;; Bioinformatics module (define-module (gn packages genenetwork) #: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 check) #:use-module (gnu packages databases) #:use-module (gnu packages cpio) #:use-module (gn packages elixir) #: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 dlang) #: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-crypto) #:use-module (gnu packages python) #:use-module (gnu packages python-web) #: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 bootstrap) #:use-module (gnu packages version-control) #:use-module (gn packages bioinformatics) #:use-module (gn packages gemma) #:use-module (gn packages javascript) #:use-module (gn packages phewas) #:use-module (gn packages python) #:use-module (gn packages statistics) #: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 gn-server (let ((md5 "93e745e9c")) (package (name "gn-server") (version "0.0.1") (source (origin (method url-fetch) (uri "http://files.genenetwork.org/raw_database/md5sum.txt") ; any old file (file-name (string-append name "-" md5)) (sha256 (base32 "1cnkiwid4h0nnf93rm647ji9vhfzjl23arp1xj374la7mmic9jqs")))) (build-system trivial-build-system) (native-inputs `(("unzip" ,unzip) ("source" ,source))) (inputs `(("sassc" ,sassc))) (propagated-inputs `(("python" ,python) ("elixir" ,elixir) ("mysql" ,mysql) ("gnu-make" ,gnu-make) ; needed for mysqlex )) (arguments `(#:modules ((guix build utils)) #:builder (begin (use-modules (guix build utils)) (let ((target (string-append (assoc-ref %outputs "out") "/share"))) (write target) (mkdir-p target) ; (copy-recursively (assoc-ref %build-inputs "source") target) #t)))) (home-page "http://github.com/genenetwork/gn_server/") (synopsis "GN REST server API") (description "REST Server") (license license:agpl3+)))) (define-public python2-qtlreaper (let ((commit "dd9c7fb2a9d5fa40b4054e1bcb7c57905d98d5f8")) (package (name "python2-qtlreaper") (version (string-append "1.1-gn2-" (string-take commit 7) )) (source (origin (method git-fetch) (uri (git-reference ;; (url "https://github.com/genenetwork/genenetwork2.git") (url "https://github.com/pjotrp/QTLreaper.git") (commit commit))) (file-name (string-append name "-" (string-take commit 7))) (sha256 (base32 "1ldcvyk8y8w6f4ci04hzx85sknd5a3h424p5bfi4fz32sm2p7fja")))) (build-system python-build-system) (arguments `(#:python ,python-2 #:tests? #f)) ; no 'setup.py test' really! (home-page "http://qtlreaper.sourceforge.net/") (synopsis "Scan expression data for QTLs") (description "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 python-qtlreaper (let ((commit "dd9c7fb2a9d5fa40b4054e1bcb7c57905d98d5f8")) (package (name "python-qtlreaper") (version (string-append "1.1-gn2-" (string-take commit 7) )) (source (origin (method git-fetch) (uri (git-reference ;; (url "https://github.com/genenetwork/genenetwork2.git") (url "https://github.com/pjotrp/QTLreaper.git") (commit commit))) (file-name (string-append name "-" (string-take commit 7))) (sha256 (base32 "1ldcvyk8y8w6f4ci04hzx85sknd5a3h424p5bfi4fz32sm2p7fja")))) (build-system python-build-system) (arguments `( #:phases (modify-phases %standard-phases (add-after 'unpack 'fix-tests (lambda* (#:key inputs #:allow-other-keys) (substitute* '("./test/example1.py" "./test/example2.py") (("/usr/bin/python") (which "python3")))))) #:tests? #f)) ; no 'setup.py test' really! (home-page "http://qtlreaper.sourceforge.net/") (synopsis "Scan expression data for QTLs") (description "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 genenetwork2 (let ((commit "1538ffd33af19e6ac922b4ee85fe701408968dfd")) (package (name "genenetwork2") (version (string-append "2.11-guix-" (string-take commit 7) )) (source (origin (method git-fetch) (uri (git-reference (url "https://pjotrp@gitlab.com/genenetwork/gn2_diet.git") ;; (url "https://github.com/genenetwork/genenetwork2_diet.git") (commit commit))) (file-name (string-append name "-" version)) (sha256 (base32 "0ji929xgzypyhchcfy9xa1sz04w322ibs2khc8s3qiddxjqdglrz")))) (propagated-inputs `( ;; propagated for development purposes ("python" ,python-2) ;; probably superfluous ("coreutils" ,coreutils) ("git" ,git) ("vim" ,vim) ("which" ,which) ("grep" ,grep) ("r" ,r) ("r-ctl" ,r-ctl) ("r-phewas" ,r-phewas) ("r-qtl" ,r-qtl) ("r-wgcna" ,r-wgcna) ("redis" ,redis) ("mysql" ,mysql) ("gemma" ,gemma-gn2-git) ("gemma-wrapper" ,gemma-wrapper) ("genenetwork2-files-small" ,genenetwork2-files-small) ("plink-ng-gn" ,plink-ng-gn) ("pylmm-gn2" ,pylmm-gn2) ("nginx" ,nginx) ("python2-flask" ,python2-flask) ("gunicorn" ,gunicorn) ("python2-cssselect" ,python2-cssselect) ("python2-elasticsearch" ,python2-elasticsearch) ("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) ("python2-lxml" ,python2-lxml) ("python2-mechanize" ,python2-mechanize) ("python2-mysqlclient" ,python2-mysqlclient) ("python2-numarray" ,python2-numarray) ("python2-numpy" ,python2-numpy) ("python2-pandas" ,python2-pandas) ("python2-parallel" ,python2-parallel) ("python2-parameterized" ,python2-parameterized) ("python2-passlib" ,python2-passlib) ("python2-piddle-gn" ,python2-piddle-gn) ("python2-redis" ,python2-redis) ("python2-requests" ,python2-requests) ("python2-pil1" ,python2-pil1) ; should move to pillow some day ("python2-requests" ,python2-requests) ("python2-rpy2" ,python2-rpy2) ("python2-scipy" ,python2-scipy) ("python2-simplejson" ,python2-simplejson) ("python2-pyyaml" ,python2-pyyaml) ("python2-unittest2" ,python2-unittest2) ("python2-xlsxwriter" ,python2-xlsxwriter) ("python2-qtlreaper" ,python2-qtlreaper) ("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher) ("javascript-cytoscape" ,javascript-cytoscape) ("javascript-panzoom" ,javascript-cytoscape-panzoom) ("javascript-qtip" ,javascript-cytoscape-qtip) )) (build-system python-build-system) (arguments `(#:python ,python-2 #:phases (modify-phases %standard-phases (delete 'reset-gzip-timestamps) (add-after 'unpack 'fix-paths-scripts (lambda* _ (substitute* "bin/genenetwork2" (("/usr/bin/env") (which "env")) (("python ") (string-append (which "python2") " ")) (("readlink") (which "readlink")) (("dirname") (which "dirname")) (("basename") (which "basename")) (("cat") (which "cat")) (("echo") (which "echo")) (("redis-server") (which "redis-server")) (("git") (which "git")) (("grep") (which "grep")) (("rm") (which "rm")) (("which") (which "which")) ; three wiches in a row! )#t)) (add-before 'install 'fix-paths (lambda* (#:key inputs #:allow-other-keys) (let* ( (datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2" )) (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis")) (plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2")) (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma")) ) (substitute* '("etc/default_settings.py") (("^GENENETWORK_FILES +=.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )) (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" )) (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" )) ) )))) #:tests? #f)) ; no 'setup.py test' (home-page "http://genenetwork.org/") (synopsis "Full genenetwork services") (description "Genenetwork installation sumo.") (license license:agpl3+)))) ;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip ;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x (define-public genenetwork2-files-small (let ((pfff "xx")) (package (name "genenetwork2-files-small") (version "1.0") (source (origin (method url-fetch) (uri "http://files.genenetwork.org/data_files/gn2_data_s-20160303-C9E672ECED1F51B915DE419B5B2C524E.tar.lz4") (file-name (string-append name "-" pfff)) (sha256 (base32 "058ymx3af6abdhdxyxj0i9qfvb6v7j091frjpp6jh4ahks7r23lj")))) (build-system trivial-build-system) (native-inputs `(("lz4" ,lz4) ("tar" ,tar) ("source" ,source))) (arguments `(#:modules ((guix build utils)) #:builder (let* ((out (assoc-ref %outputs "out")) (name "gn2_data_s") (tarfn (string-append name ".tar")) (targetdir (string-append out "/share/genenetwork2/")) ) (begin (use-modules (guix build utils)) (let ((source (assoc-ref %build-inputs "source")) (lz4unpack (string-append (assoc-ref %build-inputs "lz4") "/bin/lz4")) (tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar")) ) (and (zero? (system* lz4unpack source "-d" tarfn)) (zero? (system* tar "xf" tarfn)) (mkdir-p targetdir) (copy-recursively name targetdir) )))))) (home-page "http://genenetwork.org/") (synopsis "Small file archive to run on genenetwork") (description "Genenetwork genotype and mapping files.") (license license:agpl3+)))) (define-public genenetwork2-database-small (let ((md5 "93e745e9c")) (package (name "genenetwork2-database-small") (version "1.0") (source (origin (method url-fetch) (uri "http://files.genenetwork.org/raw_database/db_webqtl_s.zip") (file-name (string-append name "-" md5)) (sha256 (base32 "0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x")))) (build-system trivial-build-system) (native-inputs `(("unzip" ,unzip) ("source" ,source))) (arguments `(#:modules ((guix build utils)) #:builder (begin (use-modules (guix build utils)) (let ((source (assoc-ref %build-inputs "source")) (unzip (string-append (assoc-ref %build-inputs "unzip") "/bin/unzip")) ) (and (mkdir "db") (zero? (system* unzip source "-d" "db")) (chdir "db")))))) (home-page "http://genenetwork.org/") (synopsis "Small database to run on genenetwork") (description "Genenetwork installation + database.") (license license:agpl3+)))) (define-public python-reaper (let ((commit "63391333a6619771277bfffa9bd9d33811fa0d28")) (package (name "python-reaper") (version (string-append "0.0.1-" (string-take commit 7))) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/fredmanglis/reaper.git") (commit commit))) (sha256 (base32 "1rq2qn0vrqd8k676yy8drm0zxzkj065ywhxjl0j1n2r25zifay7r")))) (build-system python-build-system) (arguments `(#:tests? #f)) (home-page "https://github.com/fredmanglis/reaper") (synopsis "Parser for .geno files") (description "Parser for .geno files. It replaces the Python2 library written in C") (license license:agpl3+)))) (define-public genenetwork3 (let (;; (commit "1538ffd33af19e6ac922b4ee85fe701408968dfd") (commit "5bff4f49dffb4ac982d36cd0d39e0a9ec6bc66e9")) (package (name "genenetwork3") (version (string-append "2.10rc5-" (string-take commit 7) )) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/fredmanglis/genenetwork2.git") ;; (url "https://pjotrp@gitlab.com/genenetwork/gn2_diet.git") ;; (url "https://github.com/genenetwork/genenetwork2_diet.git") (commit commit))) (file-name (string-append name "-" version)) (sha256 (base32 "0klgjra2qisfzs8mk0s8vzdr190l4n56xcm66dk0asqs7zswi8di" ;; "0ji929xgzypyhchcfy9xa1sz04w322ibs2khc8s3qiddxjqdglrz" )))) (propagated-inputs ;; propagated for development purposes `( ;; Agnostic to Python ("r" ,r) ("git" ,git) ("vim" ,vim) ("grep" ,grep) ("which" ,which) ("r-ctl" ,r-ctl) ("r-qtl" ,r-qtl) ("redis" ,redis) ("mysql" ,mysql) ("nginx" ,nginx) ("r-wgcna" ,r-wgcna) ;; ("r-phewas" ,r-phewas) ("coreutils" ,coreutils) ("gemma" ,gemma-gn2-git) ("plink-ng-gn" ,plink-ng-gn) ("python-lxml" ,python-lxml) ;; used for the tests ("gemma-wrapper" ,gemma-wrapper) ("python-unittest" ,python-unittest2) ;; used for the tests ("python-parameterized" ,python-parameterized) ;; used for the tests ("genenetwork2-files-small" ,genenetwork2-files-small) ("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher) ("javascript-cytoscape" ,javascript-cytoscape) ("javascript-panzoom" ,javascript-cytoscape-panzoom) ("javascript-qtip" ,javascript-cytoscape-qtip) ;; With Python3 support ("gunicorn" ,gunicorn) ("python-rpy2" ,python-rpy2) ("python-flask" ,python-flask) ("python-scipy" ,python-scipy) ("python-numpy" ,python-numpy) ("python-redis" ,python-redis) ("python-scipy" ,python-scipy) ("python-reaper" ,python-reaper) ("python-pyyaml" ,python-pyyaml) ("python-jinja2" ,python-jinja2) ("python-pandas" ,python-pandas) ("python-htmlgen" ,python-htmlgen) ("python-passlib" ,python-passlib) ("python-wrapper" ,python-wrapper) ("python-requests" ,python-requests) ("python-cssselect" ,python-cssselect) ("python-sqlalchemy" ,python-sqlalchemy) ("python-setuptools" ,python-setuptools) ("python-simplejson" ,python-simplejson) ("python-xlsxwriter" ,python-xlsxwriter) ("python-mysqlclient" ,python-mysqlclient) ("python-elasticsearch" ,python-elasticsearch) ("python-flask-sqlalchemy" ,python-flask-sqlalchemy) ;; Without Python3 support ;; ("python-qtlreaper" ,python-qtlreaper) ;; Run as an external program ;; ("pylmm-gn2" ,pylmm-gn2) ;; To be run as an external python2 program ;; ("python2-pil1" ,python2-pil1) ; should move to pillow some day. Run as external python2 program ;; ("python2-numarray" ,python2-numarray) ;; Update gn2 code and drop this (IMPORTANT) ;; ("python2-piddle-gn" ,python2-piddle-gn) ;; Run as external python2 program ;; ("python2-htmlgen-gn" ,python2-htmlgen-gn) ;; pjotrp and zsloan to give directions ;; Removed packages ;; ("python2-mechanize" ,python2-mechanize) ;; ("python2-parallel" ,python2-parallel) )) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases (delete 'reset-gzip-timestamps) (add-after 'unpack 'fix-paths-scripts (lambda* _ (substitute* "bin/genenetwork2" (("/usr/bin/env") (which "env")) (("python ") (string-append (which "python") " ")) (("readlink") (which "readlink")) (("dirname") (which "dirname")) (("basename") (which "basename")) (("cat") (which "cat")) (("echo") (which "echo")) (("redis-server") (which "redis-server")) (("git") (which "git")) (("grep") (which "grep")) (("rm") (which "rm")) (("which") (which "which"))) #t)) (add-before 'install 'fix-paths (lambda* (#:key inputs #:allow-other-keys) (let* ((datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2" )) ;; (pylmmcmd ;; (string-append ;; (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis")) (plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2")) (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma"))) (substitute* '("etc/default_settings.py") (("^GENENETWORK_FILES +=.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )) (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" )) (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n"))))))) #:tests? #f)) ; no 'setup.py test' (home-page "http://genenetwork.org/") (synopsis "Full genenetwork services") (description "Genenetwork installation sumo.") (license license:agpl3+))))