;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014, 2015 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Ben Woodcroft <donttrustben@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(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 git-download)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system perl)
  #:use-module (guix build-system python)
  #:use-module (guix build-system trivial)
  #:use-module (gnu packages)
  #:use-module (gnu packages algebra)
  #:use-module (gnu packages base)
  #:use-module (gnu packages boost)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages cpio)
  #:use-module (gnu packages file)
  #:use-module (gnu packages java)
  #:use-module (gnu packages linux)
  #:use-module (gnu packages machine-learning)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages popt)
  #:use-module (gnu packages protobuf)
  #:use-module (gnu packages python)
  #:use-module (gnu packages statistics)
  #:use-module (gnu packages swig)
  #:use-module (gnu packages tbb)
  #:use-module (gnu packages textutils)
  #:use-module (gnu packages vim)
  #:use-module (gnu packages web)
  #:use-module (gnu packages xml)
  #:use-module (gnu packages zip))

(define-public bamtools
  (package
    (name "bamtools")
    (version "2.3.0")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/pezmaster31/bamtools/archive/v"
                    version ".tar.gz"))
              (file-name (string-append name "-" version ".tar.gz"))
              (sha256
               (base32
                "1brry29bw2xr2l9pqn240rkqwayg85b8qq78zk2zs6nlspk4d018"))))
    (build-system cmake-build-system)
    (arguments
     `(#:tests? #f ;no "check" target
       #:phases
       (modify-phases %standard-phases
         (add-before
          'configure 'set-ldflags
          (lambda* (#:key outputs #:allow-other-keys)
            (setenv "LDFLAGS"
                    (string-append
                     "-Wl,-rpath="
                     (assoc-ref outputs "out") "/lib/bamtools")))))))
    (inputs `(("zlib" ,zlib)))
    (home-page "https://github.com/pezmaster31/bamtools")
    (synopsis "C++ API and command-line toolkit for working with BAM data")
    (description
     "BamTools provides both a C++ API and a command-line toolkit for handling
BAM files.")
    (license license:expat)))

(define-public bedops
  (package
    (name "bedops")
    (version "2.4.14")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/bedops/bedops/archive/v"
                                  version ".tar.gz"))
              (file-name (string-append name "-" version ".tar.gz"))
              (sha256
               (base32
                "1kqbac547wyqma81cyky9n7mkgikjpsfd3nnmcm6hpqwanqgh10v"))))
    (build-system gnu-build-system)
    (arguments
     '(#:tests? #f
       #:make-flags (list (string-append "BINDIR=" %output "/bin"))
       #:phases
       (alist-cons-after
         'unpack 'unpack-tarballs
         (lambda _
           ;; FIXME: Bedops includes tarballs of minimally patched upstream
           ;; libraries jansson, zlib, and bzip2.  We cannot just use stock
           ;; libraries because at least one of the libraries (zlib) is
           ;; patched to add a C++ function definition (deflateInit2cpp).
           ;; Until the Bedops developers offer a way to link against system
           ;; libraries we have to build the in-tree copies of these three
           ;; libraries.

           ;; See upstream discussion:
           ;; https://github.com/bedops/bedops/issues/124

           ;; Unpack the tarballs to benefit from shebang patching.
           (with-directory-excursion "third-party"
             (and (zero? (system* "tar" "xvf" "jansson-2.6.tar.bz2"))
                  (zero? (system* "tar" "xvf" "zlib-1.2.7.tar.bz2"))
                  (zero? (system* "tar" "xvf" "bzip2-1.0.6.tar.bz2"))))
           ;; Disable unpacking of tarballs in Makefile.
           (substitute* "system.mk/Makefile.linux"
             (("^\tbzcat .*") "\t@echo \"not unpacking\"\n")
             (("\\./configure") "CONFIG_SHELL=bash ./configure"))
           (substitute* "third-party/zlib-1.2.7/Makefile.in"
             (("^SHELL=.*$") "SHELL=bash\n")))
         (alist-delete 'configure %standard-phases))))
    (home-page "https://github.com/bedops/bedops")
    (synopsis "Tools for high-performance genomic feature operations")
    (description
     "BEDOPS is a suite of tools to address common questions raised in genomic
studies---mostly with regard to overlap and proximity relationships between
data sets.  It aims to be scalable and flexible, facilitating the efficient
and accurate analysis and management of large-scale genomic data.

BEDOPS provides tools that perform highly efficient and scalable Boolean and
other set operations, statistical calculations, archiving, conversion and
other management of genomic data of arbitrary scale.  Tasks can be easily
split by chromosome for distributing whole-genome analyses across a
computational cluster.")
    (license license:gpl2+)))

(define-public bedtools
  (package
    (name "bedtools")
    (version "2.22.0")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/arq5x/bedtools2/archive/v"
                                  version ".tar.gz"))
              (file-name (string-append name "-" version ".tar.gz"))
              (sha256
               (base32
                "16aq0w3dmbd0853j32xk9jin4vb6v6fgakfyvrsmsjizzbn3fpfl"))))
    (build-system gnu-build-system)
    (native-inputs `(("python" ,python-2)))
    (inputs `(("samtools" ,samtools)
              ("zlib" ,zlib)))
    (arguments
     '(#:test-target "test"
       #:phases
       (alist-cons-after
        'unpack 'patch-makefile-SHELL-definition
        (lambda _
          ;; patch-makefile-SHELL cannot be used here as it does not
          ;; yet patch definitions with `:='.  Since changes to
          ;; patch-makefile-SHELL result in a full rebuild, features
          ;; of patch-makefile-SHELL are reimplemented here.
          (substitute* "Makefile"
            (("^SHELL := .*$") (string-append "SHELL := " (which "bash") " -e \n"))))
        (alist-delete
         'configure
         (alist-replace
          'install
          (lambda* (#:key outputs #:allow-other-keys)
            (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
              (mkdir-p bin)
              (for-each (lambda (file)
                          (copy-file file (string-append bin (basename file))))
                        (find-files "bin" ".*"))))
          %standard-phases)))))
    (home-page "https://github.com/arq5x/bedtools2")
    (synopsis "Tools for genome analysis and arithmetic")
    (description
     "Collectively, the bedtools utilities are a swiss-army knife of tools for
a wide-range of genomics analysis tasks.  The most widely-used tools enable
genome arithmetic: that is, set theory on the genome.  For example, bedtools
allows one to intersect, merge, count, complement, and shuffle genomic
intervals from multiple files in widely-used genomic file formats such as BAM,
BED, GFF/GTF, VCF.")
    (license license:gpl2)))

(define-public python2-pybedtools
  (package
    (name "python2-pybedtools")
    (version "0.6.9")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://pypi.python.org/packages/source/p/pybedtools/pybedtools-"
                    version ".tar.gz"))
              (sha256
               (base32
                "1ldzdxw1p4y3g2ignmggsdypvqkcwqwzhdha4rbgpih048z5p4an"))))
    (build-system python-build-system)
    (arguments `(#:python ,python-2)) ; no Python 3 support
    (inputs
     `(("python-cython" ,python2-cython)
       ("python-matplotlib" ,python2-matplotlib)))
    (propagated-inputs
     `(("bedtools" ,bedtools)
       ("samtools" ,samtools)))
    (native-inputs
     `(("python-pyyaml" ,python2-pyyaml)
       ("python-nose" ,python2-nose)
       ("python-setuptools" ,python2-setuptools)))
    (home-page "https://pythonhosted.org/pybedtools/")
    (synopsis "Python wrapper for BEDtools programs")
    (description
     "pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs,
which are widely used for genomic interval manipulation or \"genome algebra\".
pybedtools extends BEDTools by offering feature-level manipulations from with
Python.")
    (license license:gpl2+)))

(define-public python-biopython
  (package
    (name "python-biopython")
    (version "1.65")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "http://biopython.org/DIST/biopython-"
                    version ".tar.gz"))
              (sha256
               (base32
                "13m8s9jkrw40zvdp1rl709n6lmgdh4f52aann7gzr6sfp0fwhg26"))))
    (build-system python-build-system)
    (inputs
     `(("python-numpy" ,python-numpy)))
    (native-inputs
     `(("python-setuptools" ,python2-setuptools)))
    (home-page "http://biopython.org/")
    (synopsis "Tools for biological computation in Python")
    (description
     "Biopython is a set of tools for biological computation including parsers
for bioinformatics files into Python data structures; interfaces to common
bioinformatics programs; a standard sequence class and tools for performing
common operations on them; code to perform data classification; code for
dealing with alignments; code making it easy to split up parallelizable tasks
into separate processes; and more.")
    (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE"))))

(define-public python2-biopython
  (package (inherit (package-with-python2 python-biopython))
    (inputs
     `(("python2-numpy" ,python2-numpy)))))

(define-public blast+
  (package
    (name "blast+")
    (version "2.2.31")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/"
                    version "/ncbi-blast-" version "+-src.tar.gz"))
              (sha256
               (base32
                "19gq6as4k1jrgsd26158ads6h7v4jca3h4r5dzg1y0m6ya50x5ph"))
              (modules '((guix build utils)))
              (snippet
               '(begin
                  ;; Remove bundled bzip2 and zlib
                  (delete-file-recursively "c++/src/util/compress/bzip2")
                  (delete-file-recursively "c++/src/util/compress/zlib")
                  (substitute* "c++/src/util/compress/Makefile.in"
                    (("bzip2 zlib api") "api"))
                  ;; Remove useless msbuild directory
                  (delete-file-recursively
                   "c++/src/build-system/project_tree_builder/msbuild")
                  #t))))
    (build-system gnu-build-system)
    (arguments
     `(;; There are three(!) tests for this massive library, and all fail with
       ;; "unparsable timing stats".
       ;; ERR [127] --  [util/regexp] test_pcre.sh     (unparsable timing stats)
       ;; ERR [127] --  [serial/datatool] datatool.sh     (unparsable timing stats)
       ;; ERR [127] --  [serial/datatool] datatool_xml.sh     (unparsable timing stats)
       #:tests? #f
       #:out-of-source? #t
       #:parallel-build? #f ; not supported
       #:phases
       (modify-phases %standard-phases
         (add-before
          'configure 'set-HOME
          ;; $HOME needs to be set at some point during the configure phase
          (lambda _ (setenv "HOME" "/tmp") #t))
         (add-after
          'unpack 'enter-dir
          (lambda _ (chdir "c++") #t))
         (add-after
          'enter-dir 'fix-build-system
          (lambda _
            (define (which* cmd)
              (cond ((string=? cmd "date")
                     ;; make call to "date" deterministic
                     "date -d @0")
                    ((which cmd)
                     => identity)
                    (else
                     (format (current-error-port)
                             "WARNING: Unable to find absolute path for ~s~%"
                             cmd)
                     #f)))

            ;; Rewrite hardcoded paths to various tools
            (substitute* (append '("src/build-system/configure.ac"
                                   "src/build-system/configure"
                                   "scripts/common/impl/if_diff.sh"
                                   "scripts/common/impl/run_with_lock.sh"
                                   "src/build-system/Makefile.configurables.real"
                                   "src/build-system/Makefile.in.top"
                                   "src/build-system/Makefile.meta.gmake=no"
                                   "src/build-system/Makefile.meta.in"
                                   "src/build-system/Makefile.meta_l"
                                   "src/build-system/Makefile.meta_p"
                                   "src/build-system/Makefile.meta_r"
                                   "src/build-system/Makefile.mk.in"
                                   "src/build-system/Makefile.requirements"
                                   "src/build-system/Makefile.rules_with_autodep.in")
                                 (find-files "scripts/common/check" "\\.sh$"))
              (("(/usr/bin/|/bin/)([a-z][-_.a-z]*)" all dir cmd)
               (or (which* cmd) all)))

            (substitute* (find-files "src/build-system" "^config.*")
              (("LN_S=/bin/\\$LN_S") (string-append "LN_S=" (which "ln")))
              (("^PATH=.*") ""))

            ;; rewrite "/var/tmp" in check script
            (substitute* "scripts/common/check/check_make_unix.sh"
              (("/var/tmp") "/tmp"))

            ;; do not reset PATH
            (substitute* (find-files "scripts/common/impl/" "\\.sh$")
              (("^ *PATH=.*") "")
              (("action=/bin/") "action=")
              (("export PATH") ":"))
            #t))
         (replace
          'configure
          (lambda* (#:key inputs outputs #:allow-other-keys)
            (let ((out     (assoc-ref outputs "out"))
                  (lib     (string-append (assoc-ref outputs "lib") "/lib"))
                  (include (string-append (assoc-ref outputs "include")
                                          "/include/ncbi-tools++")))
              ;; The 'configure' script doesn't recognize things like
              ;; '--enable-fast-install'.
              (zero? (system* "./configure.orig"
                              (string-append "--with-build-root=" (getcwd) "/build")
                              (string-append "--prefix=" out)
                              (string-append "--libdir=" lib)
                              (string-append "--includedir=" include)
                              (string-append "--with-bz2="
                                             (assoc-ref inputs "bzip2"))
                              (string-append "--with-z="
                                             (assoc-ref inputs "zlib"))
                              ;; Each library is built twice by default, once
                              ;; with "-static" in its name, and again
                              ;; without.
                              "--without-static"
                              "--with-dll"))))))))
    (outputs '("out"       ;  19 MB
               "lib"       ; 203 MB
               "include")) ;  32 MB
    (inputs
     `(("bzip2" ,bzip2)
       ("zlib" ,zlib)))
    (native-inputs
     `(("cpio" ,cpio)))
    (home-page "http://blast.ncbi.nlm.nih.gov")
    (synopsis "Basic local alignment search tool")
    (description
     "BLAST is a popular method of performing a DNA or protein sequence
similarity search, using heuristics to produce results quickly.  It also
calculates an “expect value” that estimates how many matches would have
occurred at a given score by chance, which can aid a user in judging how much
confidence to have in an alignment.")
    ;; Most of the sources are in the public domain, with the following
    ;; exceptions:
    ;;   * Expat:
    ;;     * ./c++/include/util/bitset/
    ;;     * ./c++/src/html/ncbi_menu*.js
    ;;   * Boost license:
    ;;     * ./c++/include/util/impl/floating_point_comparison.hpp
    ;;   * LGPL 2+:
    ;;     * ./c++/include/dbapi/driver/odbc/unix_odbc/
    ;;   * ASL 2.0:
    ;;     * ./c++/src/corelib/teamcity_*
    (license (list license:public-domain
                   license:expat
                   license:boost1.0
                   license:lgpl2.0+
                   license:asl2.0))))

(define-public bowtie
  (package
    (name "bowtie")
    (version "2.2.4")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v"
                                  version ".tar.gz"))
              (file-name (string-append name "-" version ".tar.gz"))
              (sha256
               (base32
                "15dnbqippwvhyh9zqjhaxkabk7lm1xbh1nvar1x4b5kwm117zijn"))
              (modules '((guix build utils)))
              (snippet
               '(substitute* "Makefile"
                  (("^CC = .*$") "CC = gcc")
                  (("^CPP = .*$") "CPP = g++")
                  ;; replace BUILD_HOST and BUILD_TIME for deterministic build
                  (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
                  (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))
              (patches (list (search-patch "bowtie-fix-makefile.patch")))))
    (build-system gnu-build-system)
    (inputs `(("perl" ,perl)
              ("perl-clone" ,perl-clone)
              ("perl-test-deep" ,perl-test-deep)
              ("perl-test-simple" ,perl-test-simple)
              ("python" ,python-2)))
    (arguments
     '(#:make-flags '("allall")
       #:phases
       (alist-delete
        'configure
        (alist-replace
         'install
         (lambda* (#:key outputs #:allow-other-keys)
           (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
             (mkdir-p bin)
             (for-each (lambda (file)
                         (copy-file file (string-append bin file)))
                       (find-files "." "bowtie2.*"))))
         (alist-replace
          'check
          (lambda* (#:key outputs #:allow-other-keys)
            (system* "perl"
                     "scripts/test/simple_tests.pl"
                     "--bowtie2=./bowtie2"
                     "--bowtie2-build=./bowtie2-build"))
          %standard-phases)))))
    (home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
    (synopsis "Fast and sensitive nucleotide sequence read aligner")
    (description
     "Bowtie 2 is a fast and memory-efficient tool for aligning sequencing
reads to long reference sequences.  It is particularly good at aligning reads
of about 50 up to 100s or 1,000s of characters, and particularly good at
aligning to relatively long (e.g. mammalian) genomes.  Bowtie 2 indexes the
genome with an FM Index to keep its memory footprint small: for the human
genome, its memory footprint is typically around 3.2 GB.  Bowtie 2 supports
gapped, local, and paired-end alignment modes.")
    (supported-systems '("x86_64-linux"))
    (license license:gpl3+)))

(define-public bwa
  (package
    (name "bwa")
    (version "0.7.12")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/bio-bwa/bwa-"
                                  version ".tar.bz2"))
              (sha256
               (base32
                "1330dpqncv0px3pbhjzz1gwgg39kkcv2r9qp2xs0sixf8z8wl7bh"))))
    (build-system gnu-build-system)
    (arguments
     '(#:tests? #f ;no "check" target
       #:phases
       (alist-replace
        'install
        (lambda* (#:key outputs #:allow-other-keys)
          (let ((bin (string-append
                      (assoc-ref outputs "out") "/bin"))
                (doc (string-append
                      (assoc-ref outputs "out") "/share/doc/bwa"))
                (man (string-append
                      (assoc-ref outputs "out") "/share/man/man1")))
            (mkdir-p bin)
            (mkdir-p doc)
            (mkdir-p man)
            (copy-file "bwa" (string-append bin "/bwa"))
            (copy-file "README.md" (string-append doc "/README.md"))
            (copy-file "bwa.1" (string-append man "/bwa.1"))))
        ;; no "configure" script
        (alist-delete 'configure %standard-phases))))
    (inputs `(("zlib" ,zlib)))
    (home-page "http://bio-bwa.sourceforge.net/")
    (synopsis "Burrows-Wheeler sequence aligner")
    (description
     "BWA is a software package for mapping low-divergent sequences against a
large reference genome, such as the human genome.  It consists of three
algorithms: BWA-backtrack, BWA-SW and BWA-MEM.  The first algorithm is
designed for Illumina sequence reads up to 100bp, while the rest two for
longer sequences ranged from 70bp to 1Mbp.  BWA-MEM and BWA-SW share similar
features such as long-read support and split alignment, but BWA-MEM, which is
the latest, is generally recommended for high-quality queries as it is faster
and more accurate.  BWA-MEM also has better performance than BWA-backtrack for
70-100bp Illumina reads.")
    (license license:gpl3+)))

(define-public python2-bx-python
  (package
    (name "python2-bx-python")
    (version "0.7.2")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://pypi.python.org/packages/source/b/bx-python/bx-python-"
                    version ".tar.gz"))
              (sha256
               (base32
                "0ld49idhc5zjdvbhvjq1a2qmpjj7h5v58rqr25dzmfq7g34b50xh"))
              (modules '((guix build utils)))
              (snippet
               '(substitute* "setup.py"
                  ;; remove dependency on outdated "distribute" module
                  (("^from distribute_setup import use_setuptools") "")
                  (("^use_setuptools\\(\\)") "")))))
    (build-system python-build-system)
    (arguments
     `(#:tests? #f ;tests fail because test data are not included
       #:python ,python-2))
    (inputs
     `(("python-numpy" ,python2-numpy)
       ("zlib" ,zlib)))
    (native-inputs
     `(("python-nose" ,python2-nose)
       ("python-setuptools" ,python2-setuptools)))
    (home-page "http://bitbucket.org/james_taylor/bx-python/")
    (synopsis "Tools for manipulating biological data")
    (description
     "bx-python provides tools for manipulating biological data, particularly
multiple sequence alignments.")
    (license license:expat)))

(define-public clipper
  (package
    (name "clipper")
    (version "0.3.0")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/YeoLab/clipper/archive/"
                    version ".tar.gz"))
              (sha256
               (base32
                "1q7jpimsqln7ic44i8v2rx2haj5wvik8hc1s2syd31zcn0xk1iyq"))
              (modules '((guix build utils)))
              (snippet
               ;; remove unnecessary setup dependency
               '(substitute* "setup.py"
                  (("setup_requires = .*") "")))))
    (build-system python-build-system)
    (arguments `(#:python ,python-2)) ; only Python 2 is supported
    (inputs
     `(("htseq" ,htseq)
       ("python-pybedtools" ,python2-pybedtools)
       ("python-cython" ,python2-cython)
       ("python-scikit-learn" ,python2-scikit-learn)
       ("python-matplotlib" ,python2-matplotlib)
       ("python-pysam" ,python2-pysam)
       ("python-numpy" ,python2-numpy)
       ("python-scipy" ,python2-scipy)))
    (native-inputs
     `(("python-mock" ,python2-mock) ; for tests
       ("python-pytz" ,python2-pytz) ; for tests
       ("python-setuptools" ,python2-setuptools)))
    (home-page "https://github.com/YeoLab/clipper")
    (synopsis "CLIP peak enrichment recognition")
    (description
     "CLIPper is a tool to define peaks in CLIP-seq datasets.")
    (license license:gpl2)))

(define-public couger
  (package
    (name "couger")
    (version "1.8.2")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "http://couger.oit.duke.edu/static/assets/COUGER"
                    version ".zip"))
              (sha256
               (base32
                "04p2b14nmhzxw5h72mpzdhalv21bx4w9b87z0wpw0xzxpysyncmq"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f
       #:phases
       (modify-phases %standard-phases
         (delete 'configure)
         (delete 'build)
         (replace
          'install
          (lambda* (#:key outputs #:allow-other-keys)
            (let ((out (assoc-ref outputs "out")))
              (copy-recursively "src" (string-append out "/src"))
              (mkdir (string-append out "/bin"))
              ;; Add "src" directory to module lookup path.
              (substitute* "couger"
                (("from argparse")
                 (string-append "import sys\nsys.path.append(\""
                                out "\")\nfrom argparse")))
              (copy-file "couger" (string-append out "/bin/couger")))
            #t))
         (add-after
          'install 'wrap-program
          (lambda* (#:key inputs outputs #:allow-other-keys)
            ;; Make sure 'couger' runs with the correct PYTHONPATH.
            (let* ((out (assoc-ref outputs "out"))
                   (path (getenv "PYTHONPATH")))
              (wrap-program (string-append out "/bin/couger")
                `("PYTHONPATH" ":" prefix (,path))))
            #t)))))
    (inputs
     `(("python" ,python-2)
       ("python2-pillow" ,python2-pillow)
       ("python2-numpy" ,python2-numpy)
       ("python2-scipy" ,python2-scipy)
       ("python2-matplotlib" ,python2-matplotlib)))
    (propagated-inputs
     `(("r" ,r)
       ("libsvm" ,libsvm)
       ("randomjungle" ,randomjungle)))
    (native-inputs
     `(("unzip" ,unzip)))
    (home-page "http://couger.oit.duke.edu")
    (synopsis "Identify co-factors in sets of genomic regions")
    (description
     "COUGER can be applied to any two sets of genomic regions bound by
paralogous TFs (e.g., regions derived from ChIP-seq experiments) to identify
putative co-factors that provide specificity to each TF.  The framework
determines the genomic targets uniquely-bound by each TF, and identifies a
small set of co-factors that best explain the in vivo binding differences
between the two TFs.

COUGER uses classification algorithms (support vector machines and random
forests) with features that reflect the DNA binding specificities of putative
co-factors.  The features are generated either from high-throughput TF-DNA
binding data (from protein binding microarray experiments), or from large
collections of DNA motifs.")
    (license license:gpl3+)))

(define-public clustal-omega
  (package
    (name "clustal-omega")
    (version "1.2.1")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "http://www.clustal.org/omega/clustal-omega-"
                    version ".tar.gz"))
              (sha256
               (base32
                "02ibkx0m0iwz8nscg998bh41gg251y56cgh86bvyrii5m8kjgwqf"))))
    (build-system gnu-build-system)
    (inputs
     `(("argtable" ,argtable)))
    (home-page "http://www.clustal.org/omega/")
    (synopsis "Multiple sequence aligner for protein and DNA/RNA")
    (description
     "Clustal-Omega is a general purpose multiple sequence alignment (MSA)
program for protein and DNA/RNA.  It produces high quality MSAs and is capable
of handling data-sets of hundreds of thousands of sequences in reasonable
time.")
    (license license:gpl2+)))

(define-public crossmap
  (package
    (name "crossmap")
    (version "0.1.6")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/crossmap/CrossMap-"
                                  version ".tar.gz"))
              (sha256
               (base32
                "163hi5gjgij6cndxlvbkp5jjwr0k4wbm9im6d2210278q7k9kpnp"))
              ;; patch has been sent upstream already
              (patches (list
                        (search-patch "crossmap-allow-system-pysam.patch")))
              (modules '((guix build utils)))
              ;; remove bundled copy of pysam
              (snippet
               '(delete-file-recursively "lib/pysam"))))
    (build-system python-build-system)
    (arguments
     `(#:python ,python-2
       #:phases
       (alist-cons-after
        'unpack 'set-env
        (lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1"))
        %standard-phases)))
    (inputs
     `(("python-numpy" ,python2-numpy)
       ("python-pysam" ,python2-pysam)
       ("zlib" ,zlib)))
    (native-inputs
     `(("python-cython" ,python2-cython)
       ("python-nose" ,python2-nose)
       ("python-setuptools" ,python2-setuptools)))
    (home-page "http://crossmap.sourceforge.net/")
    (synopsis "Convert genome coordinates between assemblies")
    (description
     "CrossMap is a program for conversion of genome coordinates or annotation
files between different genome assemblies.  It supports most commonly used
file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
    (license license:gpl2+)))

(define-public cutadapt
  (package
    (name "cutadapt")
    (version "1.8")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/marcelm/cutadapt/archive/v"
                    version ".tar.gz"))
              (file-name (string-append name "-" version ".tar.gz"))
              (sha256
               (base32
                "161bp87y6gd6r5bmvjpn2b1k942i3fizfpa139f0jn6jv1wcp5h5"))))
    (build-system python-build-system)
    (arguments
     ;; tests must be run after install
     `(#:phases (alist-cons-after
                 'install 'check
                 (lambda* (#:key inputs outputs #:allow-other-keys)
                   (setenv "PYTHONPATH"
                           (string-append
                            (getenv "PYTHONPATH")
                            ":" (assoc-ref outputs "out")
                            "/lib/python"
                            (string-take (string-take-right
                                          (assoc-ref inputs "python") 5) 3)
                            "/site-packages"))
                   (zero? (system* "nosetests" "-P" "tests")))
                 (alist-delete 'check %standard-phases))))
    (native-inputs
     `(("python-cython" ,python-cython)
       ("python-nose" ,python-nose)
       ("python-setuptools" ,python-setuptools)))
    (home-page "https://code.google.com/p/cutadapt/")
    (synopsis "Remove adapter sequences from nucleotide sequencing reads")
    (description
     "Cutadapt finds and removes adapter sequences, primers, poly-A tails and
other types of unwanted sequence from high-throughput sequencing reads.")
    (license license:expat)))

(define-public diamond
  (package
    (name "diamond")
    (version "0.7.9")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/bbuchfink/diamond/archive/v"
                    version ".tar.gz"))
              (file-name (string-append name "-" version ".tar.gz"))
              (sha256
               (base32
                "0hfkcfv9f76h5brbyw9fyvmc0l9cmbsxrcdqk0fa9xv82zj47p15"))
              (snippet '(begin
                          (delete-file "bin/diamond")
                          #t))))
    (build-system gnu-build-system)
    (arguments
     '(#:tests? #f  ;no "check" target
       #:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'enter-source-dir
                    (lambda _
                      (chdir "src")
                      #t))
         (delete 'configure)
         (replace 'install
                  (lambda* (#:key outputs #:allow-other-keys)
                    (let ((bin (string-append (assoc-ref outputs "out")
                                              "/bin")))
                      (mkdir-p bin)
                      (copy-file "../bin/diamond"
                                 (string-append bin "/diamond"))
                      #t))))))
    (native-inputs
     `(("bc" ,bc)))
    (inputs
     `(("boost" ,boost)
       ("zlib" ,zlib)))
    (home-page "https://github.com/bbuchfink/diamond")
    (synopsis "Accelerated BLAST compatible local sequence aligner")
    (description
     "DIAMOND is a BLAST-compatible local aligner for mapping protein and
translated DNA query sequences against a protein reference database (BLASTP
and BLASTX alignment mode).  The speedup over BLAST is up to 20,000 on short
reads at a typical sensitivity of 90-99% relative to BLAST depending on the
data and settings.")
    (license (license:non-copyleft "file://src/COPYING"
                                   "See src/COPYING in the distribution."))))

(define-public edirect
  (package
    (name "edirect")
    (version "2.50")
    (source (origin
              (method url-fetch)
              ;; Note: older versions are not retained.
              (uri "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/edirect.zip")
              (sha256
               (base32
                "08afhz2ph66h8h381hl1mqyxkdi5nbvzsyj9gfw3jfbdijnpi4qj"))))
    (build-system perl-build-system)
    (arguments
     `(#:tests? #f ;no "check" target
       #:phases
       (modify-phases %standard-phases
         (delete 'configure)
         (delete 'build)
         (replace 'install
                  (lambda* (#:key outputs #:allow-other-keys)
                    (let ((target (string-append (assoc-ref outputs "out")
                                                 "/bin")))
                      (mkdir-p target)
                      (copy-file "edirect.pl"
                                 (string-append target "/edirect.pl"))
                      #t)))
         (add-after
          'install 'wrap-program
          (lambda* (#:key inputs outputs #:allow-other-keys)
            ;; Make sure 'edirect.pl' finds all perl inputs at runtime.
            (let* ((out (assoc-ref outputs "out"))
                   (path (getenv "PERL5LIB")))
              (wrap-program (string-append out "/bin/edirect.pl")
                `("PERL5LIB" ":" prefix (,path)))))))))
    (inputs
     `(("perl-html-parser" ,perl-html-parser)
       ("perl-encode-locale" ,perl-encode-locale)
       ("perl-file-listing" ,perl-file-listing)
       ("perl-html-tagset" ,perl-html-tagset)
       ("perl-html-tree" ,perl-html-tree)
       ("perl-http-cookies" ,perl-http-cookies)
       ("perl-http-date" ,perl-http-date)
       ("perl-http-message" ,perl-http-message)
       ("perl-http-negotiate" ,perl-http-negotiate)
       ("perl-lwp-mediatypes" ,perl-lwp-mediatypes)
       ("perl-lwp-protocol-https" ,perl-lwp-protocol-https)
       ("perl-net-http" ,perl-net-http)
       ("perl-uri" ,perl-uri)
       ("perl-www-robotrules" ,perl-www-robotrules)
       ("perl" ,perl)))
    (native-inputs
     `(("unzip" ,unzip)))
    (home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288")
    (synopsis "Tools for accessing the NCBI's set of databases")
    (description
     "Entrez Direct (EDirect) is a method for accessing the National Center
for Biotechnology Information's (NCBI) set of interconnected
databases (publication, sequence, structure, gene, variation, expression,
etc.) from a terminal.  Functions take search terms from command-line
arguments.  Individual operations are combined to build multi-step queries.
Record retrieval and formatting normally complete the process.

EDirect also provides an argument-driven function that simplifies the
extraction of data from document summaries or other results that are returned
in structured XML format.  This can eliminate the need for writing custom
software to answer ad hoc questions.")
    (license license:public-domain)))

(define-public express
  (package
    (name "express")
    (version "1.5.1")
    (source (origin
              (method url-fetch)
              (uri
               (string-append
                "http://bio.math.berkeley.edu/eXpress/downloads/express-"
                version "/express-" version "-src.tgz"))
              (sha256
               (base32
                "03rczxd0gjp2l1jxcmjfmf5j94j77zqyxa6x063zsc585nj40n0c"))))
    (build-system cmake-build-system)
    (arguments
     `(#:tests? #f ;no "check" target
       #:phases
       (alist-cons-after
        'unpack 'use-shared-boost-libs-and-set-bamtools-paths
        (lambda* (#:key inputs #:allow-other-keys)
          (substitute* "CMakeLists.txt"
            (("set\\(Boost_USE_STATIC_LIBS ON\\)")
             "set(Boost_USE_STATIC_LIBS OFF)")
            (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include")
             (string-append (assoc-ref inputs "bamtools") "/include/bamtools")))
          (substitute* "src/CMakeLists.txt"
            (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib")
             (string-append (assoc-ref inputs "bamtools") "/lib/bamtools")))
          #t)
        %standard-phases)))
    (inputs
     `(("boost" ,boost)
       ("bamtools" ,bamtools)
       ("protobuf" ,protobuf)
       ("zlib" ,zlib)))
    (home-page "http://bio.math.berkeley.edu/eXpress")
    (synopsis "Streaming quantification for high-throughput genomic sequencing")
    (description
     "eXpress is a streaming tool for quantifying the abundances of a set of
target sequences from sampled subsequences.  Example applications include
transcript-level RNA-Seq quantification, allele-specific/haplotype expression
analysis (from RNA-Seq), transcription factor binding quantification in
ChIP-Seq, and analysis of metagenomic data.")
    (license license:artistic2.0)))

(define-public fasttree
  (package
   (name "fasttree")
   (version "2.1.8")
   (source (origin
             (method url-fetch)
             (uri (string-append
                   "http://www.microbesonline.org/fasttree/FastTree-"
                   version ".c"))
             (sha256
              (base32
               "0dzqc9vr9iiiw21y159xfjl2z90vw0y7r4x6456pcaxiy5hd2wmi"))))
   (build-system gnu-build-system)
   (arguments
    `(#:tests? #f ; no "check" target
      #:phases
      (modify-phases %standard-phases
        (delete 'unpack)
        (delete 'configure)
        (replace 'build
                 (lambda* (#:key source #:allow-other-keys)
                   (and (zero? (system* "gcc"
                                        "-O3"
                                        "-finline-functions"
                                        "-funroll-loops"
                                        "-Wall"
                                        "-o"
                                        "FastTree"
                                        source
                                        "-lm"))
                        (zero? (system* "gcc"
                                        "-DOPENMP"
                                        "-fopenmp"
                                        "-O3"
                                        "-finline-functions"
                                        "-funroll-loops"
                                        "-Wall"
                                        "-o"
                                        "FastTreeMP"
                                        source
                                        "-lm")))))
        (replace 'install
                 (lambda* (#:key outputs #:allow-other-keys)
                   (let ((bin (string-append (assoc-ref outputs "out")
                                             "/bin")))
                     (mkdir-p bin)
                     (copy-file "FastTree"
                                (string-append bin "/FastTree"))
                     (copy-file "FastTreeMP"
                                (string-append bin "/FastTreeMP"))
                     #t))))))
   (home-page "http://www.microbesonline.org/fasttree")
   (synopsis "Infers approximately-maximum-likelihood phylogenetic trees")
   (description
    "FastTree can handle alignments with up to a million of sequences in a
reasonable amount of time and memory.  For large alignments, FastTree is
100-1,000 times faster than PhyML 3.0 or RAxML 7.")
   (license license:gpl2+)))

(define-public fastx-toolkit
  (package
    (name "fastx-toolkit")
    (version "0.0.14")
    (source (origin
              (method url-fetch)
              (uri
               (string-append
                "https://github.com/agordon/fastx_toolkit/releases/download/"
                version "/fastx_toolkit-" version ".tar.bz2"))
              (sha256
               (base32
                "01jqzw386873sr0pjp1wr4rn8fsga2vxs1qfmicvx1pjr72007wy"))))
    (build-system gnu-build-system)
    (inputs
     `(("libgtextutils" ,libgtextutils)))
    (native-inputs
     `(("pkg-config" ,pkg-config)))
    (home-page "http://hannonlab.cshl.edu/fastx_toolkit/")
    (synopsis "Tools for FASTA/FASTQ file preprocessing")
    (description
     "The FASTX-Toolkit is a collection of command line tools for Short-Reads
FASTA/FASTQ files preprocessing.

Next-Generation sequencing machines usually produce FASTA or FASTQ files,
containing multiple short-reads sequences.  The main processing of such
FASTA/FASTQ files is mapping the sequences to reference genomes.  However, it
is sometimes more productive to preprocess the files before mapping the
sequences to the genome---manipulating the sequences to produce better mapping
results.  The FASTX-Toolkit tools perform some of these preprocessing tasks.")
    (license license:agpl3+)))

(define-public flexbar
  (package
    (name "flexbar")
    (version "2.5")
    (source (origin
              (method url-fetch)
              (uri
               (string-append "mirror://sourceforge/flexbar/"
                              version "/flexbar_v" version "_src.tgz"))
              (sha256
               (base32
                "13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf"))))
    (build-system cmake-build-system)
    (arguments
     `(#:configure-flags (list
                          (string-append "-DFLEXBAR_BINARY_DIR="
                                         (assoc-ref %outputs "out")
                                         "/bin/"))
       #:phases
       (alist-replace
        'check
        (lambda* (#:key outputs #:allow-other-keys)
          (setenv "PATH" (string-append
                          (assoc-ref outputs "out") "/bin:"
                          (getenv "PATH")))
          (chdir "../flexbar_v2.5_src/test")
          (zero? (system* "bash" "flexbar_validate.sh")))
        (alist-delete 'install %standard-phases))))
    (inputs
     `(("tbb" ,tbb)
       ("zlib" ,zlib)))
    (native-inputs
     `(("pkg-config" ,pkg-config)
       ("seqan" ,seqan)))
    (home-page "http://flexbar.sourceforge.net")
    (synopsis "Barcode and adapter removal tool for sequencing platforms")
    (description
     "Flexbar preprocesses high-throughput nucleotide sequencing data
efficiently.  It demultiplexes barcoded runs and removes adapter sequences.
Moreover, trimming and filtering features are provided.  Flexbar increases
read mapping rates and improves genome and transcriptome assemblies.  It
supports next-generation sequencing data in fasta/q and csfasta/q format from
Illumina, Roche 454, and the SOLiD platform.")
    (license license:gpl3)))

(define-public grit
  (package
    (name "grit")
    (version "2.0.2")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/nboley/grit/archive/"
                    version ".tar.gz"))
              (file-name (string-append name "-" version ".tar.gz"))
              (sha256
               (base32
                "157in84dj70wimbind3x7sy1whs3h57qfgcnj2s6lrd38fbrb7mj"))))
    (build-system python-build-system)
    (arguments
     `(#:python ,python-2
       #:phases
       (alist-cons-after
        'unpack 'generate-from-cython-sources
        (lambda* (#:key inputs outputs #:allow-other-keys)
          ;; Delete these C files to force fresh generation from pyx sources.
          (delete-file "grit/sparsify_support_fns.c")
          (delete-file "grit/call_peaks_support_fns.c")
          (substitute* "setup.py"
            (("Cython.Setup") "Cython.Build")
            ;; Add numpy include path to fix compilation
            (("pyx\", \\]")
             (string-append "pyx\", ], include_dirs = ['"
                            (assoc-ref inputs "python-numpy")
                            "/lib/python2.7/site-packages/numpy/core/include/"
                            "']"))) #t)
        %standard-phases)))
    (inputs
     `(("python-scipy" ,python2-scipy)
       ("python-numpy" ,python2-numpy)
       ("python-pysam" ,python2-pysam)
       ("python-networkx" ,python2-networkx)))
    (native-inputs
     `(("python-cython" ,python2-cython)
       ("python-setuptools" ,python2-setuptools)))
    (home-page "http://grit-bio.org")
    (synopsis "Tool for integrative analysis of RNA-seq type assays")
    (description
     "GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify
full length transcript models.  When none of these data sources are available,
GRIT can be run by providing a candidate set of TES or TSS sites.  In
addition, GRIT can merge in reference junctions and gene boundaries.  GRIT can
also be run in quantification mode, where it uses a provided GTF file and just
estimates transcript expression.")
    (license license:gpl3+)))

(define-public hisat
  (package
    (name "hisat")
    (version "0.1.4")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "http://ccb.jhu.edu/software/hisat/downloads/hisat-"
                    version "-beta-source.zip"))
              (sha256
               (base32
                "1k381ydranqxp09yf2y7w1d0chz5d59vb6jchi89hbb0prq19lk5"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ;no check target
       #:make-flags '("allall"
                      ;; Disable unsupported `popcnt' instructions on
                      ;; architectures other than x86_64
                      ,@(if (string-prefix? "x86_64"
                                            (or (%current-target-system)
                                                (%current-system)))
                            '()
                            '("POPCNT_CAPABILITY=0")))
       #:phases
       (alist-cons-after
        'unpack 'patch-sources
        (lambda _
          ;; XXX Cannot use snippet because zip files are not supported
          (substitute* "Makefile"
            (("^CC = .*$") "CC = gcc")
            (("^CPP = .*$") "CPP = g++")
            ;; replace BUILD_HOST and BUILD_TIME for deterministic build
            (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
            (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
          (substitute* '("hisat-build" "hisat-inspect")
            (("/usr/bin/env") (which "env"))))
        (alist-replace
         'install
         (lambda* (#:key outputs #:allow-other-keys)
           (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
             (mkdir-p bin)
             (for-each
              (lambda (file)
                (copy-file file (string-append bin file)))
              (find-files
               "."
               "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))))
         (alist-delete 'configure %standard-phases)))))
    (native-inputs
     `(("unzip" ,unzip)))
    (inputs
     `(("perl" ,perl)
       ("python" ,python)
       ("zlib" ,zlib)))
    (home-page "http://ccb.jhu.edu/software/hisat/index.shtml")
    (synopsis "Hierarchical indexing for spliced alignment of transcripts")
    (description
     "HISAT is a fast and sensitive spliced alignment program for mapping
RNA-seq reads.  In addition to one global FM index that represents a whole
genome, HISAT uses a large set of small FM indexes that collectively cover the
whole genome.  These small indexes (called local indexes) combined with
several alignment strategies enable effective alignment of RNA-seq reads, in
particular, reads spanning multiple exons.")
    (license license:gpl3+)))

(define-public hmmer
  (package
    (name "hmmer")
    (version "3.1b2")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "http://selab.janelia.org/software/hmmer"
                    (version-prefix version 1) "/"
                    version "/hmmer-" version ".tar.gz"))
              (sha256
               (base32
                "0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx"))))
    (build-system gnu-build-system)
    (native-inputs `(("perl", perl)))
    (home-page "http://hmmer.janelia.org")
    (synopsis "Biosequence analysis using profile hidden Markov models")
    (description
     "HMMER is used for searching sequence databases for homologs of protein
sequences, and for making protein sequence alignments.  It implements methods
using probabilistic models called profile hidden Markov models (profile
HMMs).")
    (license (list license:gpl3+
                   ;; The bundled library 'easel' is distributed
                   ;; under The Janelia Farm Software License.
                   (license:non-copyleft
                    "file://easel/LICENSE"
                    "See easel/LICENSE in the distribution.")))))

(define-public htseq
  (package
    (name "htseq")
    (version "0.6.1")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://pypi.python.org/packages/source/H/HTSeq/HTSeq-"
                    version ".tar.gz"))
              (sha256
               (base32
                "1i85ppf2j2lj12m0x690qq5nn17xxk23pbbx2c83r8ayb5wngzwv"))))
    (build-system python-build-system)
    (arguments `(#:python ,python-2)) ; only Python 2 is supported
    (inputs
     `(("python-numpy" ,python2-numpy)
       ("python-setuptools" ,python2-setuptools)))
    (home-page "http://www-huber.embl.de/users/anders/HTSeq/")
    (synopsis "Analysing high-throughput sequencing data with Python")
    (description
     "HTSeq is a Python package that provides infrastructure to process data
from high-throughput sequencing assays.")
    (license license:gpl3+)))

(define-public htsjdk
  (package
    (name "htsjdk")
    (version "1.129")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/samtools/htsjdk/archive/"
                    version ".tar.gz"))
              (file-name (string-append name "-" version ".tar.gz"))
              (sha256
               (base32
                "0asdk9b8jx2ij7yd6apg9qx03li8q7z3ml0qy2r2qczkra79y6fw"))
              (modules '((guix build utils)))
              ;; remove build dependency on git
              (snippet '(substitute* "build.xml"
                          (("failifexecutionfails=\"true\"")
                           "failifexecutionfails=\"false\"")))))
    (build-system gnu-build-system)
    (arguments
     `(#:modules ((srfi srfi-1)
                  (guix build gnu-build-system)
                  (guix build utils))
       #:phases (alist-replace
                 'build
                 (lambda _
                   (setenv "JAVA_HOME" (assoc-ref %build-inputs "jdk"))
                   (zero? (system* "ant" "all"
                                   (string-append "-Ddist="
                                                  (assoc-ref %outputs "out")
                                                  "/share/java/htsjdk/"))))
                 (fold alist-delete %standard-phases
                       '(configure install check)))))
    (native-inputs
     `(("ant" ,ant)
       ("jdk" ,icedtea6 "jdk")))
    (home-page "http://samtools.github.io/htsjdk/")
    (synopsis "Java API for high-throughput sequencing data (HTS) formats")
    (description
     "HTSJDK is an implementation of a unified Java library for accessing
common file formats, such as SAM and VCF, used for high-throughput
sequencing (HTS) data.  There are also an number of useful utilities for
manipulating HTS data.")
    (license license:expat)))

(define-public htslib
  (package
    (name "htslib")
    (version "1.2.1")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/samtools/htslib/releases/download/"
                    version "/htslib-" version ".tar.bz2"))
              (sha256
               (base32
                "1c32ssscbnjwfw3dra140fq7riarp2x990qxybh34nr1p5r17nxx"))))
    (build-system gnu-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after
          'unpack 'patch-tests
          (lambda _
            (substitute* "test/test.pl"
              (("/bin/bash") (which "bash")))
            #t)))))
    (inputs
     `(("zlib" ,zlib)))
    (native-inputs
     `(("perl" ,perl)))
    (home-page "http://www.htslib.org")
    (synopsis "C library for reading/writing high-throughput sequencing data")
    (description
     "HTSlib is a C library for reading/writing high-throughput sequencing
data.  It also provides the bgzip, htsfile, and tabix utilities.")
    ;; Files under cram/ are released under the modified BSD license;
    ;; the rest is released under the Expat license
    (license (list license:expat license:bsd-3))))

(define-public idr
  (package
    (name "idr")
    (version "2.0.0")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/nboley/idr/archive/"
                    version ".tar.gz"))
              (file-name (string-append name "-" version ".tar.gz"))
              (sha256
               (base32
                "1k3x44biak00aiv3hpm1yd6nn4hhp7n0qnbs3zh2q9sw7qr1qj5r"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after
          'install 'wrap-program
          (lambda* (#:key inputs outputs #:allow-other-keys)
            (let* ((out (assoc-ref outputs "out"))
                   (python-version (string-take (string-take-right
                                                 (assoc-ref inputs "python") 5) 3))
                   (path (string-join
                          (map (lambda (name)
                                 (string-append (assoc-ref inputs name)
                                                "/lib/python" python-version
                                                "/site-packages"))
                               '("python-scipy"
                                 "python-numpy"
                                 "python-matplotlib"))
                          ":")))
              (wrap-program (string-append out "/bin/idr")
                `("PYTHONPATH" ":" prefix (,path))))
            #t)))))
    (inputs
     `(("python-scipy" ,python-scipy)
       ("python-numpy" ,python-numpy)
       ("python-matplotlib" ,python-matplotlib)))
    (native-inputs
     `(("python-cython" ,python-cython)
       ("python-setuptools" ,python-setuptools)))
    (home-page "https://github.com/nboley/idr")
    (synopsis "Tool to measure the irreproducible discovery rate (IDR)")
    (description
     "The IDR (Irreproducible Discovery Rate) framework is a unified approach
to measure the reproducibility of findings identified from replicate
experiments and provide highly stable thresholds based on reproducibility.")
    (license license:gpl3+)))

(define-public macs
  (package
    (name "macs")
    (version "2.1.0.20140616")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://pypi.python.org/packages/source/M/MACS2/MACS2-"
                    version ".tar.gz"))
              (sha256
               (base32
                "11lmiw6avqhwn75sn59g4lfkrr2kk20r3rgfbx9xfqb8rg9mi2n6"))))
    (build-system python-build-system)
    (arguments
     `(#:python ,python-2 ; only compatible with Python 2.7
       #:tests? #f)) ; no test target
    (inputs
     `(("python-numpy" ,python2-numpy)))
    (native-inputs
     `(("python-setuptools" ,python2-setuptools)))
    (home-page "http://github.com/taoliu/MACS/")
    (synopsis "Model based analysis for ChIP-Seq data")
    (description
     "MACS is an implementation of a ChIP-Seq analysis algorithm for
identifying transcript factor binding sites named Model-based Analysis of
ChIP-Seq (MACS).  MACS captures the influence of genome complexity to evaluate
the significance of enriched ChIP regions and it improves the spatial
resolution of binding sites through combining the information of both
sequencing tag position and orientation.")
    (license license:bsd-3)))

(define-public miso
  (package
    (name "miso")
    (version "0.5.3")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://pypi.python.org/packages/source/m/misopy/misopy-"
                    version ".tar.gz"))
              (sha256
               (base32
                "0x446867az8ir0z8c1vjqffkp0ma37wm4sylixnkhgawllzx8v5w"))
              (modules '((guix build utils)))
              (snippet
               '(substitute* "setup.py"
                  ;; Use setuptools, or else the executables are not
                  ;; installed.
                  (("distutils.core") "setuptools")
                  ;; use "gcc" instead of "cc" for compilation
                  (("^defines")
                   "cc.set_executables(
compiler='gcc',
compiler_so='gcc',
linker_exe='gcc',
linker_so='gcc -shared'); defines")))))
    (build-system python-build-system)
    (arguments
     `(#:python ,python-2 ; only Python 2 is supported
       #:tests? #f)) ; no "test" target
    (inputs
     `(("samtools" ,samtools)
       ("python-numpy" ,python2-numpy)
       ("python-pysam" ,python2-pysam)
       ("python-scipy" ,python2-scipy)
       ("python-matplotlib" ,python2-matplotlib)))
    (native-inputs
     `(("python-mock" ,python2-mock) ;for tests
       ("python-pytz" ,python2-pytz) ;for tests
       ("python-setuptools" ,python2-setuptools)))
    (home-page "http://genes.mit.edu/burgelab/miso/index.html")
    (synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation")
    (description
     "MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates
the expression level of alternatively spliced genes from RNA-Seq data, and
identifies differentially regulated isoforms or exons across samples.  By
modeling the generative process by which reads are produced from isoforms in
RNA-Seq, the MISO model uses Bayesian inference to compute the probability
that a read originated from a particular isoform.")
    (license license:gpl2)))

(define-public orfm
  (package
    (name "orfm")
    (version "0.4.1")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/wwood/OrfM/releases/download/v"
                    version "/orfm-" version ".tar.gz"))
              (sha256
               (base32
                "05fmw145snk646ly076zby0fjav0k7ysbclck5d4s9pmgcfpijc2"))))
    (build-system gnu-build-system)
    (inputs `(("zlib" ,zlib)))
    (synopsis "Simple and not slow open reading frame (ORF) caller")
    (description
     "An ORF caller finds stretches of DNA that when translated are not
interrupted by stop codons.  OrfM finds and prints these ORFs.")
    (home-page "https://github.com/wwood/OrfM")
    (license license:lgpl3+)))

(define-public python2-pbcore
  (package
    (name "python2-pbcore")
    (version "0.9.3")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/PacificBiosciences/pbcore/archive/"
                    version ".tar.gz"))
              (file-name (string-append name "-" version ".tar.gz"))
              (sha256
               (base32
                "1z46rwjac93jm87cbj2zgjg6qvsgs65140wkbbxsvxps7ai4pm09"))))
    (build-system python-build-system)
    (arguments `(#:python ,python-2)) ; pbcore requires Python 2.7
    (inputs
     `(("python-cython" ,python2-cython)
       ("python-numpy" ,python2-numpy)
       ("python-pysam" ,python2-pysam)
       ("python-h5py" ,python2-h5py)))
    (native-inputs
     `(("python-setuptools" ,python2-setuptools)))
    (home-page "http://pacificbiosciences.github.io/pbcore/")
    (synopsis "Library for reading and writing PacBio data files")
    (description
     "The pbcore package provides Python APIs for interacting with PacBio data
files and writing bioinformatics applications.")
    (license license:bsd-3)))

(define-public python2-warpedlmm
  (package
    (name "python2-warpedlmm")
    (version "0.21")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://pypi.python.org/packages/source/W/WarpedLMM/WarpedLMM-"
             version ".zip"))
       (sha256
        (base32
         "1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j"))))
    (build-system python-build-system)
    (arguments
     `(#:python ,python-2  ; requires Python 2.7
       #:phases
       (modify-phases %standard-phases
         (add-after
          'install 'remove-bin-directory
          (lambda* (#:key outputs #:allow-other-keys)
            ;; The "bin" directory only contains wrappers for running
            ;; the module tests.  They are not needed after the
            ;; "check" phase.
            (delete-file-recursively
             (string-append (assoc-ref outputs "out") "/bin"))
            #t)))))
    (propagated-inputs
     `(("python-scipy" ,python2-scipy)
       ("python-numpy" ,python2-numpy)
       ("python-matplotlib" ,python2-matplotlib)
       ("python-fastlmm" ,python2-fastlmm)
       ("python-pandas" ,python2-pandas)
       ("python-pysnptools" ,python2-pysnptools)))
    (native-inputs
     `(("python-setuptools" ,python2-setuptools)
       ("python-mock" ,python2-mock)
       ("python-nose" ,python2-nose)
       ("unzip" ,unzip)))
    (home-page "https://github.com/PMBio/warpedLMM")
    (synopsis "Implementation of warped linear mixed models")
    (description
     "WarpedLMM is a Python implementation of the warped linear mixed model,
which automatically learns an optimal warping function (or transformation) for
the phenotype as it models the data.")
    (license license:asl2.0)))

(define-public pbtranscript-tofu
  (let ((commit "c7bbd5472"))
    (package
      (name "pbtranscript-tofu")
      (version (string-append "0.4.1." commit))
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/PacificBiosciences/cDNA_primer.git")
                      (commit commit)))
                (file-name (string-append name "-" version ".tar.gz"))
                (sha256
                 (base32
                  "148xkzi689c49g6fdhckp6mnmj2qhjdf1j4wifm6ja7ij95d7fxx"))))
      (build-system python-build-system)
      (arguments
       `(#:python ,python-2
         ;; With standard flags, the install phase attempts to create a zip'd
         ;; egg file, and fails with an error: 'ZIP does not support timestamps
         ;; before 1980'
         #:configure-flags '("--single-version-externally-managed"
                             "--record=pbtranscript-tofu.txt")
         #:phases
         (alist-cons-after
          'unpack 'enter-directory-and-clean-up
          (lambda _
            (chdir "pbtranscript-tofu/pbtranscript/")
            ;; Delete clutter
            (delete-file-recursively "dist/")
            (delete-file-recursively "build/")
            (delete-file-recursively "setuptools_cython-0.2.1-py2.6.egg/")
            (delete-file-recursively "pbtools.pbtranscript.egg-info")
            (delete-file "Cython-0.20.1.tar.gz")
            (delete-file "setuptools_cython-0.2.1-py2.7.egg")
            (delete-file "setuptools_cython-0.2.1.tar.gz")
            (delete-file "setup.cfg")
            (for-each delete-file
                      (find-files "." "\\.so$"))
            ;; files should be writable for install phase
            (for-each (lambda (f) (chmod f #o755))
                      (find-files "." "\\.py$")))
          %standard-phases)))
      (inputs
       `(("python-cython" ,python2-cython)
         ("python-numpy" ,python2-numpy)
         ("python-bx-python" ,python2-bx-python)
         ("python-networkx" ,python2-networkx)
         ("python-scipy" ,python2-scipy)
         ("python-pbcore" ,python2-pbcore)))
      (native-inputs
       `(("python-nose" ,python2-nose)
         ("python-setuptools" ,python2-setuptools)))
      (home-page "https://github.com/PacificBiosciences/cDNA_primer")
      (synopsis "Analyze transcriptome data generated with the Iso-Seq protocol")
      (description
       "pbtranscript-tofu contains scripts to analyze transcriptome data
generated using the PacBio Iso-Seq protocol.")
      (license license:bsd-3))))

(define-public prodigal
  (package
    (name "prodigal")
    (version "2.6.2")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/hyattpd/Prodigal/archive/v"
                    version ".tar.gz"))
              (file-name (string-append name "-" version ".tar.gz"))
              (sha256
               (base32
                "0m8sb0fg6lmxrlpzna0am6svbnlmd3dckrhgzxxgb3gxr5fyj284"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ;no check target
       #:make-flags (list (string-append "INSTALLDIR="
                                         (assoc-ref %outputs "out")
                                         "/bin"))
       #:phases
       (modify-phases %standard-phases
         (delete 'configure))))
    (home-page "http://prodigal.ornl.gov")
    (synopsis "Protein-coding gene prediction for Archaea and Bacteria")
    (description
     "Prodigal runs smoothly on finished genomes, draft genomes, and
metagenomes, providing gene predictions in GFF3, Genbank, or Sequin table
format.  It runs quickly, in an unsupervised fashion, handles gaps, handles
partial genes, and identifies translation initiation sites.")
    (license license:gpl3+)))

(define-public rsem
  (package
    (name "rsem")
    (version "1.2.20")
    (source
     (origin
       (method url-fetch)
       (uri
        (string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-"
                       version ".tar.gz"))
       (sha256
        (base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q"))
       (patches (list (search-patch "rsem-makefile.patch")))
       (modules '((guix build utils)))
       (snippet
        '(begin
           ;; remove bundled copy of boost
           (delete-file-recursively "boost")
           #t))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ;no "check" target
       #:phases
       (modify-phases %standard-phases
         ;; No "configure" script.
         ;; Do not build bundled samtools library.
         (replace 'configure
                  (lambda _
                    (substitute* "Makefile"
                      (("^all : sam/libbam.a") "all : "))
                    #t))
         (replace 'install
                  (lambda* (#:key outputs #:allow-other-keys)
                    (let* ((out (string-append (assoc-ref outputs "out")))
                           (bin (string-append out "/bin/"))
                           (perl (string-append out "/lib/perl5/site_perl")))
                      (mkdir-p bin)
                      (mkdir-p perl)
                      (for-each (lambda (file)
                                  (copy-file file
                                             (string-append bin (basename file))))
                                (find-files "." "rsem-.*"))
                      (copy-file "rsem_perl_utils.pm"
                                 (string-append perl "/rsem_perl_utils.pm")))
                    #t))
         (add-after
          'install 'wrap-program
          (lambda* (#:key outputs #:allow-other-keys)
            (let ((out (assoc-ref outputs "out")))
              (for-each (lambda (prog)
                          (wrap-program (string-append out "/bin/" prog)
                            `("PERL5LIB" ":" prefix
                              (,(string-append out "/lib/perl5/site_perl")))))
                        '("rsem-plot-transcript-wiggles"
                          "rsem-calculate-expression"
                          "rsem-generate-ngvector"
                          "rsem-run-ebseq"
                          "rsem-prepare-reference")))
            #t)))))
    (inputs
     `(("boost" ,boost)
       ("ncurses" ,ncurses)
       ("r" ,r)
       ("perl" ,perl)
       ("samtools" ,samtools-0.1)
       ("zlib" ,zlib)))
    (home-page "http://deweylab.biostat.wisc.edu/rsem/")
    (synopsis "Estimate gene expression levels from RNA-Seq data")
    (description
     "RSEM is a software package for estimating gene and isoform expression
levels from RNA-Seq data.  The RSEM package provides a user-friendly
interface, supports threads for parallel computation of the EM algorithm,
single-end and paired-end read data, quality scores, variable-length reads and
RSPD estimation.  In addition, it provides posterior mean and 95% credibility
interval estimates for expression levels.  For visualization, it can generate
BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.")
    (license license:gpl3+)))

(define-public rseqc
  (package
    (name "rseqc")
    (version "2.6.1")
    (source
     (origin
       (method url-fetch)
       (uri
        (string-append "mirror://sourceforge/rseqc/"
                       version "/RSeQC-" version ".tar.gz"))
       (sha256
        (base32 "15ly0254yi032qzkdplg00q144qfdsd986gh62829rl5bkxhj330"))
       (modules '((guix build utils)))
       (snippet
        '(begin
           ;; remove bundled copy of pysam
           (delete-file-recursively "lib/pysam")
           (substitute* "setup.py"
             ;; remove dependency on outdated "distribute" module
             (("^from distribute_setup import use_setuptools") "")
             (("^use_setuptools\\(\\)") "")
             ;; do not use bundled copy of pysam
             (("^have_pysam = False") "have_pysam = True"))))))
    (build-system python-build-system)
    (arguments `(#:python ,python-2))
    (inputs
     `(("python-cython" ,python2-cython)
       ("python-pysam" ,python2-pysam)
       ("python-numpy" ,python2-numpy)
       ("python-setuptools" ,python2-setuptools)
       ("zlib" ,zlib)))
    (native-inputs
     `(("python-nose" ,python2-nose)))
    (home-page "http://rseqc.sourceforge.net/")
    (synopsis "RNA-seq quality control package")
    (description
     "RSeQC provides a number of modules that can comprehensively evaluate
high throughput sequence data, especially RNA-seq data.  Some basic modules
inspect sequence quality, nucleotide composition bias, PCR bias and GC bias,
while RNA-seq specific modules evaluate sequencing saturation, mapped reads
distribution, coverage uniformity, strand specificity, etc.")
    (license license:gpl3+)))

(define-public samtools
  (package
    (name "samtools")
    (version "1.2")
    (source
     (origin
       (method url-fetch)
       (uri
        (string-append "mirror://sourceforge/samtools/"
                       version "/samtools-" version ".tar.bz2"))
       (sha256
        (base32
         "1akdqb685pk9xk1nb6sa9aq8xssjjhvvc06kp4cpdqvz2157l3j2"))))
    (build-system gnu-build-system)
    (arguments
     `(;; There are 87 test failures when building on non-64-bit architectures
       ;; due to invalid test data.  This has since been fixed upstream (see
       ;; <https://github.com/samtools/samtools/pull/307>), but as there has
       ;; not been a new release we disable the tests for all non-64-bit
       ;; systems.
       #:tests? ,(string=? (or (%current-system) (%current-target-system))
                           "x86_64-linux")
       #:modules ((ice-9 ftw)
                  (ice-9 regex)
                  (guix build gnu-build-system)
                  (guix build utils))
       #:make-flags (list "LIBCURSES=-lncurses"
                          (string-append "prefix=" (assoc-ref %outputs "out")))
       #:phases
       (alist-cons-after
        'unpack
        'patch-tests
        (lambda* (#:key inputs #:allow-other-keys)
          (let ((bash (assoc-ref inputs "bash")))
            (substitute* "test/test.pl"
              ;; The test script calls out to /bin/bash
              (("/bin/bash")
               (string-append bash "/bin/bash"))
              ;; There are two failing tests upstream relating to the "stats"
              ;; subcommand in test_usage_subcommand ("did not have Usage"
              ;; and "usage did not mention samtools stats"), so we disable
              ;; them.
              (("(test_usage_subcommand\\(.*\\);)" cmd)
               (string-append "unless ($subcommand eq 'stats') {" cmd "};")))))
        (alist-cons-after
         'install 'install-library
         (lambda* (#:key outputs #:allow-other-keys)
           (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
             (mkdir-p lib)
             (copy-file "libbam.a" (string-append lib "/libbam.a"))))
         (alist-cons-after
          'install 'install-headers
          (lambda* (#:key outputs #:allow-other-keys)
            (let ((include (string-append (assoc-ref outputs "out")
                                          "/include/samtools/")))
              (mkdir-p include)
              (for-each (lambda (file)
                          (copy-file file (string-append include
                                                         (basename file))))
                        (scandir "." (lambda (name) (string-match "\\.h$" name))))
              #t))
          (alist-delete 'configure %standard-phases))))))
    (native-inputs `(("pkg-config" ,pkg-config)))
    (inputs `(("ncurses" ,ncurses)
              ("perl" ,perl)
              ("python" ,python)
              ("zlib" ,zlib)))
    (home-page "http://samtools.sourceforge.net")
    (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments")
    (description
     "Samtools implements various utilities for post-processing nucleotide
sequence alignments in the SAM, BAM, and CRAM formats, including indexing,
variant calling (in conjunction with bcftools), and a simple alignment
viewer.")
    (license license:expat)))

(define-public samtools-0.1
  ;; This is the most recent version of the 0.1 line of samtools.  The input
  ;; and output formats differ greatly from that used and produced by samtools
  ;; 1.x and is still used in many bioinformatics pipelines.
  (package (inherit samtools)
    (version "0.1.19")
    (source
     (origin
       (method url-fetch)
       (uri
        (string-append "mirror://sourceforge/samtools/"
                       version "/samtools-" version ".tar.bz2"))
       (sha256
        (base32 "1m33xsfwz0s8qi45lylagfllqg7fphf4dr0780rsvw75av9wk06h"))))
    (arguments
     (substitute-keyword-arguments (package-arguments samtools)
       ((#:tests? tests) #f) ;no "check" target
       ((#:phases phases)
        `(modify-phases ,phases
           (replace 'install
                    (lambda* (#:key outputs #:allow-other-keys)
                      (let ((bin (string-append
                                  (assoc-ref outputs "out") "/bin")))
                        (mkdir-p bin)
                        (copy-file "samtools"
                                   (string-append bin "/samtools")))))
           (delete 'patch-tests)))))))

(define-public ngs-sdk
  (package
    (name "ngs-sdk")
    (version "1.1.1")
    (source
     (origin
       (method url-fetch)
       (uri
        (string-append "https://github.com/ncbi/ngs/archive/"
                       version ".tar.gz"))
       (file-name (string-append name "-" version ".tar.gz"))
       (sha256
        (base32
         "1x58gpm574n0xmk2a98gmikbgycq78ia0bvnb42k5ck34fmd5v8y"))))
    (build-system gnu-build-system)
    (arguments
     `(#:parallel-build? #f ; not supported
       #:tests? #f ; no "check" target
       #:phases
       (alist-replace
        'configure
        (lambda* (#:key outputs #:allow-other-keys)
          (let ((out (assoc-ref outputs "out")))
            ;; The 'configure' script doesn't recognize things like
            ;; '--enable-fast-install'.
            (zero? (system* "./configure"
                            (string-append "--build-prefix=" (getcwd) "/build")
                            (string-append "--prefix=" out)))))
        (alist-cons-after
         'unpack 'enter-dir
         (lambda _ (chdir "ngs-sdk") #t)
         %standard-phases))))
    (native-inputs `(("perl" ,perl)))
    (home-page "https://github.com/ncbi/ngs")
    (synopsis "API for accessing Next Generation Sequencing data")
    (description
     "NGS is a domain-specific API for accessing reads, alignments and pileups
produced from Next Generation Sequencing.  The API itself is independent from
any particular back-end implementation, and supports use of multiple back-ends
simultaneously.")
    (license license:public-domain)))

(define-public ngs-java
  (package (inherit ngs-sdk)
    (name "ngs-java")
    (arguments
     `(,@(substitute-keyword-arguments
             `(#:modules ((guix build gnu-build-system)
                          (guix build utils)
                          (srfi srfi-1)
                          (srfi srfi-26))
                         ,@(package-arguments ngs-sdk))
           ((#:phases phases)
            `(alist-cons-after
              'enter-dir 'fix-java-symlink-installation
              (lambda _
                ;; Only replace the version suffix, not the version number in
                ;; the directory name.  Reported here:
                ;; https://github.com/ncbi/ngs/pull/4
                (substitute* "Makefile.java"
                  (((string-append "\\$\\(subst "
                                   "(\\$\\(VERSION[^\\)]*\\)),"
                                   "(\\$\\([^\\)]+\\)),"
                                   "(\\$\\([^\\)]+\\)|\\$\\@)"
                                   "\\)")
                    _ pattern replacement target)
                   (string-append "$(patsubst "
                                  "%" pattern ","
                                  "%" replacement ","
                                  target ")"))))
              (alist-replace
               'enter-dir (lambda _ (chdir "ngs-java") #t)
               ,phases))))))
    (inputs
     `(("jdk" ,icedtea6 "jdk")
       ("ngs-sdk" ,ngs-sdk)))
    (synopsis "Java bindings for NGS SDK")))

(define-public ncbi-vdb
  (package
    (name "ncbi-vdb")
    (version "2.4.5-5")
    (source
     (origin
       (method url-fetch)
       (uri
        (string-append "https://github.com/ncbi/ncbi-vdb/archive/"
                       version ".tar.gz"))
       (file-name (string-append name "-" version ".tar.gz"))
       (sha256
        (base32
         "1cj8nk6if8sqagv20vx36v566fdvhcaadf0x1ycnbgql6chbs6vy"))))
    (build-system gnu-build-system)
    (arguments
     `(#:parallel-build? #f ; not supported
       #:tests? #f ; no "check" target
       #:phases
       (alist-replace
        'configure
        (lambda* (#:key inputs outputs #:allow-other-keys)
          (let ((out (assoc-ref outputs "out")))
            ;; Only replace the version suffix, not the version number in the
            ;; directory name; fixed in commit 4dbba5c6a809 (no release yet).
            (substitute* "setup/konfigure.perl"
              (((string-append "\\$\\(subst "
                               "(\\$\\(VERSION[^\\)]*\\)),"
                               "(\\$\\([^\\)]+\\)),"
                               "(\\$\\([^\\)]+\\)|\\$\\@)"
                               "\\)")
                _ pattern replacement target)
               (string-append "$(patsubst "
                              "%" pattern ","
                              "%" replacement ","
                              target ")")))

            ;; Override include path for libmagic
            (substitute* "setup/package.prl"
              (("name => 'magic', Include => '/usr/include'")
               (string-append "name=> 'magic', Include => '"
                              (assoc-ref inputs "libmagic")
                              "/include" "'")))

            ;; Install kdf5 library (needed by sra-tools)
            (substitute* "build/Makefile.install"
              (("LIBRARIES_TO_INSTALL =")
               "LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)"))

            ;; The 'configure' script doesn't recognize things like
            ;; '--enable-fast-install'.
            (zero? (system*
                    "./configure"
                    (string-append "--build-prefix=" (getcwd) "/build")
                    (string-append "--prefix=" (assoc-ref outputs "out"))
                    (string-append "--debug")
                    (string-append "--with-xml2-prefix="
                                   (assoc-ref inputs "libxml2"))
                    (string-append "--with-ngs-sdk-prefix="
                                   (assoc-ref inputs "ngs-sdk"))
                    (string-append "--with-ngs-java-prefix="
                                   (assoc-ref inputs "ngs-java"))
                    (string-append "--with-hdf5-prefix="
                                   (assoc-ref inputs "hdf5"))))))
        (alist-cons-after
         'install 'install-interfaces
         (lambda* (#:key outputs #:allow-other-keys)
           ;; Install interface libraries.  On i686 the interface libraries
           ;; are installed to "linux/gcc/i386", so we need to use the Linux
           ;; architecture name ("i386") instead of the target system prefix
           ;; ("i686").
           (mkdir (string-append (assoc-ref outputs "out") "/ilib"))
           (copy-recursively (string-append "build/ncbi-vdb/linux/gcc/"
                                            ,(system->linux-architecture
                                              (or (%current-target-system)
                                                  (%current-system)))
                                            "/rel/ilib")
                             (string-append (assoc-ref outputs "out")
                                            "/ilib"))
           ;; Install interface headers
           (copy-recursively "interfaces"
                             (string-append (assoc-ref outputs "out")
                                            "/include")))
         %standard-phases))))
    (inputs
     `(("libxml2" ,libxml2)
       ("ngs-sdk" ,ngs-sdk)
       ("ngs-java" ,ngs-java)
       ("libmagic" ,file)
       ("hdf5" ,hdf5)))
    (native-inputs `(("perl" ,perl)))
    (home-page "https://github.com/ncbi/ncbi-vdb")
    (synopsis "Database engine for genetic information")
    (description
     "The NCBI-VDB library implements a highly compressed columnar data
warehousing engine that is most often used to store genetic information.
Databases are stored in a portable image within the file system, and can be
accessed/downloaded on demand across HTTP.")
    (license license:public-domain)))

(define-public plink
  (package
    (name "plink")
    (version "1.07")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-"
             version "-src.zip"))
       (sha256
        (base32 "0as8gxm4pjyc8dxmm1sl873rrd7wn5qs0l29nqfnl31x8i467xaa"))
       (patches (list (search-patch "plink-1.07-unclobber-i.patch")))))
    (build-system gnu-build-system)
    (arguments
     '(#:tests? #f ;no "check" target
       #:make-flags (list (string-append "LIB_LAPACK="
                                         (assoc-ref %build-inputs "lapack")
                                         "/lib/liblapack.so")
                          "WITH_LAPACK=1"
                          "FORCE_DYNAMIC=1"
                          ;; disable phoning home
                          "WITH_WEBCHECK=")
       #:phases
       (modify-phases %standard-phases
         ;; no "configure" script
         (delete 'configure)
         (replace 'install
                  (lambda* (#:key outputs #:allow-other-keys)
                    (let ((bin (string-append (assoc-ref outputs "out")
                                              "/bin/")))
                      (mkdir-p bin)
                      (copy-file "plink" (string-append bin "plink"))
                      #t))))))
    (inputs
     `(("zlib" ,zlib)
       ("lapack" ,lapack)))
    (native-inputs
     `(("unzip" ,unzip)))
    (home-page "http://pngu.mgh.harvard.edu/~purcell/plink/")
    (synopsis "Whole genome association analysis toolset")
    (description
     "PLINK is a whole genome association analysis toolset, designed to
perform a range of basic, large-scale analyses in a computationally efficient
manner.  The focus of PLINK is purely on analysis of genotype/phenotype data,
so there is no support for steps prior to this (e.g. study design and
planning, generating genotype or CNV calls from raw data).  Through
integration with gPLINK and Haploview, there is some support for the
subsequent visualization, annotation and storage of results.")
    ;; Code is released under GPLv2, except for fisher.h, which is under
    ;; LGPLv2.1+
    (license (list license:gpl2 license:lgpl2.1+))))

(define-public preseq
  (package
    (name "preseq")
    (version "1.0.2")
    (source (origin
              (method url-fetch)
              (uri
               (string-append "http://smithlabresearch.org/downloads/preseq-"
                              version ".tar.bz2"))
              (sha256
               (base32 "0r7sw07p6nv8ygvc17gd78lisbw5336v3vhs86b5wv8mw3pwqksc"))
              (patches (list (search-patch "preseq-1.0.2-install-to-PREFIX.patch")
                             (search-patch "preseq-1.0.2-link-with-libbam.patch")))
              (modules '((guix build utils)))
              (snippet
               ;; Remove bundled samtools.
               '(delete-file-recursively "preseq-master/samtools"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ;no "check" target
       #:phases
       (modify-phases %standard-phases
         (add-after
          'unpack 'enter-dir
          (lambda _
            (chdir "preseq-master")
            #t))
         (add-after
          'enter-dir 'use-samtools-headers
          (lambda _
            (substitute* '("smithlab_cpp/SAM.cpp"
                           "smithlab_cpp/SAM.hpp")
              (("sam.h") "samtools/sam.h"))
            #t))
         (delete 'configure))
       #:make-flags (list (string-append "PREFIX="
                                         (assoc-ref %outputs "out"))
                          (string-append "LIBBAM="
                                         (assoc-ref %build-inputs "samtools")
                                         "/lib/libbam.a"))))
    (inputs
     `(("gsl" ,gsl)
       ("samtools" ,samtools-0.1)
       ("zlib" ,zlib)))
    (home-page "http://smithlabresearch.org/software/preseq/")
    (synopsis "Program for analyzing library complexity")
    (description
     "The preseq package is aimed at predicting and estimating the complexity
of a genomic sequencing library, equivalent to predicting and estimating the
number of redundant reads from a given sequencing depth and how many will be
expected from additional sequencing using an initial sequencing experiment.
The estimates can then be used to examine the utility of further sequencing,
optimize the sequencing depth, or to screen multiple libraries to avoid low
complexity samples.")
    (license license:gpl3+)))

(define-public sra-tools
  (package
    (name "sra-tools")
    (version "2.4.5-5")
    (source
     (origin
       (method url-fetch)
       (uri
        (string-append "https://github.com/ncbi/sra-tools/archive/"
                       version ".tar.gz"))
       (file-name (string-append name "-" version ".tar.gz"))
       (sha256
        (base32
         "11nrnvz7a012f4iryf0wiwrid0h111grsfxbxa9j51h3f2xbvgns"))))
    (build-system gnu-build-system)
    (arguments
     `(#:parallel-build? #f ; not supported
       #:tests? #f ; no "check" target
       #:phases
       (alist-replace
        'configure
        (lambda* (#:key inputs outputs #:allow-other-keys)
          ;; The build system expects a directory containing the sources and
          ;; raw build output of ncbi-vdb, including files that are not
          ;; installed.  Since we are building against an installed version of
          ;; ncbi-vdb, the following modifications are needed.
          (substitute* "setup/konfigure.perl"
            ;; Make the configure script look for the "ilib" directory of
            ;; "ncbi-vdb" without first checking for the existence of a
            ;; matching library in its "lib" directory.
            (("^            my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);")
             "my $f = File::Spec->catdir($ilibdir, $ilib);")
            ;; Look for interface libraries in ncbi-vdb's "ilib" directory.
            (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);")
             "my $ilibdir = File::Spec->catdir($dir, 'ilib');"))

          ;; The 'configure' script doesn't recognize things like
          ;; '--enable-fast-install'.
          (zero? (system*
                  "./configure"
                  (string-append "--build-prefix=" (getcwd) "/build")
                  (string-append "--prefix=" (assoc-ref outputs "out"))
                  (string-append "--debug")
                  (string-append "--with-fuse-prefix="
                                 (assoc-ref inputs "fuse"))
                  (string-append "--with-magic-prefix="
                                 (assoc-ref inputs "libmagic"))
                  ;; TODO: building with libxml2 fails with linker errors
                  ;; (string-append "--with-xml2-prefix="
                  ;;                (assoc-ref inputs "libxml2"))
                  (string-append "--with-ncbi-vdb-sources="
                                 (assoc-ref inputs "ncbi-vdb"))
                  (string-append "--with-ncbi-vdb-build="
                                 (assoc-ref inputs "ncbi-vdb"))
                  (string-append "--with-ngs-sdk-prefix="
                                 (assoc-ref inputs "ngs-sdk"))
                  (string-append "--with-hdf5-prefix="
                                 (assoc-ref inputs "hdf5")))))
        %standard-phases)))
    (native-inputs `(("perl" ,perl)))
    (inputs
     `(("ngs-sdk" ,ngs-sdk)
       ("ncbi-vdb" ,ncbi-vdb)
       ("libmagic" ,file)
       ("fuse" ,fuse)
       ("hdf5" ,hdf5)
       ("zlib" ,zlib)))
    (home-page "http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software")
    (synopsis "Tools and libraries for reading and writing sequencing data")
    (description
     "The SRA Toolkit from NCBI is a collection of tools and libraries for
reading of sequencing files from the Sequence Read Archive (SRA) database and
writing files into the .sra format.")
    (license license:public-domain)))

(define-public seqan
  (package
    (name "seqan")
    (version "1.4.2")
    (source (origin
              (method url-fetch)
              (uri (string-append "http://packages.seqan.de/seqan-library/"
                                  "seqan-library-" version ".tar.bz2"))
              (sha256
               (base32
                "05s3wrrwn50f81aklfm65i4a749zag1vr8z03k21xm0pdxy47yvp"))))
    ;; The documentation is 7.8MB and the includes are 3.6MB heavy, so it
    ;; makes sense to split the outputs.
    (outputs '("out" "doc"))
    (build-system trivial-build-system)
    (arguments
     `(#:modules ((guix build utils))
       #:builder
       (begin
         (use-modules (guix build utils))
         (let ((tar  (assoc-ref %build-inputs "tar"))
               (bzip (assoc-ref %build-inputs "bzip2"))
               (out  (assoc-ref %outputs "out"))
               (doc  (assoc-ref %outputs "doc")))
           (setenv "PATH" (string-append tar "/bin:" bzip "/bin"))
           (system* "tar" "xvf" (assoc-ref %build-inputs "source"))
           (chdir (string-append "seqan-library-" ,version))
           (copy-recursively "include" (string-append out "/include"))
           (copy-recursively "share"  (string-append doc "/share"))))))
    (native-inputs
     `(("source" ,source)
       ("tar" ,tar)
       ("bzip2" ,bzip2)))
    (home-page "http://www.seqan.de")
    (synopsis "Library for nucleotide sequence analysis")
    (description
     "SeqAn is a C++ library of efficient algorithms and data structures for
the analysis of sequences with the focus on biological data.  It contains
algorithms and data structures for string representation and their
manipulation, online and indexed string search, efficient I/O of
bioinformatics file formats, sequence alignment, and more.")
    (license license:bsd-3)))

(define-public star
  (package
    (name "star")
    (version "2.4.2a")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/alexdobin/STAR/archive/STAR_"
                    version ".tar.gz"))
              (sha256
               (base32
                "1c3rnm7r5l0kl3d04gl1g7938xqf1c2l0mla87rlplqg1hcns5mc"))
              (modules '((guix build utils)))
              (snippet
               '(substitute* "source/Makefile"
                  (("/bin/rm") "rm")))))
    (build-system gnu-build-system)
    (arguments
     '(#:tests? #f ;no check target
       #:make-flags '("STAR")
       #:phases
       (alist-cons-after
        'unpack 'enter-source-dir (lambda _ (chdir "source"))
        (alist-replace
         'install
         (lambda* (#:key outputs #:allow-other-keys)
           (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
             (mkdir-p bin)
             (copy-file "STAR" (string-append bin "STAR"))))
         (alist-delete
          'configure %standard-phases)))))
    (native-inputs
     `(("vim" ,vim))) ; for xxd
    (inputs
     `(("zlib" ,zlib)))
    (home-page "https://github.com/alexdobin/STAR")
    (synopsis "Universal RNA-seq aligner")
    (description
     "The Spliced Transcripts Alignment to a Reference (STAR) software is
based on a previously undescribed RNA-seq alignment algorithm that uses
sequential maximum mappable seed search in uncompressed suffix arrays followed
by seed clustering and stitching procedure.  In addition to unbiased de novo
detection of canonical junctions, STAR can discover non-canonical splices and
chimeric (fusion) transcripts, and is also capable of mapping full-length RNA
sequences.")
    ;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
    (license license:gpl3+)))

(define-public subread
  (package
    (name "subread")
    (version "1.4.6-p2")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "mirror://sourceforge/subread/subread-"
                    version "-source.tar.gz"))
              (sha256
               (base32
                "06sv9mpcsdj6p68y15d6gi70lca3lxmzk0dn61hg0kfsa7rxmsr3"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ;no "check" target
       #:make-flags '("-f" "Makefile.Linux")
       #:phases
       (alist-cons-after
        'unpack 'enter-dir
        (lambda _ (chdir "src") #t)
        (alist-replace
         'install
         (lambda* (#:key outputs #:allow-other-keys)
           (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
             (mkdir-p bin)
             (copy-recursively "../bin" bin)))
         ;; no "configure" script
         (alist-delete 'configure %standard-phases)))))
    (inputs `(("zlib" ,zlib)))
    (home-page "http://bioinf.wehi.edu.au/subread-package/")
    (synopsis "Tool kit for processing next-gen sequencing data")
    (description
     "The subread package contains the following tools: subread aligner, a
general-purpose read aligner; subjunc aligner: detecting exon-exon junctions
and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic
features; exactSNP: a SNP caller that discovers SNPs by testing signals
against local background noises.")
    (license license:gpl3+)))

(define-public shogun
  (package
    (name "shogun")
    (version "4.0.0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "ftp://shogun-toolbox.org/shogun/releases/"
             (version-major+minor version)
             "/sources/shogun-" version ".tar.bz2"))
       (sha256
        (base32
         "159nlijnb7mnrv9za80wnm1shwvy45hgrqzn51hxy7gw4z6d6fdb"))
       (modules '((guix build utils)
                  (ice-9 rdelim)))
       (snippet
        '(begin
           ;; Remove non-free sources and files referencing them
           (for-each delete-file
                     (find-files "src/shogun/classifier/svm/"
                                 "SVMLight\\.(cpp|h)"))
           (for-each delete-file
                     (find-files "examples/undocumented/libshogun/"
                                 (string-append
                                  "(classifier_.*svmlight.*|"
                                  "evaluation_cross_validation_locked_comparison).cpp")))
           ;; Remove non-free functions.
           (define (delete-ifdefs file)
             (with-atomic-file-replacement file
               (lambda (in out)
                 (let loop ((line (read-line in 'concat))
                            (skipping? #f))
                   (if (eof-object? line)
                       #t
                       (let ((skip-next?
                              (or (and skipping?
                                       (not (string-prefix?
                                             "#endif //USE_SVMLIGHT" line)))
                                  (string-prefix?
                                   "#ifdef USE_SVMLIGHT" line))))
                         (when (or (not skipping?)
                                   (and skipping? (not skip-next?)))
                           (display line out))
                         (loop (read-line in 'concat) skip-next?)))))))
           (for-each delete-ifdefs (find-files "src/shogun/kernel/"
                                               "^Kernel\\.(cpp|h)"))))))
    (build-system cmake-build-system)
    (arguments
     '(#:tests? #f ;no check target
       #:phases
       (alist-cons-after
        'unpack 'delete-broken-symlinks
        (lambda _
          (for-each delete-file '("applications/arts/data"
                                  "applications/asp/data"
                                  "applications/easysvm/data"
                                  "applications/msplicer/data"
                                  "applications/ocr/data"
                                  "examples/documented/data"
                                  "examples/documented/matlab_static"
                                  "examples/documented/octave_static"
                                  "examples/undocumented/data"
                                  "examples/undocumented/matlab_static"
                                  "examples/undocumented/octave_static"
                                  "tests/integration/data"
                                  "tests/integration/matlab_static"
                                  "tests/integration/octave_static"
                                  "tests/integration/python_modular/tests"))
          #t)
        (alist-cons-after
         'unpack 'change-R-target-path
         (lambda* (#:key outputs #:allow-other-keys)
           (substitute* '("src/interfaces/r_modular/CMakeLists.txt"
                          "src/interfaces/r_static/CMakeLists.txt"
                          "examples/undocumented/r_modular/CMakeLists.txt")
             (("\\$\\{R_COMPONENT_LIB_PATH\\}")
              (string-append (assoc-ref outputs "out")
                             "/lib/R/library/")))
           #t)
         (alist-cons-after
          'unpack 'fix-octave-modules
          (lambda* (#:key outputs #:allow-other-keys)
            (substitute* '("src/interfaces/octave_modular/CMakeLists.txt"
                           "src/interfaces/octave_static/CMakeLists.txt")
              (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
               "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave"))

            ;; change target directory
            (substitute* "src/interfaces/octave_modular/CMakeLists.txt"
              (("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}")
               (string-append (assoc-ref outputs "out")
                              "/share/octave/packages")))
            #t)
          (alist-cons-before
           'build 'set-HOME
           ;; $HOME needs to be set at some point during the build phase
           (lambda _ (setenv "HOME" "/tmp") #t)
           %standard-phases))))
       #:configure-flags
       (list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE"
             "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT
             ;;"-DJavaModular=ON" ;requires unpackaged jblas
             ;;"-DRubyModular=ON" ;requires unpackaged ruby-narray
             ;;"-DPerlModular=ON" ;"FindPerlLibs" does not exist
             ;;"-DLuaModular=ON"  ;fails because lua doesn't build pkgconfig file
             "-DOctaveModular=ON"
             "-DOctaveStatic=ON"
             "-DPythonModular=ON"
             "-DPythonStatic=ON"
             "-DRModular=ON"
             "-DRStatic=ON"
             "-DCmdLineStatic=ON")))
    (inputs
     `(("python" ,python)
       ("numpy" ,python-numpy)
       ("r" ,r)
       ("octave" ,octave)
       ("swig" ,swig)
       ("hdf5" ,hdf5)
       ("atlas" ,atlas)
       ("arpack" ,arpack-ng)
       ("lapack" ,lapack)
       ("glpk" ,glpk)
       ("libxml2" ,libxml2)
       ("lzo" ,lzo)
       ("zlib" ,zlib)))
    (native-inputs
     `(("pkg-config" ,pkg-config)))
    (home-page "http://shogun-toolbox.org/")
    (synopsis "Machine learning toolbox")
    (description
     "The Shogun Machine learning toolbox provides a wide range of unified and
efficient Machine Learning (ML) methods.  The toolbox seamlessly allows to
combine multiple data representations, algorithm classes, and general purpose
tools.  This enables both rapid prototyping of data pipelines and extensibility
in terms of new algorithms.")
    (license license:gpl3+)))

(define-public vcftools
  (package
    (name "vcftools")
    (version "0.1.12b")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "mirror://sourceforge/vcftools/vcftools_"
                     version ".tar.gz"))
              (sha256
               (base32
                "148al9h7f8g8my2qdnpax51kdd2yjrivlx6frvakf4lz5r8j88wx"))))
    (build-system gnu-build-system)
    (arguments
     `(#:tests? #f ; no "check" target
       #:make-flags (list
                     "CFLAGS=-O2" ; override "-m64" flag
                     (string-append "PREFIX=" (assoc-ref %outputs "out"))
                     (string-append "MANDIR=" (assoc-ref %outputs "out")
                                    "/share/man/man1"))
       #:phases
       (alist-cons-after
        'unpack 'patch-manpage-install
        (lambda _
          (substitute* "Makefile"
            (("cp \\$\\{PREFIX\\}/cpp/vcftools.1") "cp ./cpp/vcftools.1")))
        (alist-delete 'configure %standard-phases))))
    (inputs
     `(("perl" ,perl)
       ("zlib" ,zlib)))
    (home-page "http://vcftools.sourceforge.net/")
    (synopsis "Tools for working with VCF files")
    (description
     "VCFtools is a program package designed for working with VCF files, such
as those generated by the 1000 Genomes Project.  The aim of VCFtools is to
provide easily accessible methods for working with complex genetic variation
data in the form of VCF files.")
    ;; The license is declared as LGPLv3 in the README and
    ;; at http://vcftools.sourceforge.net/license.html
    (license license:lgpl3)))