diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 56 |
1 files changed, 56 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 86e2657..6a38499 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -10,10 +10,12 @@ #: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) @@ -24,6 +26,7 @@ #: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) @@ -510,6 +513,59 @@ reads.") ;; Due to the precompiled binaries we download: (supported-systems '("x86_64-linux")))) +(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))))) + ;; TODO: Unbundle zlib, bamtools, tclap (define-public sniffles (package |