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-rw-r--r--gn/packages/bioinformatics.scm116
-rw-r--r--gn/packages/golang.scm268
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))))