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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 74 |
1 files changed, 74 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 35df225cde..fda01e00ca 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3971,6 +3971,80 @@ sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome.") (license license:gpl3+))) +(define-public transanno + (package + (name "transanno") + (version "0.3.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/informationsea/transanno") + ;; Corresponds to tag v0.3.0 + (commit "df49050c92644ea12d9d5c6fae2186ca436dbca3"))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1jpn7s3cnd9ybk4lmfbhj2arhf6cmrv7jp74n7n87m3a3irkaif1")) + (snippet + '(with-output-to-file "liftover-rs/build.rs" + (lambda _ + (format #true + "fn main() {~@ + println!(\"cargo:rustc-link-lib=lzma\");~@ + }~%")))))) + (build-system cargo-build-system) + (arguments + (list + #:install-source? #false ;fails + #:tests? #false ;"cargo test" ignores build.rs + #: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 + `(("rust-anyhow" ,rust-anyhow-1) + ("rust-autocompress" ,rust-autocompress-0.2) + ("rust-bio" ,rust-bio-0.41) + ("rust-clap" ,rust-clap-2) + ("rust-csv" ,rust-csv-1) + ("rust-flate2" ,rust-flate2-1) + ("rust-indexmap" ,rust-indexmap-1) + ("rust-log" ,rust-log-0.4) + ("rust-nom" ,rust-nom-5) + ("rust-once-cell" ,rust-once-cell-1) + ("rust-pretty-env-logger" ,rust-pretty-env-logger-0.3) + ("rust-regex" ,rust-regex-1) + ("rust-thiserror" ,rust-thiserror-1) + ("rust-serde" ,rust-serde-1) + ("rust-serde-json" ,rust-serde-json-1)) + #:cargo-development-inputs + `(("rust-clap" ,rust-clap-2) + ("rust-lazy-static" ,rust-lazy-static-1)))) + (native-inputs (list bash)) + (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 +for new genome assemblies.") + (license license:gpl3+))) + (define-public trf (package (name "trf") |