gn: Add wfmash-static.

* gn/packages/static.scm: Import (gnu packages bioinformatics), (gnu
packages compression), (gnu packages cpp), (gnu packages
jemalloc), (gnu packages maths), (guix gexp) and (guix utils).
(htslib-minimal, wfmash-static): New variables.

1 files changed, 53 insertions, 1 deletions

diff --git a/gn/packages/static.scm b/gn/packages/static.scm
index 7ce1a9c..3b0d913 100644
--- a/gn/packages/static.scm
+++ b/gn/packages/static.scm
@@ -11,11 +11,63 @@
 
 (define-module (gn packages static)
   #:use-module (gnu packages base)
+  #:use-module (gnu packages bioinformatics)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages cpp)
+  #:use-module (gnu packages jemalloc)
+  #:use-module (gnu packages maths)
   #:use-module (guix build-system gnu)
-  #:use-module (guix packages))
+  #:use-module (guix gexp)
+  #:use-module (guix packages)
+  #:use-module (guix utils))
 
 ;; Static hello, for testing
 (define-public hello-static
   (package
     (inherit (static-package hello))
     (name "hello-static")))
+
+;; A minimal version of htslib that does not depend on curl and openssl. This
+;; reduces the number of higher order dependencies in static linking.
+(define htslib-minimal
+  (package
+    (inherit htslib)
+    (arguments
+     (substitute-keyword-arguments (package-arguments htslib)
+       ((#:configure-flags flags ''())
+        ''())))
+    (inputs
+     (list bzip2 xz))))
+
+(define-public wfmash-static
+  (package
+    (inherit wfmash)
+    (arguments
+     (substitute-keyword-arguments (package-arguments wfmash)
+       ((#:configure-flags flags ''())
+        `(cons* "-DCMAKE_EXE_LINKER_FLAGS=-static"
+                "-DCMAKE_SKIP_RPATH=TRUE"
+                ,flags))
+       ((#:phases phases ''())
+        #~(modify-phases #$phases
+            ;; When static linking, we need to link against the entire
+            ;; dependency tree, not just the direct first-order dependencies.
+            (add-after 'unpack 'add-higher-order-dependencies
+              (lambda _
+                (substitute* "CMakeLists.txt"
+                  (("hts" all)
+                   (string-append all " bz2 dl lzma"))
+                  (("jemalloc" all)
+                   ;; We add atomic because riscv64 has no lock-free atomic
+                   ;; instructions.
+                   (string-append all " atomic pthread")))))))))
+    (inputs
+     (list atomic-queue
+           gsl-static
+           htslib-minimal
+           jemalloc
+           (list zlib "static")
+
+           ;; Second-order dependencies from htslib
+           (list bzip2 "static")
+           (list xz "static")))))