path: root/gn/packages/bioinformatics.scm

;; Bioinformatics module

(define-module (gn 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 ruby)
  #:use-module (guix build-system r)
  #:use-module (guix build-system trivial)
  #:use-module (gnu packages)
  #:use-module (gnu packages algebra)
  #:use-module (gnu packages base)
  #:use-module (gnu packages bioinformatics)
  #:use-module (gnu packages boost)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages databases)
  #:use-module (gnu packages cpio)
  #:use-module (gnu packages file)
  #:use-module (gnu packages gcc)
  #:use-module (gnu packages graphviz)
  #: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 ruby)
  #:use-module (gnu packages statistics)
  #: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)
  #:use-module (gnu packages bootstrap)
  #:use-module (gn packages python)
  #:use-module (srfi srfi-1))

(define-public my-deploy
  (package
    (name "my-deploy")
    (version "0.0.1")
    (source #f)
    (build-system trivial-build-system)
    (arguments
     `(#:guile ,%bootstrap-guile
       #:modules ((guix build utils))
       #:builder
       (let* ((out  (assoc-ref %outputs "out"))
              (bash (assoc-ref %build-inputs "bash"))
              (foo  (string-append out "/foo")))
         (begin
           (use-modules (guix build utils))
           (mkdir out)
           (call-with-output-file foo
             (lambda (p)
               (format p
                       "#!~a~%echo \"${GUIX_FOO} ${GUIX_BAR}\"~%"
                       bash)))
           (chmod foo #o777)
           ;; wrap-program uses `which' to find bash for the wrapper
           ;; shebang, but it can't know about the bootstrap bash in
           ;; the store, since it's not named "bash".  Help it out a
           ;; bit by providing a symlink it this package's output.
           (symlink bash (string-append out "/bash"))
           (setenv "PATH" out)
           (wrap-program foo `("GUIX_FOO" prefix ("hello")))
           (wrap-program foo `("GUIX_BAR" prefix ("world")))
           #t))))
    (inputs `(("bash" ,(search-bootstrap-binary "bash"
                                                (%current-system)))))

    (home-page #f)
    (synopsis #f)
    (description #f)
    (license #f)))

(define-public r-wgcna
(package
  (name "r-wgcna")
  (version "1.48")
  (source
    (origin
      (method url-fetch)
      (uri (cran-uri "WGCNA" version))
      (sha256
        (base32
          "18yl2v3s279saq318vd5hlwnqfm89rxmjjji778d2d26vviaf6bn"))))
  (properties `((upstream-name . "WGCNA")))
  (build-system r-build-system)
  ;; (propagated-inputs
    ;; `( ;; ("r-annotationdbi" ,r-annotationdbi)
       ;; ("r-doparallel" ,r-doparallel)
       ;; ("r-dynamictreecut" ,r-dynamictreecut)
       ;; ("r-fastcluster" ,r-fastcluster)
       ;; ("r-foreach" ,r-foreach)
       ;; ("r-go.db" ,r-go.db)
       ;; ("r-grdevices" ,r-grdevices)
       ;; ("r-hmisc" ,r-hmisc)
       ;; ("r-impute" ,r-impute)
       ;; ("r-matrixstats" ,r-matrixstats)
       ;; ("r-parallel" ,r-parallel)
       ;; ("r-preprocesscore" ,r-preprocesscore)
       ;; ("r-splines" ,r-splines)
       ;; ("r-stats" ,r-stats)
       ;; ("r-survival" ,r-survival)
       ;; ("r-utils" ,r-utils)))
  (home-page
    "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
  (synopsis
    "Weighted Correlation Network Analysis")
  (description
    "Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data.  Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits.  Also includes a number of utility functions for data manipulation and visualization.")
  (license license:gpl2+)))

(define-public qtlreaper
  (package
    (name "qtlreaper")
    (version "1.1.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "mirror://sourceforge/qtlreaper/qtlreaper-" version ".tar.gz"
             ;; "http://downloads.sourceforge.net/project/qtlreaper/qtlreaper/1.1.1/qtlreaper-1.1.1.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fqtlreaper%2Ffiles%2Flatest%2Fdownload&ts=1358975786&use_mirror=iweb"))
             ))
       (file-name (string-append name "-" version ".tar.gz"))
       (sha256
        (base32
         "0rbf030940nbbbkggdq2dxiy3c0jv8l4y3vvyfxhqimgj0qv3l1x"))))
    (build-system python-build-system)
    ;; (native-inputs
    ;; `(("python-setuptools" ,python-setuptools)))
    (arguments
     `(#:python ,python-2
       #:tests? #f))   ; no 'setup.py test'
    (home-page "http://qtlreaper.sourceforge.net/")
    (synopsis "Tool for scanning expression data for QTLs")
    (description
     "It is essentially the batch-oriented version of WebQTL. It
requires, as input, expression data from members of a set of
recombinant inbred lines and genotype information for the same
lines.  It searches for an association between each expression trait
and all genotypes and evaluates that association by a permutation
test.  For the permutation test, it performs only as many permutations
as are necessary to define the empirical P-value to a reasonable
precision. It also performs bootstrap resampling to estimate the
confidence region for the location of a putative QTL.")
    (license license:gpl2)))

(define-public plink2
  (package
    (name "plink2")
    (version "1.90b3")
    (source
     (origin
      (method url-fetch)
      ;; https://github.com/chrchang/plink-ng/archive/v1.90b3.tar.gz
       (uri (string-append
             "https://github.com/chrchang/plink-ng/archive/v"
             version ".tar.gz"))
       (sha256
        (base32 "03fzib1al5qkr9vxv63wxmv6y2pfb1rmir0h8jpi72r87hczqjig"))
       (patches (list (search-patch "plink-ng-Makefile-zlib.patch")))))
    (build-system gnu-build-system)
    (arguments
     '(#:tests? #f ;no "check" target
       #:phases
       (modify-phases %standard-phases
        (delete 'configure)
        (replace 'build
                 (lambda _
                   (zero? (system* "make" "-f" "Makefile.std"))
                   ))                 
        (replace 'install
                  (lambda* (#:key outputs #:allow-other-keys)
                    (let ((bin (string-append (assoc-ref outputs "out")
                                              "/bin/")))
                      (install-file "plink2" bin)
                      #t))))))
    (inputs
     `(("zlib" ,zlib)
       ("openblas" ,openblas)
       ("atlas" ,atlas)
       ("lapack" ,lapack)
       ("gfortran" ,gfortran)
       ))
    (native-inputs
     `(("unzip" ,unzip)))
    (home-page "https://www.cog-genomics.org/plink2")
    (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 plink-ng
  (let ((commit "516d730f9"))
  (package
    (name "plink-ng")
    (version (string-append "1.90b3-" commit ))
    (source (origin
             (method git-fetch)
             (uri (git-reference
                   (url "https://github.com/chrchang/plink-ng.git")
                   (commit commit)))
             (file-name (string-append name "-" commit)) 
             (sha256
              (base32
               "0cv824wkdml9h9imsc30s2x3l8g65j44cpjbr1ydkk49g5qmf580"))
    (patches (list (search-patch "plink-ng-Makefile-zlib-git.patch")))))
    (build-system gnu-build-system)
    (arguments
     '(#:tests? #f ;no "check" target
       #:phases
       (modify-phases %standard-phases
        (delete 'configure)
        (replace 'build
                 (lambda _
                   (zero? (system* "make" "-f" "Makefile.std"))
                   ))                 
        (replace 'install
                  (lambda* (#:key outputs #:allow-other-keys)
                    (let ((bin (string-append (assoc-ref outputs "out")
                                              "/bin/")))
                      (install-file "plink2" bin)
                      #t))))))
    (inputs
     `(("zlib" ,zlib)
       ("openblas" ,openblas)
       ("atlas" ,atlas)
       ("lapack" ,lapack)
       ("gfortran" ,gfortran)
       ))
    (native-inputs
     `(("unzip" ,unzip)))
    (home-page "https://www.cog-genomics.org/plink2")
    (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.")
    (license license:gpl3+))))

(define-public gemma-git
  (let ((commit "2de4bfab3"))
  (package
    (name "gemma-git")
    (version (string-append "0.9.5-" commit ))
    (source (origin
             (method git-fetch)
             (uri (git-reference
                   (url "https://github.com/genenetwork/GEMMA.git")
                   (commit commit)))
             (file-name (string-append name "-" commit)) 
             (sha256
              (base32
               "1drffdgwbzgiw9sf55ghl3zjv58f8i9kfz0zys5mp6n06syp4ira"))))
    (inputs `(
              ("gsl" ,gsl)
              ("lapack" ,lapack)
              ("zlib" ,zlib)
              ))
    (build-system gnu-build-system)
    (arguments
     `(#:make-flags '(" FORCE_DYNAMIC=1")
       #:phases
        (modify-phases %standard-phases
         (delete 'configure)
         (add-before 'build 'bin-mkdir
                     (lambda _
                       (mkdir-p "bin")
                       ))
         (replace 'install
                  (lambda* (#:key outputs #:allow-other-keys)
                           (let ((out (assoc-ref outputs "out")))
                             (install-file "bin/gemma" (string-append out "/bin"))))))
       #:tests? #f))
    (home-page "")
    (synopsis "Tool for genome-wide efficient mixed model association")
    (description "GEMMA is the software implementing the Genome-wide
Efficient Mixed Model Association algorithm for a standard linear
mixed model and some of its close relatives for genome-wide
association studies (GWAS).")
    (license license:gpl3))))


(define-public genenetwork1
  (let ((commit "d622c803b"))
  (package
    (name "genenetwork1")
    (version (string-append "1.0-" commit ))
    (source (origin
             (method git-fetch)
             (uri (git-reference
                   (url "https://github.com/genenetwork/genenetwork.git")
                   ;; (url "https://github.com/pjotrp/genenetwork.git")
                   (commit commit)))
             (file-name (string-append name "-" commit)) 
             (sha256
              (base32
               "14fzfcm4vl20mlhxjslfa01i1nmxpk8lbxmfvpq6dyfc22ir62py"))))
    (propagated-inputs `(
              ("python" ,python-2) ;; probably superfluous
              ("r" ,r) 
    ))
    (inputs `(
              ;; http://spring211.uthsc.edu/gn/thirdparty.tbz
              ;; graphviz-2.22.2  htmlgen  json  numarray-1.5.2  piddle  PIL  pp-1.5.7  pyx  pyXLWriter  svg
              ("mysql" ,mysql)
              ("nginx" ,nginx)
              ("graphviz" ,graphviz)
              ; ("python2-jinja2" ,python2-jinja2)
              ; ("python2-sqlalchemy" ,python2-sqlalchemy)
              ; ("python2-setuptools" ,python2-setuptools)
              ; ("python2-scipy" ,python2-scipy)
              ;; looks like python-numarray is not needed
              ; ("python2-numpy" ,python2-numpy)
              ; ("python2-pandas" ,python2-pandas)
              ; ("python2-passlib" ,python2-passlib)
              ; ("python2-redis" ,python2-redis)
              ; ("python2-requests" ,python2-requests)
              ; ("python2-simplejson" ,python2-simplejson)
              ; ("python2-pyyaml" ,python2-pyyaml)
              ;; python-yolk is not needed
              ("python2-pil" ,python2-pil)
              ("python2-numarray" ,python2-numarray)
              ("plink" ,plink) ;; gn1
              ; ("r-qtl" ,r-qtl)
              ))
    (build-system python-build-system)
    (arguments
     `(#:python ,python-2
       #:tests? #f))   ; no 'setup.py test'
    (home-page "http://genenetwork.org/")
    (synopsis "Full genenetwork services")
    (description "Genenetwork installation sumo.")
    (license license:agpl3+))))

(define-public genenetwork2
  (let ((commit "9e9475053"))
  (package
    (name "genenetwork2")
    (version (string-append "2.0-" commit ))
    (source (origin
             (method git-fetch)
             (uri (git-reference
                   ;; (url "https://github.com/genenetwork/genenetwork2.git")
                   (url "https://github.com/pjotrp/genenetwork2.git")
                   (commit commit)))
             (file-name (string-append name "-" commit)) 
             (sha256
              (base32
               "09hvy9mf4dnmkb8qg49viffzrxk53m2kr4r955m84dxaa5pdrjhd"))))
    (propagated-inputs `(  ;; propagated for development purposes
              ("python" ,python-2) ;; probably superfluous
              ("r" ,r)
              ("redis" ,redis)
              ("mysql" ,mysql)
              ("gemma" ,gemma-git)
              ("plink2" ,plink-ng)
              ("nginx" ,nginx)
              ("python2-flask" ,python2-flask)
              ("python2-htmlgen-gn" ,python2-htmlgen-gn)
              ("python2-jinja2" ,python2-jinja2)
              ("python2-sqlalchemy" ,python2-sqlalchemy)
              ("python2-flask-sqlalchemy" ,python2-flask-sqlalchemy)
              ("python2-setuptools" ,python2-setuptools)
              ("python2-scipy" ,python2-scipy)
              ;; looks like python-numarray is not needed
              ("python2-mysqlclient" ,python2-mysqlclient)
              ("python2-numarray" ,python2-numarray)
              ("python2-numpy" ,python2-numpy)
              ("python2-pandas" ,python2-pandas)
              ("python2-parallel" ,python2-parallel)
              ("python2-passlib" ,python2-passlib)
              ("python2-piddle" ,python2-piddle)
              ("python2-redis" ,python2-redis)
              ("python2-requests" ,python2-requests)
              ("python2-rpy2" ,python2-rpy2)
              ("python2-scipy" ,python2-scipy)
              ("python2-simplejson" ,python2-simplejson)
              ("python2-pyyaml" ,python2-pyyaml)
              ("python2-xlsxwriter" ,python2-xlsxwriter)
              ;; python-yolk is not needed
              ("plink" ,plink) 
              ("qtlreaper" ,qtlreaper) 
              ("r-qtl" ,r-qtl)
              ))
    (build-system python-build-system)
    (arguments
     `(#:python ,python-2
       #:tests? #f))   ; no 'setup.py test'
    (home-page "http://genenetwork.org/")
    (synopsis "Full genenetwork services")
    (description "Genenetwork installation sumo.")
    (license license:agpl3+))))

(define-public rdmd
  (let ((commit "4dba6877c481c1a911a7d50714da8fbd80022f0e"))
    (package
      (name "rdmd")
      (version "20160217")
      (source (origin
                (method git-fetch)
                (uri (git-reference
                      (url "https://github.com/D-Programming-Language/tools.git")
                      (commit commit)))
                (file-name (string-append name "-" commit)) 
                (sha256
                 (base32
                  "1pcx5lyqzrip86f4vv60x292rpvnwsq2hvl1znm9x9rn68f34m45"))))
      (build-system gnu-build-system)
      (arguments
       '(#:phases
         (modify-phases %standard-phases
           (delete 'configure)
           (delete 'check)
           (replace
            'build
            (lambda* _
              (zero? (system* "ldc2" "rdmd.d"))))
           (replace
            'install
            (lambda* (#:key outputs #:allow-other-keys)
              (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
                (mkdir-p bin)
                (copy-file "rdmd" (string-append bin "/rdmd"))))))))
      (native-inputs
       `(("gcc" ,gcc)
         ("ldc" ,ldc)))
      (home-page "https://github.com/D-Programming-Language/tools/")
      (synopsis "Tool for the D language which is used for compiling")
      (description
       "rdmd is a companion to the dmd compiler that simplifies the typical
edit-compile-link-run or edit-make-run cycle to a rapid edit-run cycle. Like
make and other tools, rdmd uses the relative dates of the files involved to
minimize the amount of work necessary. Unlike make, rdmd tracks dependencies
and freshness without requiring additional information from the user.")
      (license license:boost1.0))))

(define-public sambamba
  (package
    (name "sambamba")
    (version "0.5.9")
    (source (origin
              (method url-fetch)
              (uri (string-append
                    "https://github.com/lomereiter/sambamba/archive/v"
                    version ".tar.gz"))
              (file-name (string-append "sambamba-" version ".tar.gz"))
              (sha256
               (base32 "152zbg4m10ikr7xgk20c0nwqwrqvydmpc73p2c1fqmbhpk0l0ws6"))))
    (build-system gnu-build-system)
    (inputs
     `(("ldc" ,ldc)
       ;; These are currently included in "ldc".
       ;;("druntime-ldc" ,druntime-ldc)
       ;;("phobos2-ldc" ,phobos2-ldc)
       ("lz4" ,lz4)))
    (native-inputs
     `(("ldc" ,ldc)
       ;;("druntime-ldc" ,druntime-ldc)
       ;;("phobos2-ldc" ,phobos2-ldc)
       ("lz4" ,lz4)
       ("gcc" ,gcc)
       ("rdmd" ,rdmd)
       ("htslib-src"
        ,(origin
           (method url-fetch)
           (uri (string-append
                 "https://github.com/lomereiter/htslib/archive/0.2.0-rc10.tar.gz"))
           (file-name (string-append "htslib-0.2.0-rc10.tar.gz"))
           (sha256
            (base32 "1k6dlf6m8yayhcp7b4yisgw1xqdy1xg2xyrllss6ld0wg00hfcbs"))))
       ("biod-src"
        ,(origin
           (method git-fetch)
           (uri (git-reference
                 (url "https://github.com/biod/BioD.git")
                 (commit "7efdb8a2f7fdcd71c9ad9596be48d1262bb1bd5b")))
           (sha256
            (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf"))
           (file-name "biod")))))
    (arguments
     '(#:phases 
       (modify-phases %standard-phases
         (delete 'configure)
         (add-after 'unpack 'unpack-htslib-sources
           (lambda* (#:key inputs #:allow-other-keys)
             ;; Unfortunately, the current build compiles htslib statically
             ;; into the executable.  Instead of patching the build files
             ;; for Guix, this should be resolved on Sambamba upstream.  For
             ;; now, just extract the source code to the desired directory.
             (and (with-directory-excursion "htslib"
                    (zero? (system* "tar" "xvf" (assoc-ref inputs "htslib-src")
                                    "--strip-components=1")))
                  (zero? (system* "cp" "-R" (assoc-ref inputs "biod-src") "BioD")))))
         ;; Building a production-quality executable is done with a
         ;; non-default make target. Adding it with #:make-flags breaks
         ;; building tests.  Therefore, the default make got replaced by this.
         (replace
          'build
          (lambda* (#:key (make-flags '()) #:allow-other-keys)
            (zero? (system* "make" "sambamba-ldmd2-64" make-flags)))))))
    (home-page "https://github.com/lomereiter/sambamba")
    (synopsis "A tool for working with SAM and BAM files written in D.")
    (description
     "Sambamba is a high performance modern robust and fast tool (and
library), written in the D programming language, for working with SAM
and BAM files.  Current parallelised functionality is an important
subset of samtools functionality, including view, index, sort,
markdup, and depth.")
    (license license:gpl2+)))

(define-public picard
  (package
    (name "picard")
    (version "2.1.0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "https://github.com/broadinstitute/picard/archive/"
             version ".tar.gz"))
       (sha256
        (base32 ""))))
    (build-system gnu-build-system)
    (home-page "http://broadinstitute.github.io/picard/")
    (synopsis "A set of Java command line tools for manipulating high-throughput
sequencing data (HTS) data and formats")
    (description "Picard comprises Java-based command-line utilities that
manipulate SAM files, and a Java API (HTSJDK) for creating new programs that
read and write SAM files. Both SAM text format and SAM binary (BAM) format are
supported.")
    ;; The license is MIT.
    (license license:expat)
))

(define-public fastqc
  (package
    (name "fastqc")
    (version "0.11.4")
    (source
     (origin
       (method url-fetch)
       (uri (string-append
             "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v"
             version "_source.zip"))
       (sha256
        (base32 ""))))
    (build-system gnu-build-system)
    (arguments
     `(("perl" ,perl) ; Needed to run the java command.
       ("jdk" ,icedtea "jdk")))
    (native-inputs
     `(("ant" ,ant) ; TODO: Most Java packages need Ant, but in this case, IDK..
       ("jdk" ,icedtea "jdk")
       ;;("htsjdk" ,htsjdk) ; It is based on htsjdk, but it ships its own copy.
       ("unzip" ,unzip)))
    (home-page "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/")
    (synopsis "A quality control tool for high throughput sequence data")
    (description
     "FastQC aims to provide a QC report which can spot problems which originate either in the sequencer or in the starting library material. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.")
    (license license:gpl3+)))