;; 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 gemma (let ((commit "2de4bfab3")) (package (name "gemma") (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 `( ("python" ,python-2) ;; probably superfluous ("r" ,r) )) (inputs `( ("mysql" ,mysql) ("gemma" ,gemma) ("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+))))