldc2")
+         ;;#:make-flags 
          #:phases
          (modify-phases %standard-phases
            (delete 'configure)
+           (delete 'check)
            (add-after 'unpack 'unpack-htslib-sources
              (lambda* (#:key inputs #:allow-other-keys)
                ;; Unfortunately, the current build compiles htslib statically
@@ -384,14 +386,16 @@ and freshness without requiring additional information from the user.")
                     (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")))))
+                    (and (zero? (system* "rm" "-r" "BioD"))
+                         (zero? (system* "ln" "--symbolic" "--no-target-directory"
+                                         (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")))))))
+            (lambda* (#:key inputs make-flags #:allow-other-keys)
+              (zero? (system* "make" "-f" "Makefile.guix" "CC=gcc" "D_COMPILER=ldc2")))))))
       (home-page "https://github.com/lomereiter/sambamba")
       (synopsis "A tool for working with SAM and BAM files written in D.")
       (description