diff options
| author | Efraim Flashner <efraim@flashner.co.il> | 2020-03-15 23:21:34 +0200 |
|---|---|---|
| committer | Efraim Flashner <efraim@flashner.co.il> | 2020-03-22 09:53:57 +0200 |
| commit | 7d13a942158a73cfe4bf9b9a266edac144e040a1 (patch) | |
| tree | 4198c10341592c5ffae618d3cabbdfa457d1107e /gnu/packages/bioinformatics.scm | |
| parent | 073c64dc792c79c2a988edae9f4e568d3b09f3b5 (diff) | |
| download | patches-7d13a942158a73cfe4bf9b9a266edac144e040a1.tar patches-7d13a942158a73cfe4bf9b9a266edac144e040a1.tar.gz | |
gnu: Add edirect-go-programs.
* gnu/packages/bioinformatics.scm (edirect-go-programs): New variable.
(edirect)[source]: Adjust snippet to not use non-free software.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 57 |
1 files changed, 54 insertions, 3 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6dfc23c1dc..242aafc632 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -42,6 +42,7 @@ #:use-module (guix build-system ant) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) + #:use-module (guix build-system go) #:use-module (guix build-system haskell) #:use-module (guix build-system meson) #:use-module (guix build-system ocaml) @@ -68,15 +69,17 @@ #:use-module (gnu packages documentation) #:use-module (gnu packages databases) #:use-module (gnu packages datastructures) + #:use-module (gnu packages dlang) #:use-module (gnu packages file) #:use-module (gnu packages flex) #:use-module (gnu packages gawk) #:use-module (gnu packages gcc) #:use-module (gnu packages gd) - #:use-module (gnu packages gtk) + #:use-module (gnu packages golang) #:use-module (gnu packages glib) #:use-module (gnu packages graph) #:use-module (gnu packages groff) + #:use-module (gnu packages gtk) #:use-module (gnu packages guile) #:use-module (gnu packages guile-xyz) #:use-module (gnu packages haskell-check) @@ -87,7 +90,6 @@ #:use-module (gnu packages java) #:use-module (gnu packages java-compression) #:use-module (gnu packages jemalloc) - #:use-module (gnu packages dlang) #:use-module (gnu packages linux) #:use-module (gnu packages lisp-xyz) #:use-module (gnu packages logging) @@ -2766,7 +2768,12 @@ quantitative phenotypes.") "093zp7klv81ph0y8mm8d78a9hnpfxbv2kdym70gzdf3vz176rw33")) (modules '((guix build utils))) (snippet - '(begin (delete-file "Mozilla-CA.tar.gz") #t)))) + '(begin (delete-file "Mozilla-CA.tar.gz") + (substitute* "rchive.go" + ;; This go library does not have any license. + (("github.com/fiam/gounidecode/unidecode") + "golang.org/rainycape/unidecode")) + #t)))) (build-system perl-build-system) (arguments `(#:phases @@ -2826,6 +2833,50 @@ in structured XML format. This can eliminate the need for writing custom software to answer ad hoc questions.") (license license:public-domain))) +(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 + (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))))) + (define-public exonerate (package (name "exonerate") |