From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:470:142:3::10]:52007) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jDk5b-0007k4-Gb for guix-patches@gnu.org; Mon, 16 Mar 2020 03:23:09 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1jDk5a-0008Gp-52 for guix-patches@gnu.org; Mon, 16 Mar 2020 03:23:07 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:58274) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1jDk5X-0008FA-4r for guix-patches@gnu.org; Mon, 16 Mar 2020 03:23:06 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1jDk5W-0001Sq-1D for guix-patches@gnu.org; Mon, 16 Mar 2020 03:23:02 -0400 Subject: [bug#40086] [PATCH 10/11] gnu: Add edirect-go-programs. References: <20200316070412.12364-1-efraim@flashner.co.il> In-Reply-To: <20200316070412.12364-1-efraim@flashner.co.il> Resent-Message-ID: From: Efraim Flashner Date: Mon, 16 Mar 2020 09:15:58 +0200 Message-Id: <20200316071559.13930-11-efraim@flashner.co.il> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: 40086@debbugs.gnu.org Cc: Efraim Flashner * gnu/packages/bioinformatics.scm (edirect-go-programs): New variable. (edirect)[source]: Adjust snippet to not use non-free software. --- gnu/packages/bioinformatics.scm | 57 +++++++++++++++++++++++++++++++-- 1 file changed, 54 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4dedee6223..1f0619ebb6 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") -- 2.25.1