diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 116 |
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 |