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gnu: Add edirect-go-programs. 

* gnu/packages/bioinformatics.scm (edirect-go-programs): New variable.
(edirect)[source]: Adjust snippet to not use non-free software.
master
Efraim Flashner 2020-03-15 23:21:34 +02:00
parent 073c64dc79
commit 7d13a94215
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1 changed files with 54 additions and 3 deletions
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57
gnu/packages/bioinformatics.scm
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@ -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")