sharlatan pushed a commit to branch go-team
in repository guix.
commit acbff09fe5c4e61c0eab61da05dcfbbac86b92d7
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Wed Jan 22 20:45:58 2025 +0000
gnu: Add go-github-com-biogo-hts.
This change merges all extracted subdirs under the same variable as it's
distributed in single module according to project's go.mod.
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-bam,
go-github-com-biogo-hts-bgzf, go-github-com-biogo-hts-cram,
go-github-com-biogo-hts-csi, go-github-com-biogo-hts-fai,
go-github-com-biogo-hts-sam, go-github-com-biogo-hts-tabix): Delete
variables.
(go-github-com-biogo-hts): New variable.
[arguments] <skip-build?>: No go files in project's root.
<import-path>: Set as seen in go.mod.
<test-flags>: Skip 2 tests requiring network access.
(go-github-com-biogo-biogo) [propagated-inputs]: Remove
go-github-com-biogo-hts-bam, add go-github-com-biogo-hts.
Change-Id: I2cace7a0c732e7590b3b34865323bc38b41b0d86
---
gnu/packages/bioinformatics.scm | 101 +++++++---------------------------------
1 file 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")
