diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 101 |
1 files changed, 16 insertions, 85 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c98f6022bf..170651d991 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -24401,9 +24401,9 @@ useful for bioinformatic analysis.") go-github-com-kr-pretty)) (synopsis "Step store for biogo"))) -(define-public go-github-com-biogo-hts-bam +(define-public go-github-com-biogo-hts (package - (name "go-github-com-biogo-hts-bam") + (name "go-github-com-biogo-hts") (version "1.4.4") (source (origin (method git-fetch) @@ -24416,91 +24416,22 @@ useful for bioinformatic analysis.") "1vkcqxyajghx5p5j7g2i376nbsxh8q2smk0smlv8mi34yr7hlw5b")))) (build-system go-build-system) (arguments - '(#:import-path "github.com/biogo/hts/bam" - #:unpack-path "github.com/biogo/hts")) - (propagated-inputs - (list go-gopkg-in-check-v1)) - (home-page "https://github.com/biogo/hts") - (synopsis "HTS BAM module for biogo") - (description "This package provides tools for handling BAM files.") - (license license:bsd-3))) - -(define-public go-github-com-biogo-hts-sam - (package - (inherit go-github-com-biogo-hts-bam) - (name "go-github-com-biogo-hts-sam") - (arguments - '(#:import-path "github.com/biogo/hts/sam" - #:unpack-path "github.com/biogo/hts")) - (propagated-inputs - (list go-gopkg-in-check-v1)) - (synopsis "HTS SAM module for biogo") - (description "This package provides tools for handling SAM files."))) - -(define-public go-github-com-biogo-hts-tabix - (package - (inherit go-github-com-biogo-hts-bam) - (name "go-github-com-biogo-hts-tabix") - (arguments - '(#:import-path "github.com/biogo/hts/tabix" - #:unpack-path "github.com/biogo/hts")) - (propagated-inputs - (list go-gopkg-in-check-v1)) - (synopsis "HTS Tabix module for biogo") - (description "This package provides tools for handling Tabix files."))) - -(define-public go-github-com-biogo-hts-bgzf - (package - (inherit go-github-com-biogo-hts-bam) - (name "go-github-com-biogo-hts-bgzf") - (arguments - '(#:import-path "github.com/biogo/hts/bgzf" - #:unpack-path "github.com/biogo/hts")) - (propagated-inputs + (list + #:skip-build? #t + #:import-path "github.com/biogo/hts" + ;; Tests try to get samples from <https://github.com/samtools/htslib>. + #:test-flags #~(list "-skip" "TestHasEOF|TestRead"))) + (native-inputs (list go-gopkg-in-check-v1)) - (synopsis "HTS bgzf module for biogo") - (description "This package provides tools for handling bgzf files."))) - -(define-public go-github-com-biogo-hts-cram - (package - (inherit go-github-com-biogo-hts-bam) - (name "go-github-com-biogo-hts-cram") - (arguments - '(#:import-path "github.com/biogo/hts/cram" - #:unpack-path "github.com/biogo/hts" - #:tests? #false)) ;require network access (propagated-inputs - (list go-gopkg-in-check-v1 - go-github-com-ulikunitz-xz + (list go-github-com-ulikunitz-xz go-github-com-kortschak-utter)) - (synopsis "HTS CRAM module for biogo") - (description "This package provides tools for handling CRAM files."))) - -(define-public go-github-com-biogo-hts-csi - (package - (inherit go-github-com-biogo-hts-bam) - (name "go-github-com-biogo-hts-csi") - (arguments - '(#:import-path "github.com/biogo/hts/csi" - #:unpack-path "github.com/biogo/hts")) - (propagated-inputs - (list go-gopkg-in-check-v1)) - (synopsis "Coordinate sorted indexing for biogo") - (description "This package implements CSIv1 and CSIv2 coordinate sorted -indexing."))) - -(define-public go-github-com-biogo-hts-fai - (package - (inherit go-github-com-biogo-hts-bam) - (name "go-github-com-biogo-hts-fai") - (arguments - '(#:import-path "github.com/biogo/hts/fai" - #:unpack-path "github.com/biogo/hts")) - (propagated-inputs - (list go-gopkg-in-check-v1)) - (synopsis "Fasta sequence file index handling for biogo") - (description "This package implements FAI fasta sequence file index -handling."))) + (home-page "https://github.com/biogo/hts") + (synopsis "HTS module for biogo") + (description + "This package provides tools for handling BAM, SAM, Tabix, bgzf, CRAM, +CSIv1, CSIv2 and FAI files.") + (license license:bsd-3))) (define-public go-github-com-biogo-biogo (package @@ -24524,7 +24455,7 @@ handling."))) go-github-com-biogo-store-kdtree go-github-com-biogo-store-llrb go-github-com-biogo-store-step - go-github-com-biogo-hts-bam + go-github-com-biogo-hts go-github-com-biogo-graph)) (home-page "https://github.com/biogo/biogo") (synopsis "Bioinformatics library for Go") |