gn: edirect-gn: Build go packages from source.

2 files changed, 324 insertions, 0 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 86e2657..6a38499 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -10,10 +10,12 @@
   #:use-module (guix build-system ant)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system go)
   #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module (guix build-system waf)
   #:use-module (gnu packages)
+  #:use-module (gn packages golang)
   #:use-module (gn packages python)
   #:use-module (gnu packages bioconductor)
   #:use-module (gnu packages bioinformatics)
@@ -24,6 +26,7 @@
   #:use-module (gnu packages datastructures)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gcc)
+  #:use-module (gnu packages golang)
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages jemalloc)
@@ -510,6 +513,59 @@ reads.")
     ;; Due to the precompiled binaries we download:
     (supported-systems '("x86_64-linux"))))
 
+(define-public edirect-go-programs
+  (package
+    (inherit edirect)
+    (name "edirect-go-programs")
+    (build-system go-build-system)
+    (arguments
+     `(#:install-source? #f
+       #:tests? #f      ; No tests.
+       #:import-path "ncbi.nlm.nih.gov/entrez/edirect"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'replace-go-dependency
+           ;; This go library does not have any license.
+           ;; TODO: This should move to a source snippet.
+           (lambda* (#:key import-path #:allow-other-keys)
+             (with-directory-excursion (string-append "src/" import-path)
+               (substitute* "rchive.go"
+                 (("github.com/fiam/gounidecode/unidecode")
+                  "golang.org/rainycape/unidecode"))
+               #t)))
+         (replace 'build
+           (lambda* (#:key import-path #:allow-other-keys)
+             (with-directory-excursion (string-append "src/" import-path)
+               (invoke "go" "build" "-v" "-x" "j2x.go")
+               (invoke "go" "build" "-v" "-x" "t2x.go")
+               (invoke "go" "build" "-v" "-x" "-o"
+                       "xtract.Linux" "xtract.go" "common.go")
+               (invoke "go" "build" "-v" "-x" "-o"
+                       "rchive.Linux" "rchive.go" "common.go")
+               (invoke "go" "build" "-v" "-x" "-o" "symbols.Linux" "s2p.go"))))
+         (replace 'install
+           (lambda* (#:key outputs import-path #:allow-other-keys)
+             (let ((dest    (string-append (assoc-ref outputs "out") "/bin"))
+                   (source  (string-append "src/" import-path "/")))
+               (for-each (lambda (file)
+                           (format #t "installing ~a~%" file)
+                           (install-file (string-append source file) dest))
+                         '("j2x" "t2x" "symbols.Linux" "xtract.Linux" "rchive.Linux"))
+               #t))))))
+    (native-inputs '())
+    (propagated-inputs '())
+    (inputs
+     `(("go-github-com-fatih-color" ,go-github-com-fatih-color)
+       ("go-github-com-fogleman-gg" ,go-github-com-fogleman-gg)
+       ("go-github-com-gedex-inflector" ,go-github-com-gedex-inflector)
+       ("go-github-com-golang-freetype" ,go-github-com-golang-freetype)
+       ("go-github-com-klauspost-cpuid" ,go-github-com-klauspost-cpuid)
+       ("go-github-com-pbnjay-memory" ,go-github-com-pbnjay-memory)
+       ("go-github-com-surgebase-porter2" ,go-github-com-surgebase-porter2)
+       ("go-golang-org-rainycape-unidecode" ,go-golang-org-rainycape-unidecode)
+       ("go-golang-org-x-image" ,go-golang-org-x-image)
+       ("go-golang-org-x-text" ,go-golang-org-x-text)))))
+
 ;; TODO: Unbundle zlib, bamtools, tclap
 (define-public sniffles
   (package
diff --git a/gn/packages/golang.scm b/gn/packages/golang.scm
new file mode 100644
index 0000000..56eed66
--- /dev/null
+++ b/gn/packages/golang.scm
@@ -0,0 +1,268 @@
+(define-module (gn packages golang)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix git-download)
+  #:use-module (guix packages)
+  #:use-module (guix utils)
+  #:use-module (guix build-system go)
+  #:use-module (gnu packages golang)
+  )
+
+(define-public go-golang-org-x-image
+  (let ((commit "58c23975cae11f062d4b3b0c143fe248faac195d")
+        (revision "1"))
+    (package
+      (name "go-golang-org-x-image")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://go.googlesource.com/image")
+                       (commit commit)))
+                (file-name (string-append "go.googlesource.com-image-"
+                                          version "-checkout"))
+                (sha256
+                 (base32
+                  "0i2p2girc1sfcic6xs6vrq0fp3szfx057xppksb67kliywjjrm5x"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "golang.org/x/image"
+         ; Source-only package
+         #:tests? #f
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'build))))
+      (home-page "https://go.googlesource.com/image")
+      (synopsis "Supplemental Go image libraries")
+      (description "This package provides supplemental Go libraries for image
+processing.")
+      (license license:bsd-3))))
+
+(define-public go-github-com-fiam-gounidecode
+  (let ((commit "311ebb7422d3ff70cc1d064c5a297520ff5f304a")
+        (revision "1"))
+    (package
+      (name "go-github-com-fiam-gounidecode")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/fiam/gounidecode")
+                       (commit commit)))
+                (file-name (string-append "go-github-com-fiam-gounidecode-"
+                                          version "-checkout"))
+                (sha256
+                 (base32
+                  "107c2qnlgl9d55pww3kh3x5m5pqw7ijzzqbpsrpxnzn5jls44xbs"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:unpack-path "github.com/fiam/gounidecode"
+         #:import-path "github.com/fiam/gounidecode/unidecode"))
+      (home-page "https://github.com/fiam/gounidecode/")
+      (synopsis "Unicode transliterator for Go")
+      (description "Unicode transliterator for Go.")
+      (license #f))))       ; No license listed.
+
+(define-public go-golang-org-rainycape-unidecode
+  (let ((commit "cb7f23ec59bec0d61b19c56cd88cee3d0cc1870c")
+        (revision "1"))
+    (package
+      (name "go-golang-org-rainycape-unidecode")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/rainycape/unidecode")
+                       (commit commit)))
+                (file-name (string-append "go-golang-org-rainycape-unidecode-"
+                                          version "-checkout"))
+                (sha256
+                 (base32
+                  "1wvzdijd640blwkgmw6h09frkfa04kcpdq87n2zh2ymj1dzla5v5"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "golang.org/rainycape/unidecode"))
+      (home-page "https://github.com/rainycape/unidecode")
+      (synopsis "Unicode transliterator in Golang")
+      (description "Unicode transliterator in Golang - Replaces non-ASCII
+characters with their ASCII approximations.")
+      (license license:asl2.0))))
+
+(define-public go-github-com-golang-freetype
+  (let ((commit "e2365dfdc4a05e4b8299a783240d4a7d5a65d4e4")
+        (revision "1"))
+    (package
+      (name "go-github-com-golang-freetype")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/golang/freetype")
+                       (commit commit)))
+                (file-name (string-append "go-github-com-golang-freetype-"
+                                          version "-checkout"))
+                (sha256
+                 (base32
+                  "194w3djc6fv1rgcjqds085b9fq074panc5vw582bcb8dbfzsrqxc"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "github.com/golang/freetype"))
+      (propagated-inputs
+       `(("go-golang-org-x-image" ,go-golang-org-x-image)))
+      (home-page "https://github.com/golang/freetype")
+      (synopsis "Freetype font rasterizer in the Go programming language")
+      (description "The Freetype font rasterizer in the Go programming language.")
+      (license (list license:freetype
+                     license:gpl2+)))))
+
+(define-public go-github-com-fogleman-gg
+  (package
+    (name "go-github-com-fogleman-gg")
+    (version "1.3.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://github.com/fogleman/gg")
+                     (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1nkldjghbqnzj2djfaxhiv35kk341xhcrj9m2dwq65v684iqkk8n"))))
+    (build-system go-build-system)
+    (arguments
+     `(#:tests? #f      ; Issue with test flags.
+       #:import-path "github.com/fogleman/gg"))
+    (propagated-inputs
+     `(("go-github-com-golang-freetype" ,go-github-com-golang-freetype)))
+    (home-page "https://github.com/fogleman/gg")
+    (synopsis "2D rendering in Go")
+    (description "@code{gg} is a library for rendering 2D graphics in pure Go.")
+    (license license:expat)))
+
+(define-public go-github-com-gedex-inflector
+  (let ((commit "16278e9db8130ac7ec405dc174cfb94344f16325")
+        (revision "1"))
+    (package
+      (name "go-github-com-gedex-inflector")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/gedex/inflector")
+                       (commit commit)))
+                (file-name (string-append "go-github-com-gedex-inflector-"
+                                          version "-checkout"))
+                (sha256
+                 (base32
+                  "05hjqw1m71vww4914d9h6nqa9jw3lgjzwsy7qaffl02s2lh1amks"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "github.com/gedex/inflector"))
+      (home-page "https://github.com/gedex/inflector")
+      (synopsis "Go library that pluralizes and singularizes English nouns")
+      (description "Go library that pluralizes and singularizes English nouns.")
+      (license license:bsd-2))))
+
+(define-public go-github-com-klauspost-cpuid
+  (package
+    (name "go-github-com-klauspost-cpuid")
+    (version "1.2.3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://github.com/klauspost/cpuid")
+                     (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1s510210wdj5dkamii1qrk7v87k4qpdcrrjzflp5ha9iscw6b06l"))))
+    (build-system go-build-system)
+    (arguments
+     `(#:import-path "github.com/klauspost/cpuid"))
+    (home-page "https://github.com/klauspost/cpuid")
+    (synopsis "CPU feature identification for Go")
+    (description "@code{cpuid} provides information about the CPU running the
+current program.  CPU features are detected on startup, and kept for fast access
+through the life of the application. Currently x86 / x64 (AMD64) is supported,
+and no external C (cgo) code is used, which should make the library very eas
+to use.")
+    (license license:expat)))
+
+(define-public go-github-com-pbnjay-memory
+  (let ((commit "974d429e7ae40c89e7dcd41cfcc22a0bfbe42510")
+        (revision "1"))
+    (package
+      (name "go-github-com-pbnjay-memory")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/pbnjay/memory")
+                       (commit commit)))
+                (file-name (string-append "go-github-com-pbnjay-memory-"
+                                          version "-checkout"))
+                (sha256
+                 (base32
+                  "0kazg5psdn90pqadrzma5chdwh0l2by9z31sspr47gx93fhjmkkq"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "github.com/pbnjay/memory"))
+      (home-page "https://github.com/gedex/inflector")
+      (synopsis "Go library to report total system memory")
+      (description "@code{memory} provides a single method reporting total
+physical system memory accessible to the kernel. It does not account for memory
+used by other processes.")
+      (license license:bsd-3))))
+
+(define-public go-github-com-surgebase-porter2
+  (let ((commit "56e4718818e8dc4ea5ba6348402fc7661863732a")
+        (revision "1"))
+    (package
+      (name "go-github-com-surgebase-porter2")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/surgebase/porter2")
+                       (commit commit)))
+                (file-name (string-append "go-github-com-surgebase-porter2-"
+                                          version "-checkout"))
+                (sha256
+                 (base32
+                  "1ivcf83jlj9s7q5y9dfbpyl0br35cz8fcp0dm8sxxvqh54py06v2"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "github.com/surgebase/porter2"))
+      (native-inputs
+       `(("go-github-com-stretchr-testify" ,go-github-com-stretchr-testify)
+         ("go-github-com-surge-glog" ,go-github-com-surge-glog)))
+      (home-page "https://github.com/surgebase/porter2")
+      (synopsis "Go library implementing english Porter2 stemmer")
+      (description "Porter2 implements the
+@url{http://snowball.tartarus.org/algorithms/english/stemmer.html, english
+Porter2 stemmer}.  It is written completely using finite state machines to do
+suffix comparison, rather than the string-based or tree-based approaches.")
+      (license license:asl2.0))))
+
+(define-public go-github-com-surge-glog
+  (let ((commit "2578deb2b95c665e6b1ebabf304ce2085c9e1985")
+        (revision "1"))
+    (package
+      (name "go-github-com-surge-glog")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/surge/glog")
+                       (commit commit)))
+                (file-name (string-append "go-github-com-surge-glog-"
+                                          version "-checkout"))
+                (sha256
+                 (base32
+                  "1bxcwxvsvr2hfpjz9hrrn0wrgykwmrbyk567102k3vafw9xdcwk4"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "github.com/surge/glog"))
+      (home-page "https://github.com/surge/glog")
+      (synopsis "Leveled execution logs for Go")
+      (description "Leveled execution logs for Go.")
+      (license license:asl2.0))))