diff options
| -rw-r--r-- | README.md | 26 | ||||
| -rw-r--r-- | gn/packages/bioinformatics.scm | 39 |
2 files changed, 61 insertions, 4 deletions
diff --git a/README.md b/README.md index 7b700b2..5cb1dd7 100644 --- a/README.md +++ b/README.md @@ -31,13 +31,31 @@ Install the common workflow language tool cwltool with ## Install R/qtl - git clone https://github.com/genenetwork/guix-bioinformatics.git - export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/ +R-qtl is part of main stream GNU Guix: + guix package -i r-qtl r R library(qtl) +# Development tips + +## Override individual packages + +The cheerful way of overriding a version of a package: + + (use-modules (guix) (gnu packages emacs)) + + (package + (inherit emacs) + (name "emacs-snapshot") + (source "/path/to/some-file-or-directory.tar.gz")) + +and then run: + + guix package --install-from-file=that-file.scm + + ## LICENSE -These package descriptions are distributed by the same license as GNU -Guix, i.e. GPL3+ +These package descriptions (so-called Guix expressions) are +distributed by the same license as GNU Guix, i.e. GPL3+ diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 6238dfb..f319532 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -38,5 +38,44 @@ #:use-module (gnu packages web) #:use-module (gnu packages xml) #:use-module (gnu packages zip) + #:use-module (gnu packages bootstrap) #:use-module (srfi srfi-1)) +(define-public my-deploy + (package + (name "my-deploy") + (version "0.0.1") + (source #f) + (build-system trivial-build-system) + (arguments + `(#:guile ,%bootstrap-guile + #:modules ((guix build utils)) + #:builder + (let* ((out (assoc-ref %outputs "out")) + (bash (assoc-ref %build-inputs "bash")) + (foo (string-append out "/foo"))) + (begin + (use-modules (guix build utils)) + (mkdir out) + (call-with-output-file foo + (lambda (p) + (format p + "#!~a~%echo \"${GUIX_FOO} ${GUIX_BAR}\"~%" + bash))) + (chmod foo #o777) + ;; wrap-program uses `which' to find bash for the wrapper + ;; shebang, but it can't know about the bootstrap bash in + ;; the store, since it's not named "bash". Help it out a + ;; bit by providing a symlink it this package's output. + (symlink bash (string-append out "/bash")) + (setenv "PATH" out) + (wrap-program foo `("GUIX_FOO" prefix ("hello"))) + (wrap-program foo `("GUIX_BAR" prefix ("world"))) + #t)))) + (inputs `(("bash" ,(search-bootstrap-binary "bash" + (%current-system))))) + + (home-page #f) + (synopsis #f) + (description #f) + (license #f))) |