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;; 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 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 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 `(
("python" ,python-2) ;; probably superfluous
("r" ,r)
))
(inputs `(
("mysql" ,mysql)
("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)
("python-xlsxwriter" ,python-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+))))