bioinformatics: iqtree3: Use packaged cmaple and lsd2.

* guix-science/packages/bioinformatics.scm (iqtree3)
  [source]: Disable recursive git fetch.
  [arguments]<#:phases>: Copy cmaple and lsd2 sources where expected.
  [native-inputs]: Add (package-source cmaple) and (package-source lsd2).

1 files changed, 13 insertions, 15 deletions

diff --git a/guix-science/packages/bioinformatics.scm b/guix-science/packages/bioinformatics.scm
index 53f06ed..c3f7654 100644
--- a/guix-science/packages/bioinformatics.scm
+++ b/guix-science/packages/bioinformatics.scm
@@ -2582,14 +2582,13 @@ This package provides IQ-TREE version 2.")
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/iqtree/iqtree3")
-             (commit (string-append "v" version))
-             (recursive? #t)))
+             (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1i0pz0iwv3rgh6syc48icsfchl1h0pmc9fha5yj8l2hjnsxvz779"))
+        (base32 "14vqa36gxip2hh46wnhsq84abf2hq89d2xvs6rasn6m4zanmy5h9"))
        (modules '((guix build utils)))
        ;; FIXME: Look for further opportunities to get rid of vendored
-       ;; dependencies, such as cmaple, lsd2 or ncl.
+       ;; dependencies, such as ncl.
        (snippet #~(for-each delete-file-recursively
                             (list "yaml-cpp" "zlib-1.2.7")))))
     (build-system cmake-build-system)
@@ -2606,27 +2605,26 @@ This package provides IQ-TREE version 2.")
                  ""))))
           (add-after 'unpack 'use-system-libraries
             (lambda _
+              ;; cmaple
+              (copy-recursively #$(package-source cmaple) "cmaple")
+              ;; lsd2
+              (copy-recursively #$(package-source lsd2) "lsd2")
               ;; yaml-cpp
               (substitute* "CMakeLists.txt"
                 (("add_subdirectory\\(yaml-cpp\\)")
                  "find_package(yaml-cpp REQUIRED CONFIG)
-include_directories(${yaml-cpp_INCLUDE_DIRS})"))
-              ;; googletest
-              (substitute* "cmaple/CMakeLists.txt"
-                (("URL .*googletest.*")
-                 "GIT_REPOSITORY https://github.com/google/googletest.git
-FIND_PACKAGE_ARGS NAMES GTest"))))
+include_directories(${yaml-cpp_INCLUDE_DIRS})"))))
           (delete 'check)
           (add-after 'install 'check
             (lambda* (#:key tests? #:allow-other-keys)
               (when tests?
                 (let ((iqtree3 (string-append #$output "/bin/iqtree3")))
-                  (invoke iqtree3 "-s"
-                          (string-append #$source "/example/example.phy")
-                          "--prefix"
-                          (string-append (getcwd) "/example")))))))))
+                  (with-directory-excursion "../source/example"
+                    (invoke iqtree3 "-s" "example.phy")))))))))
     (inputs (list boost eigen yaml-cpp zlib))
-    (native-inputs (list googletest))
+    (native-inputs (list googletest
+                         (package-source cmaple)
+                         (package-source lsd2)))
     (home-page "https://iqtree.github.io/")
     (synopsis "Efficient and versatile phylogenomic inference (version 3)")
     (description