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gnu: transanno: Fix build.

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* 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.
This commit is contained in:
Efraim Flashner 2023-10-13 13:50:19 +03:00
parent 0a2f10ac11
commit 4fcf042532
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1 changed files with 3 additions and 11 deletions
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gnu/packages/bioinformatics.scm
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@ -4696,26 +4696,17 @@ (define-public transanno
(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 @@ (define-public transanno
#: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