(define-module (gnu packages bioinformatics)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix utils)
  #:use-module (guix download)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system trivial)
  #:use-module (gnu packages)
  #:use-module (gnu packages base)
  #:use-module (gnu packages boost)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages mpi)
  #:use-module (gnu packages perl)
  #:use-module (srfi srfi-1))

(define-public bless
  (package
    (name "bless")
    (version "v1p02")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/bless-ec/bless."
                                  version ".tgz"))
              (file-name (string-append name "." version ".tgz"))
              (sha256
               (base32
		"0rm0gw2s18dqwzzpl3c2x1z05ni2v0xz5dmfk3d33j6g4cgrlrdd"))
	      ))
    (build-system gnu-build-system)
    (native-inputs `(("perl" ,perl)
                     ("zlib" ,zlib)))
    (inputs `(("openmpi" ,openmpi)
	      ("pigz" ,pigz)))
    (arguments
     '(#:tests? #f ;no "check" target
       #:phases
       (alist-cons-after 'unpack 'unpack-tarballs
	  (lambda* (#:key inputs outputs #:allow-other-keys)
             (substitute* "Makefile"
	       (("-I ./zlib/install/include")
	         (string-append "-I " (assoc-ref inputs "zlib") "/include"))
               (("./zlib/install/lib/libz.a")
		(string-append (assoc-ref inputs "zlib") "/lib/libz.a"))
	       ((".(ZLIB) ") "")
	       (("cd pigz/pigz-2.3.3; make") "")
	       )
	     ;;(substitute* "define.hpp"
             ;;  (("pigz/pigz-2.3.3") (string-append (assoc-ref inputs "pigz")))
             ;;  (("kmc/bin") ".")
	     (substitute* "parse_args.cpp"
	       (("kmc_binary = .*")
		 (string-append "kmc_binary = \"" (assoc-ref outputs "out") "/bin/kmc\";"))
	       (("pigz_binary = .*")
		(string-append "pigz_binary = \"" (assoc-ref inputs "pigz") "/bin/pigz\";"))
	     )
 	     #t)
        (alist-replace
         'install
         (lambda* (#:key outputs #:allow-other-keys)
           (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
             (for-each (lambda (file)
                         (install-file file bin))
		       '("bless" "kmc/bin/kmc")
                       )))
	  
       (alist-delete 'configure %standard-phases)))))
    (home-page "http://sourceforge.net/projects/bless-ec/wiki/Home/")
    (synopsis "Bloom-filter-based Error Correction Tool for NGS reads")
    (description
     "Developed by ESCAD Group, Computational Comparative Genomics
Lab, and IMACT Group in university of Illinois at Urbana-Champaign")
    (license license:gpl3+))
  )