gn: Upstream edirect-gn

2 files changed, 1 insertions, 383 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 45e88c7..78a55fc 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -10,12 +10,10 @@
   #: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)
@@ -26,7 +24,6 @@
   #: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)
@@ -421,118 +418,7 @@ reads.")
     (license license:non-copyleft)))
 
 (define-public edirect-gn
-  (package
-    (inherit edirect)
-    (name "edirect-gn")
-    (arguments
-      (substitute-keyword-arguments (package-arguments edirect)
-        ((#:phases phases)
-         `(modify-phases ,phases
-            (add-after 'unpack 'patch-programs
-              (lambda* (#:key inputs #:allow-other-keys)
-                ;; Ignore errors about missing xtract.Linux and rchive.Linux.
-                (substitute* "pm-refresh"
-                  (("cat \\\"\\$target")
-                   "grep ^[[:digit:]] \"$target"))
-                #t))
-            (replace 'install
-              (lambda* (#:key inputs outputs #:allow-other-keys)
-                (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
-                      (edirect-go (assoc-ref inputs "edirect-go-programs")))
-                  (for-each
-                    (lambda (file)
-                      (install-file file bin))
-                    '("archive-pubmed" "asp-cp" "asp-ls" "download-ncbi-data"
-                      "download-pubmed" "edirect.pl" "efetch" "epost" "esearch"
-                      "fetch-pubmed" "ftp-cp" "ftp-ls" "has-asp" "index-pubmed"
-                      "pm-prepare" "pm-refresh" "pm-stash" "pm-collect"
-                      "pm-index" "pm-invert" "pm-merge" "pm-promote"))
-                  (symlink (string-append edirect-go "/bin/xtract.Linux")
-                           (string-append bin "/xtract"))
-                  (symlink (string-append edirect-go "/bin/rchive.Linux")
-                           (string-append bin "/rchive")))
-                #t))
-            (replace 'wrap-program
-              (lambda* (#:key outputs #:allow-other-keys)
-                ;; Make sure everything can run in a pure environment.
-                (let ((out (assoc-ref outputs "out"))
-                      (path (getenv "PERL5LIB")))
-                  (for-each
-                    (lambda (file)
-                      (wrap-program file
-                                    `("PERL5LIB" ":" prefix (,path)))
-                      (wrap-program file
-                                    `("PATH" ":" prefix (,(string-append out "/bin")
-                                                         ,(dirname (which "sed"))
-                                                         ,(dirname (which "gzip"))
-                                                         ,(dirname (which "grep"))
-                                                         ,(dirname (which "perl"))
-                                                         ,(dirname (which "uname"))))))
-                    (find-files out ".")))
-                #t))))))
-    (inputs
-     `(("edirect-go-programs" ,edirect-go-programs)
-       ,@(package-inputs edirect)))
-    (native-search-paths
-     ;; Ideally this should be set for LWP somewhere.
-     (list (search-path-specification
-            (variable "PERL_LWP_SSL_CA_FILE")
-            (file-type 'regular)
-            (separator #f)
-            (files '("/etc/ssl/certs/ca-certificates.crt")))))))
-
-(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)))))
+  (deprecated-package "edirect-gn" edirect))
 
 ;; TODO: Unbundle zlib, bamtools, tclap
 (define-public sniffles
diff --git a/gn/packages/golang.scm b/gn/packages/golang.scm
deleted file mode 100644
index 56eed66..0000000
--- a/gn/packages/golang.scm
+++ /dev/null
@@ -1,268 +0,0 @@
-(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))))