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603 lines
26 KiB
603 lines
26 KiB
;; Bioinformatics module
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(define-module (gn packages genenetwork)
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (guix packages)
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#:use-module (guix utils)
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#:use-module (guix download)
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#:use-module (guix git-download)
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#:use-module (guix build-system cargo)
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#:use-module (guix build-system gnu)
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#:use-module (guix build-system python)
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#:use-module (guix build-system trivial)
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#:use-module (guix graph)
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#:use-module (guix scripts graph)
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#:use-module (guix store)
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#:use-module (guix gexp)
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#:use-module (gnu packages)
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#:use-module (gnu packages base)
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#:use-module (gnu packages bioconductor)
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#:use-module (gnu packages bioinformatics)
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#:use-module (gnu packages check)
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#:use-module (gnu packages cran)
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#:use-module (gnu packages crates-io)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages databases)
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#:use-module (gnu packages ghostscript)
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#:use-module (gnu packages golang)
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#:use-module (gnu packages graph)
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#:use-module (gnu packages graphviz)
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#:use-module (gnu packages parallel)
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#:use-module (gnu packages python)
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#:use-module (gnu packages python-check)
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#:use-module (gnu packages python-crypto)
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#:use-module (gnu packages python-science)
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#:use-module (gnu packages python-web)
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#:use-module (gnu packages python-xyz)
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#:use-module (gnu packages rdf)
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#:use-module (gnu packages rust)
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#:use-module (gnu packages scheme)
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#:use-module (gnu packages statistics)
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#:use-module (gnu packages version-control)
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; #:use-module (gnu packages vim)
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#:use-module (gnu packages web)
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; #:use-module (gnu packages wget)
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#:use-module (gnu packages xml)
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#:use-module (gn packages bioinformatics)
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#:use-module (gn packages gemma)
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#:use-module (gn packages javascript)
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#:use-module (gn packages python)
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#:use-module (gn packages statistics)
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#:use-module (gn packages twint)
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#:use-module (gn packages web)
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#:use-module (srfi srfi-1))
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(define-public rust-qtlreaper
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(let ((commit "2e7fed6d45b0b602d80fa2a55835f96ef1cba9e3")
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(revision "1"))
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(package
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(name "rust-qtlreaper")
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(version "0.1.4")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/chfi/rust-qtlreaper.git")
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(commit commit)))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"0h70aalsplmc6xn1w7ha102n3bsi3gqkbnbrjvjm2za37c07gv0g"))))
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(build-system cargo-build-system)
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(arguments
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`(#:cargo-inputs
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(("rust-rand" ,rust-rand-0.6)
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("rust-structopt" ,rust-structopt-0.2)
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("rust-rayon" ,rust-rayon-1)
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("rust-serde" ,rust-serde-1)
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("rust-serde-json" ,rust-serde-json-1)
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("rust-ndarray" ,rust-ndarray-0.12))
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#:phases
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(modify-phases %standard-phases
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;; Test results vary based on the machine running them.
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(replace 'check
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(lambda _
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(or (assoc-ref %standard-phases 'check)
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(begin
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(substitute* "src/geneobject.rs"
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;; array![Genotype::Unk, Genotype::Unk, Genotype::Pat]
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(("0.3421367343627405") "0.3421367343627406")
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;; array![Genotype::Unk, Genotype::Unk, Genotype::Unk]
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(("-0.3223330030526561") "-0.32233300305265566"))
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(assoc-ref %standard-phases 'check)))
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#t)))))
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(home-page "https://github.com/chfi/rust-qtlreaper")
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(synopsis "Reimplementation of genenetwork/QTLReaper in Rust")
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(description "Reimplementation of genenetwork/QTLReaper in Rust")
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(license #f))))
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(define-public genenetwork3
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(let ((commit "77c274b79c3ec01de60e90db3299763cb58f715b"))
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(package
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(name "genenetwork3")
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(version (string-append "0.0.1-guix-" (string-take commit 7)))
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/genenetwork/genenetwork3.git")
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(commit commit)))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"0ha70ibr7dqz0kzmgccx5l6nrmmf2a2mj7scg6jllx232crjby72"))))
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(propagated-inputs `(("coreutils" ,coreutils)
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("gemma-wrapper" ,gemma-wrapper)
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("csvdiff" ,go-github-com-aswinkarthik-csvdiff)
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("python" ,python-wrapper)
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("python-bcrypt" ,python-bcrypt)
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("python-flask" ,python-flask)
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("python-flask-cors" ,python-flask-cors)
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("python-ipfshttpclient" ,python-ipfshttpclient)
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("python-mypy" ,python-mypy)
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("python-mypy-extensions" ,python-mypy-extensions)
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("python-mysqlclient" ,python-mysqlclient)
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("python-numpy" ,python-numpy)
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("python-pylint" ,python-pylint)
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("python-redis" ,python-redis)
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("python-requests" ,python-requests)
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("python-scipy" ,python-scipy)
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("python-plotly" ,python-plotly)
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("python-sqlalchemy-stubs"
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,python-sqlalchemy-stubs)
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("r-optparse" ,r-optparse)
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("r-qtl" ,r-qtl)
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("r-stringi" ,r-stringi)
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("r-wgcna" ,r-wgcna)
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("r-rjson" ,r-rjson)))
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(build-system python-build-system)
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(home-page "https://github.com/genenetwork/genenetwork3")
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(synopsis "GeneNetwork3 API for data science and machine learning.")
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(description "GeneNetwork3 API for data science and machine learning.")
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(license license:agpl3+))))
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(define-public genenetwork2
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(let ((commit "fe345c9f2e99be748511f6889420d6560a553a37"))
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(package
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(name "genenetwork2")
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(version (string-append "3.11-guix-" (string-take commit 7) ))
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/genenetwork/genenetwork2.git")
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(commit commit)))
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(file-name (string-append name "-" version))
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(sha256
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(base32
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"1y6psmxpm3qn78dx6xfc11rdpf22vf807qb7grnp82gl19q6408w"))))
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(native-inputs
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`(("graphviz" ,graphviz)
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;; And the graphs
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;("genenetwork-graph" ,genenetwork-graph)
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;("dag-svg-file" ,dag-svg-file)
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))
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(propagated-inputs
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`(("genenetwork3" ,genenetwork3)
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("parallel" ,parallel) ;; GNU parallel
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("coreutils" ,coreutils)
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("git" ,git)
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("which" ,which)
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("grep" ,grep)
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("r" ,r)
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("r-ctl" ,r-ctl)
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; ("r-phewas" ,r-phewas)
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("r-qtl" ,r-qtl)
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("r-wgcna" ,r-wgcna)
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("redis" ,redis)
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("mariadb" ,mariadb)
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("gemma" ,gemma-gn2)
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("gemma-wrapper" ,gemma-wrapper)
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; ("genenetwork2-files-small" ,genenetwork2-files-small)
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("plink-ng-gn" ,plink-ng-gn)
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; ("pylmm-gn2" ,pylmm-gn2)
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("rust-qtlreaper" ,rust-qtlreaper)
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("glibc-utf8-locales" ,glibc-utf8-locales)
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("nginx" ,nginx)
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("python" ,python-wrapper)
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("python-pillow" ,python-pillow)
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("python-coverage" ,python-coverage)
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("python-configparser" ,python-configparser) ;; maintenance/scripts
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("python-flask" ,python-flask)
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("gunicorn" ,gunicorn)
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("python-autopep8" ,python-autopep8)
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("python-cssselect" ,python-cssselect)
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("python-flask-debugtoolbar" ,python-flask-debugtoolbar)
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("python-elasticsearch" ,python-elasticsearch)
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("python-htmlgen" ,python-htmlgen)
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("python-jinja2" ,python-jinja2)
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("python-sqlalchemy" ,python-sqlalchemy)
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("python-flask-sqlalchemy" ,python-flask-sqlalchemy)
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("python-setuptools" ,python-setuptools)
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("python-scipy" ,python-scipy)
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("python-lxml" ,python-lxml)
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("python-mechanize" ,python-mechanize)
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("python-mysqlclient" ,python-mysqlclient)
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("python-mypy" ,python-mypy)
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("python-numpy" ,python-numpy)
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("python-pandas" ,python-pandas)
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("python-parameterized" ,python-parameterized)
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("python-passlib" ,python-passlib)
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("python-pylint" ,python-pylint)
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("python-redis" ,python-redis)
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("python-requests" ,python-requests)
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("python-simplejson" ,python-simplejson)
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("python-pyyaml" ,python-pyyaml)
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("python-markdown" ,python-markdown)
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("python-rdflib" ,python-rdflib)
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("python-twint" ,python-twint)
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("python-unittest2" ,python-unittest2)
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;; TODO: Get rid of Python R bindings
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("python-rpy2" ,python-rpy2-next)
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("python-beautifulsoup4" ,python-beautifulsoup4)
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;; Disable for now. Build fails on Penguin2
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;; ("python-flask-socketio" ,python-flask-socketio)
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("python-xlsxwriter" ,python-xlsxwriter)
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;; All the external js dependencies
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("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher)
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("javascript-cytoscape" ,javascript-cytoscape)
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("javascript-panzoom" ,javascript-cytoscape-panzoom)
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("javascript-qtip" ,javascript-cytoscape-qtip)
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("javascript-chroma" ,javascript-chroma)
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("javascript-d3-tip" ,javascript-d3-tip)
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("javascript-jscolor" ,javascript-jscolor)
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("javascript-colorbox" ,javascript-colorbox)
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("javascript-jszip" ,javascript-jszip)
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("js-jstat" ,js-jstat)
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("js-md5" ,js-md5)
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("js-parsley" ,js-parsley)
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("javascript-plotly" ,javascript-plotly)
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("javascript-typeahead" ,javascript-typeahead)
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("js-underscore" ,js-underscore)
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("js-smart-time-ago" ,js-smart-time-ago)
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("javascript-nouislider" ,javascript-nouislider)
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("javascript-purescript-genome-browser" ,javascript-purescript-genome-browser)
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("javascript-ckeditor" ,javascript-ckeditor)
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("javascript-datatables" ,javascript-datatables)
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("javascript-datatables-scroller" ,javascript-datatables-scroller)
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("javascript-datatables-buttons" ,javascript-datatables-buttons)
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("javascript-datatables-buttons-bootstrap" ,javascript-datatables-buttons-bootstrap)
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("javascript-datatables-plugins" ,javascript-datatables-plugins)
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("javascript-datatables-col-reorder" ,javascript-datatables-col-reorder)
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("javascript-datatables-col-resize" ,javascript-datatables-col-resize)
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("javascript-datatables-buttons-styles" ,javascript-datatables-buttons-styles)
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("javascript-shapiro-wilk" ,javascript-shapiro-wilk)
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("javascript-underscore-string" ,javascript-underscore-string)
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("javascript-qtip2" ,javascript-qtip2)
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("javascript-d3js" ,javascript-d3js)
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("javascript-nvd3" ,javascript-nvd3)
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("javascript-bootstrap" ,javascript-bootstrap)
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("javascript-jquery" ,javascript-jquery)
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("javascript-zxcvbn" ,javascript-zxcvbn)
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("javascript-jquery-ui" ,javascript-jquery-ui)
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("javascript-jquery-cookie" ,javascript-jquery-cookie)
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("javascript-font-awesome" ,javascript-font-awesome)))
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(inputs
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`(("javascript-colorbox" ,(package-source javascript-colorbox))))
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(build-system python-build-system)
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(arguments
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`(#:tests? #f ; no 'setup.py test'
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#:phases
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(modify-phases %standard-phases
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(delete 'reset-gzip-timestamps)
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(add-after 'unpack 'fix-paths-scripts
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(lambda _
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(substitute* "bin/genenetwork2"
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(("/usr/bin/env") (which "env"))
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(("python ") (string-append (which "python3") " "))
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(("readlink") (which "readlink"))
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(("dirname") (which "dirname"))
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(("basename") (which "basename"))
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(("cat") (which "cat"))
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(("echo") (which "echo"))
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(("redis-server") (which "redis-server"))
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(("git") (which "git"))
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(("grep") (which "grep"))
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(("rm") (which "rm"))
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(("which") (which "which")))
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#t))
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; (add-after 'unpack 'patch-javascript
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; (lambda* (#:key inputs #:allow-other-keys)
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; (let ((colorbox (assoc-ref inputs "javascript-colorbox"))
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; (gn2 "/share/genenetwork2/javascript/"))
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; (delete-file-recursively "wqflask/wqflask/static/packages/colorbox")
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; (copy-recursively colorbox "wqflask/wqflask/static/packages/colorbox")
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; #t)))
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(add-before 'install 'fix-paths
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(lambda* (#:key inputs #:allow-other-keys)
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(let* (
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; (datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2"))
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; (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis"))
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(plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2"))
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(gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma"))
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)
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(substitute* '("etc/default_settings.py")
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; (("^GENENETWORK_FILES +=.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" ))
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; (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" ))
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(("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" ))
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(("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" ))
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)
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)))
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; (add-after 'install 'generate-graph
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; (lambda* (#:key inputs outputs #:allow-other-keys)
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; (call-with-output-file
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; (string-append
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; (assoc-ref outputs "out")
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; "/lib/python"
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; (python-version (assoc-ref inputs "python"))
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; "/site-packages"
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; "/wqflask/dependency-graph.html")
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; (lambda (port)
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; (format
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; port "~a"
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; ,(call-with-output-string
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; (lambda (p)
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; (with-output-to-port p
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; (lambda ()
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; (run-with-store
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; (open-connection)
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; (export-graph
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; (list this-package)
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; p
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; #:node-type %package-node-type
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; #:backend %d3js-backend)))))))))))
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;(add-after 'install 'generate-dag-svg-file
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; (lambda* (#:key inputs outputs #:allow-other-keys)
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; (let* ((output-dir
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; (string-append
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; (assoc-ref outputs "out")
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; "/lib/python"
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; (python-version (assoc-ref inputs "python"))
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; "/site-packages/wqflask/"))
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; (dot-file
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; (string-append
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; output-dir
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; "dependency-graph.dot"))
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; (svg-file
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; (string-append
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; output-dir
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; "dependency-graph.svg")))
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; (begin
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; (call-with-output-file
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; dot-file
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; (lambda (port)
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; (format
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; port "~a"
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; ,(call-with-output-string
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; (lambda (p)
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; (with-output-to-port p
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; (lambda ()
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; (run-with-store
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; (open-connection)
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; (export-graph
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; (list this-package)
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; p
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; #:node-type %package-node-type
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; #:backend %graphviz-backend)))))))))
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; (invoke "dot" "-Tsvg" "-o" svg-file dot-file)))))
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;; TODO: Use this to replace the two previous phases.
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;(add-after 'install 'install-generated-files
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; (lambda* (#:key inputs outputs #:allow-other-keys)
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; (let ((output-dir
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; (string-append
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; (assoc-ref outputs "out")
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; "/lib/python"
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; (python-version (assoc-ref inputs "python"))
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; "/site-packages/wqflask/")))
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; (install-file (string-append %dag-svg-file "/dependency-graph.dot") output-dir)
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; (install-file (string-append %dag-svg-file "/dependency-graph.svg") output-dir)
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; (install-file (string-append %genenetwork-graph "/dependency-graph.html") output-dir)
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; #t)))
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(add-after 'install 'generate-dependency-file
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(call-with-output-file
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(string-append
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(assoc-ref outputs "out")
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"/lib/python"
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(python-version (assoc-ref inputs "python"))
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"/site-packages"
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"/wqflask/DEPENDENCIES.md")
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(lambda (port)
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(format
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port "
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#### System Inputs (generated from ~a package defined in ~a)
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|Name | Description |
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|-----|-------------|
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~a
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"
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,(package-name this-package)
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(string-append
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"[genenetwork.scm]"
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"(http://git.genenetwork.org/"
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"guix-bioinformatics/guix-bioinformatics"
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"/src/branch/master/gn/packages/"
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"genenetwork.scm)")
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,(apply
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string-append
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(map
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(lambda (input)
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(let* ((pkg (cadr input))
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(name (package-name pkg))
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(version (package-version pkg))
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(home-page (package-home-page pkg))
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(description (package-synopsis pkg)))
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(string-append
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"| **[" name "](" home-page ")** v"
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version"| "
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description " |\n")))
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(package-propagated-inputs this-package)))))))))))
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(home-page "http://genenetwork.org/")
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(synopsis "Full genenetwork services")
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(description "Genenetwork installation sumo.")
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(license license:agpl3+))))
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;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip
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;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x
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(define-public genenetwork2-files-small
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(let ((pfff "xx"))
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(package
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(name "genenetwork2-files-small")
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(version "1.0")
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(source
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(origin
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(method url-fetch)
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(uri "http://files.genenetwork.org/data_files/gn2_data_s-20160303-C9E672ECED1F51B915DE419B5B2C524E.tar.lz4")
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(file-name (string-append name "-" pfff))
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(sha256
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(base32 "058ymx3af6abdhdxyxj0i9qfvb6v7j091frjpp6jh4ahks7r23lj"))))
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(build-system trivial-build-system)
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(native-inputs `(("lz4" ,lz4)
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("tar" ,tar)
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("source" ,source)))
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(arguments
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`(#:modules ((guix build utils))
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#:builder
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(let* ((out (assoc-ref %outputs "out"))
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(name "gn2_data_s")
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(tarfn (string-append name ".tar"))
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(targetdir (string-append out "/share/genenetwork2/")))
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(begin
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(use-modules (guix build utils))
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(let ((source (assoc-ref %build-inputs "source"))
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(lz4unpack (string-append (assoc-ref %build-inputs "lz4") "/bin/lz4"))
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(tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar")))
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(and
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(zero? (system* lz4unpack source "-d" tarfn))
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(zero? (system* tar "xf" tarfn))
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(mkdir-p targetdir)
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(copy-recursively name targetdir)))))))
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(home-page "http://genenetwork.org/")
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(synopsis "Small file archive to run on genenetwork")
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(description "Genenetwork genotype and mapping files.")
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(license license:agpl3+))))
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(define-public genenetwork2-database-small
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(let ((md5 "93e745e9c"))
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(package
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(name "genenetwork2-database-small")
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(version "1.0")
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(source
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(origin
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(method url-fetch)
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(uri "http://files.genenetwork.org/raw_database/db_webqtl_s.zip")
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(file-name (string-append name "-" md5))
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(sha256
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(base32 "0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x"))))
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(build-system trivial-build-system)
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(native-inputs `(("unzip" ,unzip)
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("source" ,source)))
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(arguments
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`(#:modules ((guix build utils))
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#:builder (begin
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(use-modules (guix build utils))
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(let ((source (assoc-ref %build-inputs "source"))
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(unzip (string-append (assoc-ref %build-inputs "unzip") "/bin/unzip")))
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(and (mkdir "db")
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(zero? (system* unzip source "-d" "db"))
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(chdir "db"))))))
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(home-page "http://genenetwork.org/")
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(synopsis "Small database to run on genenetwork")
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(description "Genenetwork installation + database.")
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(license license:agpl3+))))
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(define (genenetwork-graph)
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(with-imported-modules '((guix build utils))
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(gexp->derivation "genenetwork-graph"
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#~(begin
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(use-modules (guix build utils)
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(srfi srfi-1))
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(define (python-version package)
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(let* ((version (last (string-split
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package
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#\-)))
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(components (string-split version #\.))
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(major+minor (take components 2)))
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(string-join major+minor ".")))
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(let ((html-file (string-append #$output
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"/lib/python"
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(python-version #$python)
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"/site-packages/wqflask"
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"/dependency-graph.html")))
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(mkdir-p (dirname html-file))
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(call-with-output-file html-file
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(lambda (port)
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(format
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port "~a"
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#$(call-with-output-string
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(lambda (p)
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(with-output-to-port p
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(lambda ()
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(run-with-store
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(open-connection)
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(export-graph
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(list genenetwork2)
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p
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#:node-type %package-node-type
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#:backend %d3js-backend))))))))))))))
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;(define (computed-genenetwork-graph)
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; (with-imported-modules '((guix build utils))
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; (computed-file "genenetwork-graph"
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; #~(begin
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; (use-modules (guix build utils))
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; (call-with-output-file #$output
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; (lambda (port)
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; (format
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; port "~a"
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; #$(call-with-output-string
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; (lambda (p)
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; (with-output-to-port p
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; (lambda ()
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; (run-with-store
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; (open-connection)
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; (export-graph
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; (list genenetwork1)
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; p
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; #:node-type %package-node-type
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; #:backend %d3js-backend)))))))))))))
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(define (dag-svg-file)
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(with-imported-modules '((guix build utils))
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(gexp->derivation "dag-svg-file"
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#~(begin
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(use-modules (guix build utils)
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(srfi srfi-1))
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|
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(define (python-version package)
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(let* ((version (last (string-split
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package
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#\-)))
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(components (string-split version #\.))
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(major+minor (take components 2)))
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(string-join major+minor ".")))
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(let* ((dest-dir (string-append #$output
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"/lib/python"
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(python-version #$python)
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"/site-packages/wqflask"))
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(dot-file (string-append dest-dir "/dependency-graph.dot"))
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(svg-file (string-append dest-dir "/dependency-graph.svg")))
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(mkdir-p dest-dir)
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(call-with-output-file dot-file
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(lambda (port)
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(format
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port "~a"
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#$(call-with-output-string
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(lambda (p)
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(with-output-to-port p
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(lambda ()
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(run-with-store
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(open-connection)
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(export-graph
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(list genenetwork2)
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p
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#:node-type %package-node-type
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#:backend %graphviz-backend)))))))))
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(invoke #+(file-append graphviz "/bin/dot")
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"-Tsvg" "-o" svg-file dot-file))))))
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;(define-public genenetwork2-combined
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; (directory-union
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; "genenetwork2"
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; (list genenetwork2 genenetwork-graph dag-svg-file)))
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