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-rw-r--r--gn/packages/bioinformatics.scm116
1 files changed, 1 insertions, 115 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