diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 116 | ||||
| -rw-r--r-- | gn/packages/golang.scm | 268 |
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)))) |