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gn: add bam2fastx

stable-20210528
Efraim Flashner 1 year ago
parent
commit
787df9a889
Signed by: efraim GPG Key ID: 41AAE7DCCA3D8351
  1. 57
      gn/packages/bioinformatics.scm

57
gn/packages/bioinformatics.scm

@ -10,6 +10,7 @@
#:use-module (guix build-system ant)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
#:use-module (guix build-system meson)
#:use-module (guix build-system python)
#:use-module (guix build-system trivial)
#:use-module (guix build-system waf)
@ -1767,3 +1768,59 @@ to the user.")
(license:non-copyleft ; Blat, In-Silico PCR
"http://www.kentinformatics.com/index.html"
"Free for universities and non-profit institutions.")))))
(define-public bam2fastx
(package
(name "bam2fastx")
(version "1.3.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/PacificBiosciences/bam2fastx")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0pyfmvh874w29kaq6gbb1bd86135qs2jc4f8giw98kxw1b2gjdh0"))))
(build-system meson-build-system)
(arguments
`(#:configure-flags '("-Dtests=true")))
(inputs
`(("boost" ,boost)
;("htslib" ,htslib)
("pbbam" ,pbbam)
("pbcopper" ,pbcopper)
("zlib" ,zlib)))
(native-inputs
`(("pkg-config" ,pkg-config)
("python-cram" ,python-cram)
("python-wrapper" ,python-wrapper)))
(home-page "https://github.com/PacificBiosciences/bam2fastx")
(synopsis "Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files")
(description "Conversion of PacBio BAM files into gzipped fasta and fastq files, including splitting of barcoded data.")
(license license:bsd-3)))
(define-public pbcopper
(package
(name "pbcopper")
(version "1.9.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/PacificBiosciences/pbcopper")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1pphklil5kn1ds796ch41bgvdf7yq03z6w5rgi572s8xg8k5b0xn"))))
(build-system meson-build-system)
(inputs
`(("boost" ,boost)))
(native-inputs
`(("googletest" ,googletest)))
(home-page "https://github.com/PacificBiosciences/pbcopper")
(synopsis "Core C++ library for data structures, algorithms, and utilities")
(description "The pbcopper library provides a suite of data structures, algorithms, and utilities for PacBio C++ applications.")
(license license:bsd-3)))

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