From: Efraim Flashner <efraim@flashner.co.il>
To: 40086@debbugs.gnu.org
Cc: Efraim Flashner <efraim@flashner.co.il>
Subject: [bug#40086] [PATCH 10/11] gnu: Add edirect-go-programs.
Date: Mon, 16 Mar 2020 09:15:58 +0200 [thread overview]
Message-ID: <20200316071559.13930-11-efraim@flashner.co.il> (raw)
In-Reply-To: <20200316070412.12364-1-efraim@flashner.co.il>
* 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
next prev parent reply other threads:[~2020-03-16 7:23 UTC|newest]
Thread overview: 14+ messages / expand[flat|nested] mbox.gz Atom feed top
2020-03-16 7:04 [bug#40086] [PATCH 00/11] Expand edirect programs Efraim Flashner
2020-03-16 7:15 ` [bug#40086] [PATCH 01/11] gnu: Add go-golang-org-x-image Efraim Flashner
2020-03-16 7:15 ` [bug#40086] [PATCH 02/11] gnu: Add go-golang-org-rainycape-unidecode Efraim Flashner
2020-03-16 7:15 ` [bug#40086] [PATCH 03/11] gnu: Add go-github-com-golang-freetype Efraim Flashner
2020-03-16 7:15 ` [bug#40086] [PATCH 04/11] gnu: Add go-github-com-fogleman-gg Efraim Flashner
2020-03-16 7:15 ` [bug#40086] [PATCH 05/11] gnu: Add go-github-com-gedex-inflector Efraim Flashner
2020-03-16 7:15 ` [bug#40086] [PATCH 06/11] gnu: Add go-github-com-klauspost-cpuid Efraim Flashner
2020-03-16 7:15 ` Efraim Flashner
2020-03-16 7:15 ` [bug#40086] [PATCH 07/11] gnu: Add go-github-com-pbnjay-memory Efraim Flashner
2020-03-16 7:15 ` [bug#40086] [PATCH 08/11] gnu: Add go-github-com-surge-glog Efraim Flashner
2020-03-16 7:15 ` [bug#40086] [PATCH 09/11] gnu: Add go-github-com-surgebase-porter2 Efraim Flashner
2020-03-16 7:15 ` Efraim Flashner [this message]
2020-03-16 7:15 ` [bug#40086] [PATCH 11/11] gnu: edirect: Install more programs Efraim Flashner
2020-03-22 7:59 ` bug#40086: [PATCH 00/11] Expand edirect programs Efraim Flashner
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