;; 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 cargo)
#:use-module (guix build-system python)
#:use-module (guix build-system trivial)
#:use-module (gnu packages)
#:use-module (gnu packages base)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages bootstrap)
#:use-module (gnu packages check)
#:use-module (gnu packages cran)
#:use-module (gnu packages compression)
#:use-module (gnu packages databases)
#:use-module (gnu packages python)
#:use-module (gnu packages python-crypto)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages statistics)
#:use-module (gnu packages version-control)
#:use-module (gnu packages vim)
#:use-module (gnu packages web)
#:use-module (gn packages bioinformatics)
#:use-module (gn packages crates-io)
#:use-module (gn packages elixir)
#:use-module (gn packages gemma)
#:use-module (gn packages javascript)
#:use-module (gn packages phewas)
#:use-module (gn packages python)
#:use-module (gn packages python24)
#:use-module (gn packages statistics))
(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 to 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" ,(bootstrap-executable "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 "442c217b90393380a8634ff8636b44992f5c53dd"))
(package
(name "python2-qtlreaper")
(version (string-append "1.11-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
"1rrbm1ap2zzyjxmrs9aa1d18sgiba5dhj1fmkl7wmab06jv3j1hm"))))
(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 python24-qtlreaper
(let ((commit "dd9c7fb2a9d5fa40b4054e1bcb7c57905d98d5f8"))
(package
(name "python24-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-2.4
#:tests? #f)) ; no 'setup.py test' really!
(native-inputs
`(("python24-setuptools" ,python24-setuptools)))
(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 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-1.0)
("rust-serde" ,rust-serde-1.0)
("rust-serde-json" ,rust-serde-json-1.0)
("rust-ndarray" ,rust-ndarray-0.12))
#:cargo-development-inputs
(("rust-ansi-term" ,rust-ansi-term-0.11)
("rust-arrayvec" ,rust-arrayvec-0.4)
("rust-atty" ,rust-atty-0.2)
("rust-autocfg" ,rust-autocfg-0.1)
("rust-bitflags" ,rust-bitflags-1.0)
("rust-cfg-if" ,rust-cfg-if-0.1)
("rust-clap" ,rust-clap-2.33)
("rust-cloudabi" ,rust-cloudabi-0.0)
("rust-crossbeam-deque" ,rust-crossbeam-deque-0.2)
("rust-crossbeam-epoch" ,rust-crossbeam-epoch-0.3)
("rust-crossbeam-utils" ,rust-crossbeam-utils-0.2)
("rust-either" ,rust-either-1.5)
("rust-fuchsia-cprng" ,rust-fuchsia-cprng-0.1)
("rust-heck" ,rust-heck-0.3)
("rust-itertools" ,rust-itertools-0.7)
("rust-itoa" ,rust-itoa-0.4)
("rust-lazy-static" ,rust-lazy-static-1.3)
("rust-libc" ,rust-libc-0.2)
("rust-maxtrixmultiply" ,rust-matrixmultiply-0.1)
("rust-memoffset" ,rust-memoffset-0.2)
("rust-nodrop" ,rust-nodrop-0.1)
("rust-num-complex" ,rust-num-complex-0.2)
("rust-num-cpus" ,rust-num-cpus-1.10)
("rust-num-traits" ,rust-num-traits-0.2)
("rust-numtoa" ,rust-numtoa-0.1)
("rust-proc-macro2" ,rust-proc-macro2-0.4)
("rust-quote" ,rust-quote-0.6)
("rust-rand" ,rust-rand-0.6)
("rust-rand-chacha" ,rust-rand-chacha-0.1)
("rust-rand-core-0.4" ,rust-rand-core-0.4)
("rust-rand-core-0.3" ,rust-rand-core-0.3)
("rust-rand-hc" ,rust-rand-hc-0.1)
("rust-rand-isaac" ,rust-rand-isaac-0.1)
("rust-rand-jitter" ,rust-rand-jitter-0.1)
("rust-rand-os" ,rust-rand-os-0.1)
("rust-rand-pcg" ,rust-rand-pcg-0.1)
("rust-rand-xorshift" ,rust-rand-xorshift-0.1)
("rust-rawpointer" ,rust-rawpointer-0.1)
("rust-rayon" ,rust-rayon-1.0)
("rust-rayon-core" ,rust-rayon-core-1.4)
("rust-rdrand" ,rust-rdrand-0.4)
("rust-redox-syscall" ,rust-redox-syscall-0.1)
("rust-redox-termios" ,rust-redox-termios-0.1)
("rust-ryu" ,rust-ryu-1.0)
("rust-scopeguard" ,rust-scopeguard-0.3)
("rust-serde" ,rust-serde-1.0)
("rust-serde-derive" ,rust-serde-derive-1.0)
("rust-serde-json" ,rust-serde-json-1.0)
("rust-strsim" ,rust-strsim-0.8)
("rust-structopt" ,rust-structopt-0.2)
("rust-structopt-derive" ,rust-structopt-derive-0.2)
("rust-syn" ,rust-syn-0.15)
("rust-termion" ,rust-termion-1.5)
("rust-textwrap" ,rust-textwrap-0.11)
("rust-unicode-segmentation" ,rust-unicode-segmentation-1.3)
("rust-unicode-width" ,rust-unicode-width-0.1)
("rust-unicode-xid" ,rust-unicode-xid-0.1)
("rust-vec-map" ,rust-vec-map-0.8)
("rust-winapi" ,rust-winapi-0.3)
("rust-winapi-i686-pc-windows-gnu" ,rust-winapi-i686-pc-windows-gnu-0.4)
("rust-winapi-x86-64-pc-windows-gnu" ,rust-winapi-x86-64-pc-windows-gnu-0.4))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'update-test-data
(lambda _
(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"))
#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))))
(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)
("rust-qtlreaper" ,rust-qtlreaper)
("nginx" ,nginx)
("python2-flask" ,python2-flask)
("gunicorn" ,gunicorn)
; ("python2-pillow" ,python2-pillow) - for later!
("python2-pil1" ,python2-pil1-gn)
("python2-piddle-gn" ,python2-piddle-gn)
("python2-cssselect" ,python2-cssselect)
("python2-elasticsearch" ,python2-elasticsearch)
; ("python2-htmlgen" ,python2-htmlgen)
("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-redis" ,python2-redis)
("python2-requests" ,python2-requests)
("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)
))
(inputs
`(("javascript-colorbox" ,(package-source javascript-colorbox))))
(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 whiches in a row!
)
#t))
(add-after 'unpack 'patch-javascript
(lambda* (#:key inputs #:allow-other-keys)
(let ((colorbox (assoc-ref inputs "javascript-colorbox"))
(gn2 "/share/genenetwork2/javascript/"))
(delete-file-recursively "wqflask/wqflask/static/packages/colorbox")
(copy-recursively colorbox "wqflask/wqflask/static/packages/colorbox")
#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)))
(file-name (git-file-name name version))
(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-pillow" ,python-pillow)
("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-numarray" ,python2-numarray) ;; Update gn2 code and drop this (IMPORTANT)
;; ("python2-htmlgen-gn" ,python2-htmlgen-gn) ;; pjotrp and zsloan to give directions
))
(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+))))
