diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 56 | ||||
| -rw-r--r-- | gn/packages/golang.scm | 268 |
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)))) |