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(define-module (gn packages julia)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix utils)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix build-system julia)
#:use-module (gn packages cran)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages compression)
#:use-module (gnu packages cran)
#:use-module (gnu packages statistics)
#:use-module (ice-9 match))
(define-public julia-lmgpu
(let ((commit "e9e95b5fa46f1905ca1ff32a3684a2616a7e482c")
(revision "1"))
(package
(name "julia-lmgpu")
(version (git-version "0.1.1" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ChelseaTrotter/LMGPU.jl")
(commit commit)))
;(file-name (git-file-name name version))
(file-name "LMGPU")
(sha256
(base32
"1ddx2np1lakw1l2dclpcaihxd0fcj6bjxsvaxr6g5brxjqk5j7b1"))))
(build-system julia-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
;; This is a super ugly hack. Some JULIA environment variable should
;; be tuned so it can find the artifact directory.
(add-after 'unpack 'symlink-zlib-into-artifact-directory
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((julia-dir (string-append (assoc-ref outputs "out")
"/share/julia")))
(mkdir-p julia-dir)
(symlink
(string-append (assoc-ref inputs "julia-zlib-jll")
"/share/julia/artifacts")
(string-append julia-dir "/artifacts")))
#t))
(add-after 'precompile 'check
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(builddir (string-append out "/share/julia/")))
(setenv "JULIA_LOAD_PATH"
(string-append builddir "packages/" ":"
(or (getenv "JULIA_LOAD_PATH")
"")))
(setenv "HOME" (getcwd))
(invoke "julia" "test/runtests.jl")))))))
(native-inputs
`(("r" ,r-minimal)
("r-mice" ,r-mice)
("r-qtl2" ,r-qtl2)
("r-tictoc" ,r-tictoc)
("r-tidyverse" ,r-tidyverse)))
(propagated-inputs
`(("julia-zipfile" ,julia-zipfile)))
(home-page "https://github.com/ChelseaTrotter/LMGPU.jl")
(synopsis "")
(description "")
(license license:expat))))
(define-public julia-lmgpu-myapp
(package
(inherit julia-lmgpu)
(name "julia-lmgpu-myapp")
(source
(origin (inherit (package-source julia-lmgpu))
(file-name "MyApp")))
(arguments
(substitute-keyword-arguments (package-arguments julia-lmgpu)
((#:phases phases)
`(modify-phases ,phases
(add-after 'unpack 'change-directory
(lambda _
(chdir "bin/MyApp") #t))))))
(propagated-inputs
`(("julia-lmgpu" ,julia-lmgpu)
,@(package-propagated-inputs julia-lmgpu)))
(native-inputs
`(("julia-packagecompiler" ,julia-packagecompiler)))))
(define-public julia-zipfile
(package
(name "julia-zipfile")
(version "0.9.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/fhs/ZipFile.jl")
(commit (string-append "v" version))))
;(file-name (git-file-name name version))
(file-name "ZipFile")
(sha256
(base32
"1fpvlhfqg5kgq5vchlf8dyc73r6dzki0dz7plddc3bnr0ld00rlw"))))
(build-system julia-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
;; This is a super ugly hack. Some JULIA environment variable should
;; be tuned so it can find the artifact directory.
(add-after 'unpack 'symlink-zlib-into-artifact-directory
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((julia-dir (string-append (assoc-ref outputs "out")
"/share/julia")))
(mkdir-p julia-dir)
(symlink
(string-append (assoc-ref inputs "julia-zlib-jll")
"/share/julia/artifacts")
(string-append julia-dir "/artifacts")))
#t)))))
(propagated-inputs
`(("julia-zlib-jll" ,julia-zlib-jll)))
(home-page "https://github.com/fhs/ZipFile.jl")
(synopsis "Read/Write ZIP archives in Julia")
(description "This module provides support for reading and writing ZIP
archives in Julia.")
(license license:expat)))
(define-public julia-zlib-jll
(package
(name "julia-zlib-jll")
(version "1.2.11+9")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaBinaryWrappers/Zlib_jll.jl")
(commit (string-append "Zlib-v" version))))
;(file-name (git-file-name name version))
(file-name "Zlib_jll")
(sha256
(base32
"0m9n8dp4bwhkyjag1szmhz02k0bxzm4ka2ia2jh8crnd1qi8w9dz"))))
(build-system julia-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'symlink-zlib-into-artifact-directory
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((artifacts (string-append (assoc-ref outputs "out")
"/share/julia/artifacts")))
(mkdir-p artifacts)
(symlink
(assoc-ref inputs "zlib")
;; from git-tree-sha1 in Artifacts.toml
(string-append
artifacts
,(match (%current-system)
("x86_64-linux" "/7846a2956a213715c2c76632f3461cef87d9d545")
("i686-linux" "/c8456cbd00982236828623bbc63f21b9b7b03821")
("armhf-linux" "/748c38025b5596a5005a87ac2b9476603cf8615b")
("aarch64-linux" "/3dd0c7cd5424c8746a1a32034ba1b10458f20b3b")
(_ "/UNSUPPORTED")))))
#t)))))
(native-inputs
`(("zlib" ,zlib)))
(home-page "https://github.com/JuliaBinaryWrappers/Zlib_jll.jl")
(synopsis "Autogenerated package constructed using BinaryBuilder.jl")
(description "This is an autogenerated package constructed using
@url{https://github.com/JuliaPackaging/BinaryBuilder.jl, BinaryBuilder.jl}.")
(license license:expat)))
(define-public julia-packagecompiler
(package
(name "julia-packagecompiler")
(version "1.1.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaLang/PackageCompiler.jl")
(commit (string-append "v" version))))
;(file-name (git-file-name name version))
(file-name "PackageCompiler")
(sha256
(base32
"1s9xc17i308fdpyvkz1w6qb1h7yncdr2jgk1szfvygxd6yzkv1b4"))))
(build-system julia-build-system)
(home-page "https://github.com/JuliaLang/PackageCompiler.jl")
(synopsis "Compile your Julia Package")
(description "PackageCompiler is a Julia package with two main purposes:
@itemize
@item Creating custom sysimages for reduced latency when working locally with
packages that has a high startup time.
@item Creating \"apps\" which are a bundle of files including an executable that
can be sent and run on other machines without Julia being installed on that machine.
@end itemize")
(license license:expat)))
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