;; 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 ldc)
#: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 "2.10rc5-" (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)
))
(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 genenetwork3
(let ((commit "1538ffd33af19e6ac922b4ee85fe701408968dfd"))
(package
(name "genenetwork3")
(version (string-append "2.10rc5-" (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
`( ;; 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)
;; 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-pyyaml" ,python-pyyaml)
("python-jinja2" ,python-jinja2)
("python-pandas" ,python-pandas)
("python-passlib" ,python-passlib)
("python-requests" ,python-requests)
("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+))))
