Merge branch 'master' of http://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics

1 files changed, 198 insertions, 0 deletions

diff --git a/gn/packages/julia.scm b/gn/packages/julia.scm
new file mode 100644
index 0000000..b55efde
--- /dev/null
+++ b/gn/packages/julia.scm
@@ -0,0 +1,198 @@
+(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)))