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-rw-r--r--gnu/packages/bioinformatics.scm187
1 files changed, 54 insertions, 133 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e68c801866..1b381f1bb8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -87,9 +87,6 @@
#:use-module (gnu packages cpp)
#:use-module (gnu packages cpio)
#:use-module (gnu packages cran)
- #:use-module (gnu packages crates-compression)
- #:use-module (gnu packages crates-io)
- #:use-module (gnu packages crates-web)
#:use-module (gnu packages curl)
#:use-module (gnu packages docbook)
#:use-module (gnu packages documentation)
@@ -2280,33 +2277,6 @@ Format (GFF) with Biopython integration.")
;; These test require a 84 GB file.
"--skip=http_two"
"--skip=http_cloud_urls_md_3")
- #:cargo-inputs
- (list rust-anyinput-0.1
- rust-bytecount-0.6
- rust-byteorder-1
- rust-bytes-1
- rust-cloud-file-0.2
- rust-derive-builder-0.20
- rust-dpc-pariter-0.4
- rust-fetch-data-0.2
- rust-futures-util-0.3
- rust-itertools-0.13
- rust-ndarray-0.16
- rust-ndarray-npy-0.9
- rust-num-traits-0.2
- rust-numpy-0.22
- rust-pyo3-0.22
- rust-pyo3-build-config-0.22
- rust-rayon-1
- rust-statrs-0.17
- rust-thiserror-1
- rust-tokio-1)
- #:cargo-development-inputs
- (list rust-anyhow-1
- rust-ndarray-rand-0.15
- rust-rusoto-credential-0.48
- rust-temp-testdir-0.2
- rust-thousands-0.2)
#:imported-modules
(append %cargo-build-system-modules
%pyproject-build-system-modules)
@@ -2418,7 +2388,7 @@ version = ~s
python-pytest-doctestplus
python-recommonmark
python-sphinx))
- (inputs (list python-wrapper))
+ (inputs (cons python-wrapper (cargo-inputs 'python-bed-reader)))
(propagated-inputs (list python-numpy python-pandas python-scipy))
(home-page "https://fastlmm.github.io/")
(synopsis "Read and write the PLINK BED format, simply and efficiently")
@@ -4697,19 +4667,9 @@ compressed files.")
"find_package(bioparser 3.0.13 CONFIG)")
(("find_package\\(biosoup 0.10.0 QUIET\\)")
"find_package(biosoup 0.10.0 CONFIG)")
- (("GTest_FOUND") "TRUE")))))
- #:cargo-inputs
- (("rust-anyhow" ,rust-anyhow-1)
- ("rust-bio" ,rust-bio-0.33)
- ("rust-chrono" ,rust-chrono-0.4)
- ("rust-docopt" ,rust-docopt-1)
- ("rust-flate2" ,rust-flate2-1)
- ("rust-indicatif" ,rust-indicatif-0.15)
- ("rust-libc" ,rust-libc-0.2)
- ("rust-serde" ,rust-serde-1)
- ("rust-seq-io" ,rust-seq-io-0.3))))
+ (("GTest_FOUND") "TRUE")))))))
(inputs
- (list bioparser biosoup))
+ (cons* bioparser biosoup (cargo-inputs 'circtools)))
(native-inputs
(list cmake-minimal pkg-config googletest))
(home-page "https://github.com/Kevinzjy/circtools")
@@ -6211,29 +6171,6 @@ setup"))))
gene predictor designed to work with assembled, aligned RNA-seq transcripts.")
(license license:gpl3+)))
-(define-public clustal-omega
- (package
- (name "clustal-omega")
- (version "1.2.4")
- (source (origin
- (method url-fetch)
- (uri (string-append "http://www.clustal.org/omega/clustal-omega-"
- version ".tar.gz"))
- (sha256
- (base32
- "1vm30mzncwdv881vrcwg11vzvrsmwy4wg80j5i0lcfk6dlld50w6"))))
- (build-system gnu-build-system)
- (inputs
- (list argtable))
- (home-page "http://www.clustal.org/omega/")
- (synopsis "Multiple sequence aligner for protein and DNA/RNA")
- (description
- "Clustal-Omega is a general purpose multiple sequence alignment (MSA)
-program for protein and DNA/RNA. It produces high quality MSAs and is capable
-of handling data-sets of hundreds of thousands of sequences in reasonable
-time.")
- (license license:gpl2+)))
-
(define-public crossmap
(package
(name "crossmap")
@@ -7156,18 +7093,17 @@ accurately delineate genomic rearrangements throughout the genome.")
(define-public transanno
(package
(name "transanno")
- (version "0.3.0")
+ (version "0.4.5")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/informationsea/transanno")
- ;; Corresponds to tag v0.3.0
- (commit "df49050c92644ea12d9d5c6fae2186ca436dbca3")))
+ (commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
- "1jpn7s3cnd9ybk4lmfbhj2arhf6cmrv7jp74n7n87m3a3irkaif1"))
+ "0x62v8qhnpw8579kcqpr9k5ldv2y3awjp7a32f1j8qky0i1jgxp1"))
(snippet
'(with-output-to-file "liftover-rs/build.rs"
(lambda _
@@ -7190,28 +7126,9 @@ accurately delineate genomic rearrangements throughout the genome.")
"/bin/bash")))
(invoke "bash" "prepare-test-files.sh")))
(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))))
+ (lambda _ (chdir "transanno"))))))
(native-inputs (list bash pkg-config))
- (inputs (list xz))
+ (inputs (cons* xz `(,zstd "lib") (cargo-inputs 'transanno)))
(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
@@ -24542,41 +24459,52 @@ 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
@@ -25401,13 +25329,6 @@ CSIv1, CSIv2 and FAI files.")
#:install-source? #false
#:features '(list "extension-module")
#:cargo-test-flags '(list "--features=extension-module")
- #:cargo-inputs
- `(("rust-csv" ,rust-csv-1)
- ("rust-itertools" ,rust-itertools-0.10)
- ("rust-pyo3" ,rust-pyo3-0.16)
- ("rust-rand" ,rust-rand-0.8)
- ("rust-rayon" ,rust-rayon-1)
- ("rust-serde" ,rust-serde-1))
#:imported-modules
(append %cargo-build-system-modules
%pyproject-build-system-modules)
@@ -25473,7 +25394,7 @@ exclude =
;; These tests need access to the internet
"-k" "not test_enrichr and not test_prerank")))))))
(inputs
- (list python-wrapper))
+ (cons python-wrapper (cargo-inputs 'python-gseapy)))
(native-inputs
(list python-pytest python-wheel))
(propagated-inputs
generated by cgit v1.2.3 (git 2.50.1) at 2025-08-24 12:23:24 +0000