Deprecate wfmash 0.14 in favour of latest.

1 files changed, 1 insertions, 48 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 5b9deff..38c3473 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -2917,53 +2917,6 @@ multiple sequence alignment.")
            zlib
            (list zstd "lib")))))
 
-(define-public wfmash-0.14
-  (package
-    (inherit wfmash)
-    (version "0.14.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "https://github.com/waveygang/wfmash/releases/download/v"
-                           version "/wfmash-v" version ".tar.gz"))
-       (sha256
-        (base32
-         "1mk3jschn3hdr45glds65g3hxk7v6nc3plkvxmfbd5pr4kyzlf13"))
-       (snippet
-        #~(begin
-            (use-modules (guix build utils))
-            ;; Unbundle atomic-queue.
-            (delete-file-recursively "src/common/atomic_queue")
-            (substitute* "src/align/include/computeAlignments.hpp"
-              (("\"common/atomic_queue/atomic_queue.h\"")
-               "<atomic_queue/atomic_queue.h>"))
-            ;; Remove compiler optimizations.
-            (substitute* (find-files "." "CMakeLists\\.txt")
-              (("-march=native ") ""))))))
-    (arguments
-     (substitute-keyword-arguments (package-arguments wfmash)
-       ((#:tests? tests? #f) #f)
-       ((#:phases phases #~%standard-phases)
-        #~(modify-phases #$phases
-            (replace 'build-check-prerequisites
-              (lambda _
-                (let ((wfa2-lib #$(string-append "../wfmash-v"
-                                                 version
-                                                 "/src/common/wflign/deps/WFA2-lib")))
-                  (substitute* (string-append wfa2-lib "/Makefile")
-                    ;; Remove architecture-specific flags.
-                    (("-march=x86-64-v3") ""))
-                  (substitute* (string-append wfa2-lib "/tests/wfa.utest.sh")
-                    ;; Fix time command.
-                    (("\\\\time -v") "time"))
-                  ;; Build wfa2-lib.
-                  (invoke "make" "-C" wfa2-lib
-                          #$(string-append "CC=" (cc-for-target))))))))))
-    (inputs
-     (modify-inputs (package-inputs wfmash)
-       (prepend jemalloc)
-       (delete "libdeflate")))))
-
 (define-public pggb
   (package
     (name "pggb")
@@ -3066,7 +3019,7 @@ multiple sequence alignment.")
            time
            vcfbub
            vg-gn
-           wfmash-0.14))
+           wfmash))
     (home-page "https://doi.org/10.1101/2023.04.05.535718")
     (synopsis "PanGenome Graph Builder")
     (description "@command{pggb} builds