guix.scm

;; 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