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  1. ;; Bioinformatics module

  2. 

  3. (define-module (gn packages bioinformatics)

  4.   #:use-module ((guix licenses) #:prefix license:)

  5.   #:use-module (guix packages)

  6.   #:use-module (guix utils)

  7.   #:use-module (guix download)

  8.   #:use-module (guix git-download)

  9.   #:use-module (guix build-system gnu)

  10.   #:use-module (guix build-system cmake)

  11.   #:use-module (guix build-system perl)

  12.   #:use-module (guix build-system python)

  13.   #:use-module (guix build-system ruby)

  14.   #:use-module (guix build-system r)

  15.   #:use-module (guix build-system trivial)

  16.   #:use-module (gnu packages)

  17.   #:use-module (gnu packages algebra)

  18.   #:use-module (gnu packages base)

  19.   #:use-module (gnu packages bioinformatics)

  20.   #:use-module (gnu packages boost)

  21.   #:use-module (gnu packages compression)

  22.   #:use-module (gnu packages databases)

  23.   #:use-module (gnu packages cpio)

  24.   #:use-module (gnu packages file)

  25.   #:use-module (gnu packages graphviz)

  26.   #:use-module (gnu packages java)

  27.   #:use-module (gnu packages linux)

  28.   #:use-module (gnu packages machine-learning)

  29.   #:use-module (gnu packages maths)

  30.   #:use-module (gnu packages ncurses)

  31.   #:use-module (gnu packages perl)

  32.   #:use-module (gnu packages pkg-config)

  33.   #:use-module (gnu packages popt)

  34.   #:use-module (gnu packages protobuf)

  35.   #:use-module (gnu packages python)

  36.   #:use-module (gnu packages ruby)

  37.   #:use-module (gnu packages statistics)

  38.   #:use-module (gnu packages tbb)

  39.   #:use-module (gnu packages textutils)

  40.   #:use-module (gnu packages vim)

  41.   #:use-module (gnu packages web)

  42.   #:use-module (gnu packages xml)

  43.   #:use-module (gnu packages zip)

  44.   #:use-module (gnu packages bootstrap)

  45.   #:use-module (gn packages python)

  46.   #:use-module (srfi srfi-1))

  47. 

  48. (define-public my-deploy

  49.   (package

  50.     (name "my-deploy")

  51.     (version "0.0.1")

  52.     (source #f)

  53.     (build-system trivial-build-system)

  54.     (arguments

  55.      `(#:guile ,%bootstrap-guile

  56.        #:modules ((guix build utils))

  57.        #:builder

  58.        (let* ((out  (assoc-ref %outputs "out"))

  59.               (bash (assoc-ref %build-inputs "bash"))

  60.               (foo  (string-append out "/foo")))

  61.          (begin

  62.            (use-modules (guix build utils))

  63.            (mkdir out)

  64.            (call-with-output-file foo

  65.              (lambda (p)

  66.                (format p

  67.                        "#!~a~%echo \"${GUIX_FOO} ${GUIX_BAR}\"~%"

  68.                        bash)))

  69.            (chmod foo #o777)

  70.            ;; wrap-program uses `which' to find bash for the wrapper

  71.            ;; shebang, but it can't know about the bootstrap bash in

  72.            ;; the store, since it's not named "bash".  Help it out a

  73.            ;; bit by providing a symlink it this package's output.

  74.            (symlink bash (string-append out "/bash"))

  75.            (setenv "PATH" out)

  76.            (wrap-program foo `("GUIX_FOO" prefix ("hello")))

  77.            (wrap-program foo `("GUIX_BAR" prefix ("world")))

  78.            #t))))

  79.     (inputs `(("bash" ,(search-bootstrap-binary "bash"

  80.                                                 (%current-system)))))

  81. 

  82.     (home-page #f)

  83.     (synopsis #f)

  84.     (description #f)

  85.     (license #f)))

  86. 

  87. (define-public r-wgcna

  88. (package

  89.   (name "r-wgcna")

  90.   (version "1.48")

  91.   (source

  92.     (origin

  93.       (method url-fetch)

  94.       (uri (cran-uri "WGCNA" version))

  95.       (sha256

  96.         (base32

  97.           "18yl2v3s279saq318vd5hlwnqfm89rxmjjji778d2d26vviaf6bn"))))

  98.   (properties `((upstream-name . "WGCNA")))

  99.   (build-system r-build-system)

  100.   ;; (propagated-inputs

  101.     ;; `( ;; ("r-annotationdbi" ,r-annotationdbi)

  102.        ;; ("r-doparallel" ,r-doparallel)

  103.        ;; ("r-dynamictreecut" ,r-dynamictreecut)

  104.        ;; ("r-fastcluster" ,r-fastcluster)

  105.        ;; ("r-foreach" ,r-foreach)

  106.        ;; ("r-go.db" ,r-go.db)

  107.        ;; ("r-grdevices" ,r-grdevices)

  108.        ;; ("r-hmisc" ,r-hmisc)

  109.        ;; ("r-impute" ,r-impute)

  110.        ;; ("r-matrixstats" ,r-matrixstats)

  111.        ;; ("r-parallel" ,r-parallel)

  112.        ;; ("r-preprocesscore" ,r-preprocesscore)

  113.        ;; ("r-splines" ,r-splines)

  114.        ;; ("r-stats" ,r-stats)

  115.        ;; ("r-survival" ,r-survival)

  116.        ;; ("r-utils" ,r-utils)))

  117.   (home-page

  118.     "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")

  119.   (synopsis

  120.     "Weighted Correlation Network Analysis")

  121.   (description

  122.     "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.")

  123.   (license license:gpl2+)))

  124. 

  125. (define-public qtlreaper

  126.   (package

  127.     (name "qtlreaper")

  128.     (version "1.1.1")

  129.     (source

  130.      (origin

  131.        (method url-fetch)

  132.        (uri (string-append

  133.              "mirror://sourceforge/qtlreaper/qtlreaper-" version ".tar.gz"

  134.              ;; "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"))

  135.              ))

  136.        (file-name (string-append name "-" version ".tar.gz"))

  137.        (sha256

  138.         (base32

  139.          "0rbf030940nbbbkggdq2dxiy3c0jv8l4y3vvyfxhqimgj0qv3l1x"))))

  140.     (build-system python-build-system)

  141.     ;; (native-inputs

  142.     ;; `(("python-setuptools" ,python-setuptools)))

  143.     (arguments

  144.      `(#:python ,python-2

  145.        #:tests? #f))   ; no 'setup.py test'

  146.     (home-page "http://qtlreaper.sourceforge.net/")

  147.     (synopsis "Tool for scanning expression data for QTLs")

  148.     (description

  149.      "It is essentially the batch-oriented version of WebQTL. It

  150. requires, as input, expression data from members of a set of

  151. recombinant inbred lines and genotype information for the same

  152. lines.  It searches for an association between each expression trait

  153. and all genotypes and evaluates that association by a permutation

  154. test.  For the permutation test, it performs only as many permutations

  155. as are necessary to define the empirical P-value to a reasonable

  156. precision. It also performs bootstrap resampling to estimate the

  157. confidence region for the location of a putative QTL.")

  158.     (license license:gpl2)))

  159. 

  160. (define-public plink2

  161.   (package

  162.     (name "plink2")

  163.     (version "1.90b3")

  164.     (source

  165.      (origin

  166.       (method url-fetch)

  167.       ;; https://github.com/chrchang/plink-ng/archive/v1.90b3.tar.gz

  168.        (uri (string-append

  169.              "https://github.com/chrchang/plink-ng/archive/v"

  170.              version ".tar.gz"))

  171.        (sha256

  172.         (base32 "03fzib1al5qkr9vxv63wxmv6y2pfb1rmir0h8jpi72r87hczqjig"))

  173.        (patches (list (search-patch "plink-ng-Makefile-zlib.patch")))))

  174.     (build-system gnu-build-system)

  175.     (arguments

  176.      '(#:tests? #t ;no "check" target

  177.        #:make-flags (list (string-append "LIB_LAPACK="

  178.                                          (assoc-ref %build-inputs "lapack")

  179.                                          "/lib/liblapack.so")

  180.                           "WITH_LAPACK=1"

  181.                           "FORCE_DYNAMIC=1"

  182.                           ;; disable phoning home

  183.                           "WITH_WEBCHECK=")

  184.        #:phases

  185.        (modify-phases %standard-phases

  186.         (delete 'configure)

  187.         (replace 'build

  188.                  (lambda _

  189.                    (system* "make" "-f" "Makefile.std")

  190.                    ))                 

  191.         (replace 'install

  192.                   (lambda* (#:key outputs #:allow-other-keys)

  193.                     (let ((bin (string-append (assoc-ref outputs "out")

  194.                                               "/bin/")))

  195.                       (install-file "plink" bin)

  196.                       #t))))))

  197.     (inputs

  198.      `(("zlib" ,zlib)

  199.        ("lapack" ,lapack)))

  200.     (native-inputs

  201.      `(("unzip" ,unzip)))

  202.     (home-page "https://www.cog-genomics.org/plink2")

  203.     (synopsis "Whole genome association analysis toolset")

  204.     (description

  205.      "PLINK is a whole genome association analysis toolset, designed to

  206. perform a range of basic, large-scale analyses in a computationally efficient

  207. manner.  The focus of PLINK is purely on analysis of genotype/phenotype data,

  208. so there is no support for steps prior to this (e.g. study design and

  209. planning, generating genotype or CNV calls from raw data).  Through

  210. integration with gPLINK and Haploview, there is some support for the

  211. subsequent visualization, annotation and storage of results.")

  212.     ;; Code is released under GPLv2, except for fisher.h, which is under

  213.     ;; LGPLv2.1+

  214.     (license (list license:gpl2 license:lgpl2.1+))))

  215. 

  216. (define-public gemma

  217.   (let ((commit "2de4bfab3"))

  218.   (package

  219.     (name "gemma")

  220.     (version (string-append "0.9.5-" commit ))

  221.     (source (origin

  222.              (method git-fetch)

  223.              (uri (git-reference

  224.                    (url "https://github.com/genenetwork/GEMMA.git")

  225.                    (commit commit)))

  226.              (file-name (string-append name "-" commit)) 

  227.              (sha256

  228.               (base32

  229.                "1drffdgwbzgiw9sf55ghl3zjv58f8i9kfz0zys5mp6n06syp4ira"))))

  230.     (inputs `(

  231.               ("gsl" ,gsl)

  232.               ("lapack" ,lapack)

  233.               ("zlib" ,zlib)

  234.               ))

  235.     (build-system gnu-build-system)

  236.     (arguments

  237.      `(#:make-flags '(" FORCE_DYNAMIC=1")

  238.        #:phases

  239.         (modify-phases %standard-phases

  240.          (delete 'configure)

  241.          (add-before 'build 'bin-mkdir

  242.                      (lambda _

  243.                        (mkdir-p "bin")

  244.                        ))

  245.          (replace 'install

  246.                   (lambda* (#:key outputs #:allow-other-keys)

  247.                            (let ((out (assoc-ref outputs "out")))

  248.                              (install-file "bin/gemma" (string-append out "/bin"))))))

  249.        #:tests? #f))

  250.     (home-page "")

  251.     (synopsis "Tool for genome-wide efficient mixed model association")

  252.     (description "GEMMA is the software implementing the Genome-wide

  253. Efficient Mixed Model Association algorithm for a standard linear

  254. mixed model and some of its close relatives for genome-wide

  255. association studies (GWAS).")

  256.     (license license:gpl3))))

  257. 

  258. 

  259. (define-public genenetwork1

  260.   (let ((commit "d622c803b"))

  261.   (package

  262.     (name "genenetwork1")

  263.     (version (string-append "1.0-" commit ))

  264.     (source (origin

  265.              (method git-fetch)

  266.              (uri (git-reference

  267.                    (url "https://github.com/genenetwork/genenetwork.git")

  268.                    ;; (url "https://github.com/pjotrp/genenetwork.git")

  269.                    (commit commit)))

  270.              (file-name (string-append name "-" commit)) 

  271.              (sha256

  272.               (base32

  273.                "14fzfcm4vl20mlhxjslfa01i1nmxpk8lbxmfvpq6dyfc22ir62py"))))

  274.     (propagated-inputs `(

  275.               ("python" ,python-2) ;; probably superfluous

  276.               ("r" ,r) 

  277.     ))

  278.     (inputs `(

  279.               ;; http://spring211.uthsc.edu/gn/thirdparty.tbz

  280.               ;; graphviz-2.22.2  htmlgen  json  numarray-1.5.2  piddle  PIL  pp-1.5.7  pyx  pyXLWriter  svg

  281.               ("mysql" ,mysql)

  282.               ("nginx" ,nginx)

  283.               ("graphviz" ,graphviz)

  284.               ; ("python2-jinja2" ,python2-jinja2)

  285.               ; ("python2-sqlalchemy" ,python2-sqlalchemy)

  286.               ; ("python2-setuptools" ,python2-setuptools)

  287.               ; ("python2-scipy" ,python2-scipy)

  288.               ;; looks like python-numarray is not needed

  289.               ; ("python2-numpy" ,python2-numpy)

  290.               ; ("python2-pandas" ,python2-pandas)

  291.               ; ("python2-passlib" ,python2-passlib)

  292.               ; ("python2-redis" ,python2-redis)

  293.               ; ("python2-requests" ,python2-requests)

  294.               ; ("python2-simplejson" ,python2-simplejson)

  295.               ; ("python2-pyyaml" ,python2-pyyaml)

  296.               ;; python-yolk is not needed

  297.               ("python2-pil" ,python2-pil)

  298.               ("python2-numarray" ,python2-numarray)

  299.               ("plink" ,plink) ;; gn1

  300.               ; ("r-qtl" ,r-qtl)

  301.               ))

  302.     (build-system python-build-system)

  303.     (arguments

  304.      `(#:python ,python-2

  305.        #:tests? #f))   ; no 'setup.py test'

  306.     (home-page "http://genenetwork.org/")

  307.     (synopsis "Full genenetwork services")

  308.     (description "Genenetwork installation sumo.")

  309.     (license license:agpl3+))))

  310. 

  311. (define-public genenetwork2

  312.   (let ((commit "9e9475053"))

  313.   (package

  314.     (name "genenetwork2")

  315.     (version (string-append "2.0-" commit ))

  316.     (source (origin

  317.              (method git-fetch)

  318.              (uri (git-reference

  319.                    ;; (url "https://github.com/genenetwork/genenetwork2.git")

  320.                    (url "https://github.com/pjotrp/genenetwork2.git")

  321.                    (commit commit)))

  322.              (file-name (string-append name "-" commit)) 

  323.              (sha256

  324.               (base32

  325.                "09hvy9mf4dnmkb8qg49viffzrxk53m2kr4r955m84dxaa5pdrjhd"))))

  326.     (propagated-inputs `(

  327.               ("python" ,python-2) ;; probably superfluous

  328.               ("r" ,r) 

  329.     ))

  330.     (inputs `(

  331.               ("mysql" ,mysql)

  332.               ("gemma" ,gemma)

  333.               ("nginx" ,nginx)

  334.               ("python2-flask" ,python2-flask)

  335.               ("python2-htmlgen-gn" ,python2-htmlgen-gn)

  336.               ("python2-jinja2" ,python2-jinja2)

  337.               ("python2-sqlalchemy" ,python2-sqlalchemy)

  338.               ("python2-flask-sqlalchemy" ,python2-flask-sqlalchemy)

  339.               ("python2-setuptools" ,python2-setuptools)

  340.               ("python2-scipy" ,python2-scipy)

  341.               ;; looks like python-numarray is not needed

  342.               ("python2-mysqlclient" ,python2-mysqlclient)

  343.               ("python2-numarray" ,python2-numarray)

  344.               ("python2-numpy" ,python2-numpy)

  345.               ("python2-pandas" ,python2-pandas)

  346.               ("python2-parallel" ,python2-parallel)

  347.               ("python2-passlib" ,python2-passlib)

  348.               ("python2-piddle" ,python2-piddle)

  349.               ("python2-redis" ,python2-redis)

  350.               ("python2-requests" ,python2-requests)

  351.               ("python2-rpy2" ,python2-rpy2)

  352.               ("python2-scipy" ,python2-scipy)

  353.               ("python2-simplejson" ,python2-simplejson)

  354.               ("python2-pyyaml" ,python2-pyyaml)

  355.               ("python-xlsxwriter" ,python-xlsxwriter)

  356.               ;; python-yolk is not needed

  357.               ("plink" ,plink) 

  358.               ("qtlreaper" ,qtlreaper) 

  359.               ("r-qtl" ,r-qtl)

  360.               ))

  361.     (build-system python-build-system)

  362.     (arguments

  363.      `(#:python ,python-2

  364.        #:tests? #f))   ; no 'setup.py test'

  365.     (home-page "http://genenetwork.org/")

  366.     (synopsis "Full genenetwork services")

  367.     (description "Genenetwork installation sumo.")

  368.     (license license:agpl3+))))