diff options
| author | Efraim Flashner <efraim@flashner.co.il> | 2023-10-13 13:50:19 +0300 |
|---|---|---|
| committer | Efraim Flashner <efraim@flashner.co.il> | 2023-10-18 11:36:31 +0300 |
| commit | 4fcf0425328d45f0204dc92ef58fdcc63caa6382 (patch) | |
| tree | df83c1b9d23b0e68b6431ea575b528222de05c1e /gnu | |
| parent | 0a2f10ac11a427ed5fe80e3e59b6ce53a1c81317 (diff) | |
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.
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 14 |
1 files changed, 3 insertions, 11 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 44eeb53e95..804693427d 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 |