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gnu: mudskipper: Update to 0.1.0-1.effd3fa.

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* gnu/packages/bioinformatics.scm (mudskipper): Update to 0.1.0-1.effd3fa.
[native-inputs]: Remove cmake-minimal.
[inputs]: Use ‘cargo-inputs’.
[arguments]<#:cargo-inputs>: Remove.
<#:install-source?>: Disable.
<#:tests?>: Enable with...
<#:phases>: ...new 'skip-doctesting-code-blocks phase.
* gnu/packages/rust-crates.scm (lookup-cargo-inputs)[mudskipper]: New entry.

Change-Id: I2e02005f5ccc35b01e396662063f02273a9f16e0
This commit is contained in:
Hilton Chain 2025-04-11 10:12:58 +08:00
parent 64955a0c53
commit 6f584ffe3a
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GPG key ID: ACC66D09CA528292
2 changed files with 396 additions and 35 deletions
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gnu/packages/bioinformatics.scm
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@ -24489,41 +24489,52 @@ assembly (small or mammalian size) and single-cell assembly.")
(license license:gpl3)))
(define-public mudskipper
(package
(name "mudskipper")
(version "0.1.0")
(source (origin
(method url-fetch)
(uri (crate-uri "mudskipper" version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1y7fnlz6irmxdmv6bxzm95w4ws4vzldlrh8npvgxmdnrz9pgb1dv"))))
(build-system cargo-build-system)
(arguments
`(#:tests? #false ;fail because the "mudskipper" crate cannot be found
#:cargo-inputs
(("rust-bio" ,rust-bio-0.39)
("rust-bio-types" ,rust-bio-types-0.12)
("rust-clap" ,rust-clap-2)
("rust-coitrees" ,rust-coitrees-0.2)
("rust-env-logger" ,rust-env-logger-0.9)
("rust-fnv" ,rust-fnv-1)
("rust-indicatif" ,rust-indicatif-0.16)
("rust-libradicl" ,rust-libradicl-0.4)
("rust-linecount" ,rust-linecount-0.1)
("rust-log" ,rust-log-0.4)
("rust-num-cpus" ,rust-num-cpus-1)
("rust-rust-htslib" ,rust-rust-htslib-0.38))))
(native-inputs
(list cmake-minimal pkg-config))
(inputs
(list zlib xz))
(home-page "https://github.com/OceanGenomics/mudskipper")
(synopsis "Convert genomic alignments to transcriptomic BAM/RAD files")
(description "Mudskipper is a tool for projecting genomic alignments to
(let ((commit "effd3fac03bc09d313e84fa680f18fdc6f3a16a0")
(revision "1"))
(package
(name "mudskipper")
(version (git-version "0.1.0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/OceanGenomics/mudskipper")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"17jm39sbrwgjlynxsn4g7lvq5hx6rwyjg86p10v4mc74fmdn5xd5"))))
(build-system cargo-build-system)
(arguments
(list #:install-source? #f
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'skip-doctesting-code-blocks
;; See also https://github.com/rust-lang/rust/issues/63193.
(lambda _
(substitute* "src/query_bam_records.rs"
(((string-append
"(pub )?fn ("
(string-join
'("get_next_query_records"
"get_next_query_records_skip"
"get_primary_record_of_sa_tag"
"get_records_from_sa_tag"
"group_records"
"group_records_skip"
"new")
"|")
")")
all)
(string-append "#[cfg(not(doctest))]\n" all))))))))
(native-inputs
(list pkg-config))
(inputs
(cons* zlib xz (cargo-inputs 'mudskipper)))
(home-page "https://github.com/OceanGenomics/mudskipper")
(synopsis "Convert genomic alignments to transcriptomic BAM/RAD files")
(description "Mudskipper is a tool for projecting genomic alignments to
transcriptomic coordinates.")
(license license:bsd-3)))
(license license:bsd-3))))
(define-public r-ascat
(package