diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 57 |
1 files changed, 57 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index a59c758..7f932cf 100644 --- a/gn/packages/bioinformatics.scm +++ b/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))) |