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|
;; To get a development container (inside emacs shell will work)
;;
;; guix shell -C -D -f guix.scm -- bash --init-file <(echo "ln -s /bin/sh /bin/bash")
;;
;; For the tests you may need /usr/bin/env. In a container create it with
;;
;; mkdir -p /usr/bin ; ln -s $GUIX_ENVIRONMENT/bin/env /usr/bin/env
;;
(use-modules
(srfi srfi-1)
(ice-9 popen)
(ice-9 rdelim)
((guix licenses) #:prefix license:)
(guix packages)
(guix utils)
(guix download)
(guix git-download)
(guix build-system gnu)
(guix gexp)
(gnu packages base)
(gnu packages bioinformatics) ; for samtools in sambamba
(gnu packages build-tools) ; for meson
(gnu packages compression)
(gnu packages curl)
(gnu packages dlang)
(gnu packages gcc)
(gnu packages pkg-config)
(gnu packages perl)
(gnu packages python)
(gnu packages ninja)
(gnu packages ruby)
(gnu packages tls)
(gnu packages version-control)
)
#!
(use-modules
(guix build-system cmake)
(guix utils)
(gnu packages base)
(gnu packages compression)
(gnu packages build-tools)
(gnu packages commencement) ; gcc-toolchain
(gnu packages curl)
(gnu packages datastructures)
(gnu packages gdb)
(gnu packages gcc)
(gnu packages jemalloc)
(gnu packages libffi)
(gnu packages mpi)
(gnu packages python)
(gnu packages python-xyz)
(gnu packages pkg-config)
(gnu packages tls)
)
!#
(define %source-dir (dirname (current-filename)))
(define %git-commit
(read-string (open-pipe "git show HEAD | head -1 | cut -d ' ' -f 2" OPEN_READ)))
(define-public sambamba-git
(package
(name "sambamba-git")
(version (git-version "1.0.0" "HEAD" %git-commit))
(source (local-file %source-dir #:recursive? #t))
(build-system gnu-build-system)
(outputs '("out" ; disable all checks for speed
"debug"))
(inputs
`(("samtools" ,samtools) ; for pileup
("bcftools" ,bcftools) ; for pileup
("meson" ,meson) ; for testing meson build system
("ninja" ,ninja)
("pkg-config" ,pkg-config)
("lz4" ,lz4)
("lz4-static" ,lz4 "static")
("zlib-static" ,zlib "static")
("zlib" ,zlib) ; also for the static build we need the includes
; ("zstd-lib" ,zstd "static")
; ("zstd" ,zstd "lib") ; same
))
(native-inputs
`(("ldc" ,ldc)
("coreutils" ,coreutils) ; for env
; ("perl" ,perl) ; Needed for building htslib
; ("ruby" ,ruby) ; Needed for building htslib
("python" ,python) ; Needed for building htslib and sambamba
("gcc" ,gcc)
("which" ,which)))
(home-page "https://github.com/lomereiter/sambamba")
(synopsis "Fast tool for working with SAM and BAM files written in D.")
(description
"Sambamba is a high performance modern robust and fast
tool (and library), written in the D programming language, for working
with SAM and BAM files. Current parallelised functionality is
an important subset of samtools functionality, including view, index,
sort, markdup, and depth.")
(license license:gpl2+)))
sambamba-git
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