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authorEfraim Flashner2021-05-20 09:56:58 +0300
committerEfraim Flashner2021-05-20 09:56:58 +0300
commit787df9a8893a7a87b60a17f123fa6d4ba9f39ea7 (patch)
tree75f52555cc291303fe1597598e436b61df5ec7b5 /gn/packages/bioinformatics.scm
parent7412a5c8bf6de07b108bd39c2cac82b471fdac2f (diff)
downloadguix-bioinformatics-787df9a8893a7a87b60a17f123fa6d4ba9f39ea7.tar.gz
gn: add bam2fastx
Diffstat (limited to 'gn/packages/bioinformatics.scm')
-rw-r--r--gn/packages/bioinformatics.scm57
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)))