02/02: gnu: transanno: Fix build.

[guix-commits]

efraim pushed a commit to branch rust-team
in repository guix.

commit 146360c736a3f7fe814de875cc95b2262e5440ab
Author: Efraim Flashner <efraim@flashner.co.il>
AuthorDate: Fri Oct 13 13:50:19 2023 +0300

    gnu: transanno: Fix build.
    
    * gnu/packages/bioinformatics.scm (transanno)[arguments]: Run the test
    suite.  Don't patch Cargo.toml in liftover-rs. Don't patch crate in
    vendor-dir.
    [native-inputs]: Add pkg-config.
    [inputs]: Add xz.
---
 gnu/packages/bioinformatics.scm | 14 +++-----------
 1 file changed, 3 insertions(+), 11 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d09eb362b2..79b81cc3f8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4696,26 +4696,17 @@ accurately delineate genomic rearrangements throughout 
the genome.")
     (arguments
      (list
       #:install-source? #false          ;fails
-      #:tests? #false                   ;"cargo test" ignores build.rs
+      #:tests? #true
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'prepare-test-files
             (lambda _
               (delete-file "Cargo.lock")
-              (substitute* "liftover-rs/Cargo.toml"
-                (("anyhow = \"1\"") "anyhow = \"1.0.65\""))
               (substitute* "liftover-rs/prepare-test.sh"
                 (("/bin/bash")
                  (string-append #$(this-package-native-input "bash")
                                 "/bin/bash")))
               (invoke "bash" "prepare-test-files.sh")))
-          (add-before 'patch-cargo-checksums 'do-not-build-xz
-            (lambda _
-              ;; Detection of liblzma (in rust-lzma-sys, pulled in by
-              ;; rust-hts-sys) doesn't seem to work, or perhaps it really does
-              ;; request a static build somewhere.
-              (substitute* "guix-vendor/rust-lzma-sys-0.1.17.tar.xz/build.rs"
-                (("if .want_static && .msvc && 
pkg_config::probe_library\\(\"liblzma\"\\).is_ok\\(\\)") ""))))
           (add-before 'install 'chdir
             (lambda _ (chdir "transanno"))))
       #:cargo-inputs
@@ -4737,7 +4728,8 @@ accurately delineate genomic rearrangements throughout 
the genome.")
       #:cargo-development-inputs
       `(("rust-clap" ,rust-clap-2)
         ("rust-lazy-static" ,rust-lazy-static-1))))
-    (native-inputs (list bash))
+    (native-inputs (list bash pkg-config))
+    (inputs (list xz))
     (home-page "https://github.com/informationsea/transanno";)
     (synopsis "LiftOver tool for new genome assemblies")
     (description "This package provides an accurate VCF/GFF3/GTF LiftOver tool