;; 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)
#:use-module (guix git-download)
#:use-module (guix build-system cargo)
#:use-module (guix build-system gnu)
#:use-module (guix build-system python)
#:use-module (guix build-system trivial)
#:use-module (guix build-system pyproject)
#:use-module (guix graph)
#:use-module (guix scripts graph)
#:use-module (guix store)
#:use-module (guix gexp)
#:use-module (guix packages)
#:use-module (gnu packages)
#:use-module (gnu packages base)
#:use-module (gnu packages certs)
#:use-module (gnu packages bioconductor)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages check)
#:use-module (gnu packages cran)
#:use-module (gnu packages crates-io)
#:use-module (gnu packages compression)
#:use-module (gnu packages databases)
#:use-module (gnu packages ghostscript)
#:use-module (gnu packages golang)
#:use-module (gnu packages graph)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages parallel)
#:use-module (gnu packages python)
#:use-module (gnu packages python-build)
#:use-module (gnu packages python-check)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-science)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages rdf)
#:use-module (gnu packages rust)
#:use-module (gnu packages scheme)
#:use-module (gnu packages search)
#:use-module (gnu packages statistics)
#:use-module (gnu packages textutils)
#:use-module (gnu packages version-control)
#:use-module (gnu packages web)
#:use-module (gnu packages xml)
#:use-module (gn packages bioinformatics)
#:use-module (gn packages crates-io)
#:use-module (gn packages gemma)
#:use-module (gn packages javascript)
#:use-module (gn packages node)
#:use-module (gn packages python)
#:use-module (gn packages statistics)
#:use-module (gn packages web)
#:use-module (gn packages python-web)
#:use-module (srfi srfi-1))
(define-public rust-qtlreaper
(let ((commit "2e7fed6d45b0b602d80fa2a55835f96ef1cba9e3")
(revision "1"))
(package
(name "rust-qtlreaper")
(version "0.1.4")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/chfi/rust-qtlreaper.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0h70aalsplmc6xn1w7ha102n3bsi3gqkbnbrjvjm2za37c07gv0g"))))
(build-system cargo-build-system)
(arguments
`(#:cargo-inputs
(("rust-rand" ,rust-rand-0.6)
("rust-structopt" ,rust-structopt-0.2)
("rust-rayon" ,rust-rayon-1)
("rust-serde" ,rust-serde-1)
("rust-serde-json" ,rust-serde-json-1)
("rust-ndarray" ,rust-ndarray-0.12))
#:phases
(modify-phases %standard-phases
;; Test results vary based on the machine running them.
(replace 'check
(lambda _
(or (assoc-ref %standard-phases 'check)
(begin
(substitute* "src/geneobject.rs"
;; array![Genotype::Unk, Genotype::Unk, Genotype::Pat]
(("0.3421367343627405") "0.3421367343627406")
;; array![Genotype::Unk, Genotype::Unk, Genotype::Unk]
(("-0.3223330030526561") "-0.32233300305265566"))
(assoc-ref %standard-phases 'check)))
#t)))))
(home-page "https://github.com/chfi/rust-qtlreaper")
(synopsis "Reimplementation of genenetwork/QTLReaper in Rust")
(description "Reimplementation of genenetwork/QTLReaper in Rust")
(license #f))))
; Tests on the upstream python-pengouin package are broken. So, we
; create this temporary workaround.
(define python-pingouin-without-tests
(package
(inherit python-pingouin)
(arguments
(substitute-keyword-arguments (package-arguments python-pingouin)
((#:tests? _ #f) #f)))))
(define-public genenetwork3
(let ((commit "5ea318ef0dc5e0e54801d5d27aa9d55c168cabb0")
(revision "5"))
(package
(name "genenetwork3")
(version (git-version "0.1.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/genenetwork/genenetwork3.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"14b8jzmwbjjrkhh6ajvp6xc7c8fsl918swjj7j6imy2pv7d9dcb3"))))
(inputs
(list python-click))
(native-inputs
(list python-hypothesis
python-mypy
python-mypy-extensions
python-pylint))
(propagated-inputs
(list csvdiff
diffutils
nss-certs
gemma-wrapper
gn-rust-correlation
python-argon2-cffi
python-authlib
python-bcrypt ;; Replace use of bcrypt with argon
python-biopython
python-email-validator
python-flask
python-flask-cors
python-lmdb
python-mysqlclient
python-numpy
python-pandas
python-pingouin-without-tests
python-plotly
python-pyld
python-pymonad
python-pytest
python-pytest-mock
python-redis
python-requests
python-scikit-learn
python-scipy
python-sparqlwrapper
python-wrapper
python-xapian-bindings
r
r-ctl
r-optparse
r-qtl
r-qtl2
r-rjson
r-stringi
r-wgcna
rust-qtlreaper))
(build-system python-build-system)
(arguments
(list #:phases
#~(modify-phases %standard-phases
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "pytest" "-k" "unit_test")))))))
(home-page "https://github.com/genenetwork/genenetwork3")
(synopsis "GeneNetwork3 API for data science and machine learning.")
(description "GeneNetwork3 API for data science and machine learning.")
(license license:agpl3+))))
(define-public genenetwork2
(let ((commit "32140f60183c008830294a9fd2f4a0477b29f3b7")
(revision "4"))
(package
(name "genenetwork2")
(version (git-version "3.11" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/genenetwork/genenetwork2.git")
(commit commit)))
(file-name (string-append name "-" version))
(sha256
(base32
"15vfwjq0y8g0kyk2qfsdisxw1k747mnbmskfisyvdgzjw5hlg184"))))
(native-inputs
(list graphviz))
(propagated-inputs
(list genenetwork3
coreutils
nss-certs
gemma
gemma-wrapper
git
glibc-utf8-locales
gn-rust-correlation
grep
gunicorn
javascript-ace
javascript-bootstrap
javascript-chroma
javascript-ckeditor
javascript-colorbox
javascript-cytoscape
javascript-cytoscape-panzoom
javascript-cytoscape-qtip
javascript-d3-tip
javascript-d3js ;; very old
javascript-d3js-7
javascript-d3panels
javascript-datatables
javascript-datatables-buttons
javascript-datatables-buttons-bootstrap
javascript-datatables-buttons-styles
javascript-datatables-col-reorder
javascript-datatables-col-resize
javascript-datatables-plugins
javascript-datatables-scroller
javascript-diff
javascript-diff2html
javascript-diff2html-ui
javascript-font-awesome
javascript-htmx
javascript-highlight
javascript-highlight-ui
javascript-jquery
javascript-jquery-cookie
javascript-jquery-ui
javascript-jscolor
javascript-jszip
javascript-linkify
javascript-linkify-html
javascript-marked
javascript-marked-highlight
javascript-nouislider
javascript-nvd3
javascript-plotly
javascript-purescript-genome-browser
javascript-qtip2
javascript-shapiro-wilk
javascript-twitter-post-fetcher
javascript-typeahead
javascript-uikit
javascript-underscore-string
javascript-zxcvbn
js-jstat
js-md5
js-parsley
js-smart-time-ago
js-underscore
mariadb
nginx
parallel
plink-ng-gn
python-authlib
python-autopep8
python-beautifulsoup4
python-configparser
python-coverage
python-cssselect
python-flask
python-flask-debugtoolbar
python-flask-session
python-htmlgen
python-ijson
python-jinja2
python-lxml
python-markdown
python-mypy
python-mysqlclient
python-numpy
python-pandas
python-pillow
python-pylint
python-pymonad
python-pytest
python-pytest-mock
python-rdflib
python-redis
python-requests
python-rpy2
python-scipy
python-setuptools
python-simplejson
python-sqlalchemy
python-wrapper
python-xlsxwriter
r
r-ctl
r-qtl
r-wgcna
redis
rust-qtlreaper
which
; javascript-xterm -- disabled until we know what to do with it, not working on production
; javascript-xterm-style
; javascript-xterm-addon-fit
))
(inputs
(list javascript-colorbox))
(build-system python-build-system)
(arguments
(list #:tests? #f
#:phases
#~(modify-phases %standard-phases
(delete 'reset-gzip-timestamps)
(add-after 'unpack 'fix-paths-to-static-files
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Set absolute store paths to installed static files.
(substitute* "gn2/wqflask/marker_regression/display_mapping_results.py"
(("\\./gn2/wqflask/static/fonts")
(string-append (site-packages inputs outputs)
"/gn2/wqflask/static/fonts")))
(substitute* "gn2/wqflask/views.py"
(("\\./gn2/wqflask/static/gif/error")
(string-append (site-packages inputs outputs)
"/gn2/wqflask/static/gif/error")))
(substitute* "gn2/wqflask/app_errors.py"
(("\\./gn2/wqflask/static/gif/error")
(string-append (site-packages inputs outputs)
"/gn2/wqflask/static/gif/error")))))
(add-after 'unpack 'fix-paths-scripts
(lambda _
(substitute* "bin/genenetwork2"
(("/usr/bin/env") (which "env"))
(("python ") (string-append (which "python3") " "))
(("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")))))
(add-before 'install 'fix-paths
(lambda* (#:key inputs #:allow-other-keys)
(let* ((plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2"))
(gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma")))
(substitute* '("gn2/default_settings.py")
(("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" ))
(("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" )))))))))
(home-page "http://genenetwork.org/")
(synopsis "Full genenetwork services")
(description "Genenetwork installation sumo.")
(license license:agpl3+))))
(define-public genenetwork3-stable
(let ((commit "e5569c3bb1c0d59ff7142273c5f51fe19f06cfe8")
(revision "1"))
(package
(inherit genenetwork3)
(name "genenetwork3-stable")
(version (string-append (git-version "3.11" revision commit)))
(arguments
(list
#:tests? #f
#:phases
#~(modify-phases %standard-phases
(add-before 'build 'update-paths
(lambda _
(for-each (lambda (fn)
(substitute* (string-append "gn3/" fn)
(("scripts/")
(string-append #$output "/scripts/"))))
'("api/rqtl.py"
"computations/wgcna.py"
"computations/ctl.py"
"api/general.py"))))
(add-before 'install 'install-scripts
(lambda _
(begin
(mkdir (string-append #$output "scripts"))
(for-each (lambda (fn)
(install-file fn
(string-append #$output "/scripts")))
'("scripts/rqtl_wrapper.R"
"scripts/ctl_analysis.R"
"scripts/wgcna_analysis.R"
))))))))
(source
(git-checkout
(url "https://github.com/genenetwork/genenetwork3")
(branch "prod"))))))
(define-public genenetwork2-stable
(let ((commit "95e634ca90d52922812b93df162686b348288651")
(revision "1"))
(package
(inherit genenetwork2)
(name "genenetwork2-stable")
(version (string-append "stable-" (git-version "3.12" revision commit)))
(source
(git-checkout
(url "https://github.com/genenetwork/genenetwork2")
(branch "prod")))
(arguments
(list
#:tests? #f
#:phases
#~(modify-phases %standard-phases
(add-before 'build 'update-font-paths
(lambda* (#:key inputs outputs #:allow-other-keys)
(for-each (lambda (fn)
(substitute* (string-append "gn2/" fn)
(("\\./gn2/wqflask/static/fonts/")
(string-append (site-packages inputs outputs) "/gn2/wqflask/static/fonts/"))))
'("utility/Plot.py"
"wqflask/marker_regression/display_mapping_results.py"))))
))))))
(define-public gn-uploader
(let ((commit "60fde66e02dba842b20fa126ff3b2ed9ec2638e6")
(version "0.0.1"))
(package
(name "gn-uploader")
(version (string-append version "-" (string-take commit 8)))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://git.genenetwork.org/gn-uploader")
(commit commit)))
(hash
(content-hash
(base32
"1q04viyf7d0q30k3424hrzsh9wxhhgs7hywlhzl3m68jki4zq1i7")))))
(build-system python-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "pytest" "-m" "unit_test")))))))
(native-inputs
(list python-mypy
python-pylint
python-pytest
python-hypothesis))
(propagated-inputs
(list gn-libs
gunicorn
nss-certs
python-redis
python-flask
python-pyyaml
python-authlib
python-pymonad
python-jsonpickle
python-mysqlclient
python-flask-session
javascript-jquery
javascript-bootstrap
node-resumablejs))
(synopsis "GeneNetwork Quality Control Application")
(description
"gn-uploader is a service allowing upload of new data into GeneNetwork,
that does quality control for the data files that is being uploaded to ensure
it fulfils all conditions before it can be accepted.")
(home-page "https://git.genenetwork.org/gn-uploader")
(license license:agpl3+))))
(define-public gn-auth
(let ((commit "346217b95a4aac17a5c7ac05c00d1205fa1855c5")
(revision "01"))
(package
(name "gn-auth")
(version (git-version "1.0.1" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://git.genenetwork.org/gn-auth")
(commit commit)))
(hash
(content-hash
(base32
"0nyxml3s778zaq3r0r9z5d7010hmbzvlwdbm5xnmrzc0xlx223g3")))))
(build-system python-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "pytest" "-k" "unit_test")))))))
(native-inputs
(list python-hypothesis
python-mypy
python-mypy-extensions
python-pylint
python-pytest
python-pytest-mock))
(propagated-inputs
(list gn-libs
gunicorn
nss-certs
python-blinker
python-argon2-cffi
python-authlib
python-email-validator
python-flask
python-flask-cors
python-mysqlclient
python-pymonad
python-redis
yoyo-migrations))
(home-page "https://github.com/genenetwork/gn-auth")
(synopsis "Authentication and Authorisation server for GeneNetwork services")
(description "Authentication and Authorisation server for GeneNetwork services.")
(license license:agpl3+))))
(define-public gn-libs
(let ((commit "4d9a29862a34b6b91829b3504b339214d010d722")
(revision "01"))
(package
(name "gn-libs")
(version (git-version "0.0.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://git.genenetwork.org/gn-libs")
(commit commit)))
(hash
(content-hash
(base32
"00ms9ma1704vgwlcsr43s87hyhb5f9jcasfrn7xqldix6rq1k4g1")))))
(build-system pyproject-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "pytest" "-k" "unit_test")))))))
(native-inputs
(list python-mypy
python-pylint
python-pytest))
(propagated-inputs
(list python-authlib
python-pymonad
python-mysqlclient))
(home-page "https://github.com/genenetwork/gn-libs")
(synopsis "Tools/utilities for GeneNetwork projects.")
(description "A collection of tools and utilities used across multiple
GeneNetwork projects.")
(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 (genenetwork-graph)
(with-imported-modules '((guix build utils))
(gexp->derivation "genenetwork-graph"
#~(begin
(use-modules (guix build utils)
(srfi srfi-1))
(define (python-version package)
(let* ((version (last (string-split
package
#\-)))
(components (string-split version #\.))
(major+minor (take components 2)))
(string-join major+minor ".")))
(let ((html-file (string-append #$output
"/lib/python"
(python-version #$python)
"/site-packages/wqflask"
"/dependency-graph.html")))
(mkdir-p (dirname html-file))
(call-with-output-file html-file
(lambda (port)
(format
port "~a"
#$(call-with-output-string
(lambda (p)
(with-output-to-port p
(lambda ()
(run-with-store
(open-connection)
(export-graph
(list genenetwork2)
p
#:node-type %package-node-type
#:backend %d3js-backend))))))))))))))
;(define (computed-genenetwork-graph)
; (with-imported-modules '((guix build utils))
; (computed-file "genenetwork-graph"
; #~(begin
; (use-modules (guix build utils))
; (call-with-output-file #$output
; (lambda (port)
; (format
; port "~a"
; #$(call-with-output-string
; (lambda (p)
; (with-output-to-port p
; (lambda ()
; (run-with-store
; (open-connection)
; (export-graph
; (list genenetwork1)
; p
; #:node-type %package-node-type
; #:backend %d3js-backend)))))))))))))
(define (dag-svg-file)
(with-imported-modules '((guix build utils))
(gexp->derivation "dag-svg-file"
#~(begin
(use-modules (guix build utils)
(srfi srfi-1))
(define (python-version package)
(let* ((version (last (string-split
package
#\-)))
(components (string-split version #\.))
(major+minor (take components 2)))
(string-join major+minor ".")))
(let* ((dest-dir (string-append #$output
"/lib/python"
(python-version #$python)
"/site-packages/wqflask"))
(dot-file (string-append dest-dir "/dependency-graph.dot"))
(svg-file (string-append dest-dir "/dependency-graph.svg")))
(mkdir-p dest-dir)
(call-with-output-file dot-file
(lambda (port)
(format
port "~a"
#$(call-with-output-string
(lambda (p)
(with-output-to-port p
(lambda ()
(run-with-store
(open-connection)
(export-graph
(list genenetwork2)
p
#:node-type %package-node-type
#:backend %graphviz-backend)))))))))
(invoke #+(file-append graphviz "/bin/dot")
"-Tsvg" "-o" svg-file dot-file))))))
;(define-public genenetwork2-combined
; (directory-union
; "genenetwork2"
; (list genenetwork2 genenetwork-graph dag-svg-file)))
