diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 54 |
1 files changed, 54 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index edf2958dac..b60f6ae846 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -143,6 +143,7 @@ #:use-module (gnu packages ruby) #:use-module (gnu packages serialization) #:use-module (gnu packages shells) + #:use-module (gnu packages skribilo) #:use-module (gnu packages sphinx) #:use-module (gnu packages sqlite) #:use-module (gnu packages statistics) @@ -16009,3 +16010,56 @@ identifying multiple clusters/cell types, learning the batch effects from the control samples and applying quantile normalization on all markers of interest.") (license license:gpl2+)))) + +(define-public ccwl + (package + (name "ccwl") + (version "0.2.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://ccwl.systemreboot.net/releases/ccwl-" + version ".tar.lz")) + (sha256 + (base32 + "1ar8rfz3zrksgygrv67zv77y8gfvvz54zcs546jn6j28y20basla")))) + (build-system gnu-build-system) + (arguments + `(#:make-flags '("GUILE_AUTO_COMPILE=0") ; to prevent guild warnings + #:modules (((guix build guile-build-system) + #:select (target-guile-effective-version)) + ,@%gnu-build-system-modules) + #:imported-modules ((guix build guile-build-system) + ,@%gnu-build-system-modules) + #:phases + (modify-phases %standard-phases + (add-after 'install 'wrap + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (effective-version (target-guile-effective-version))) + (wrap-program (string-append out "/bin/ccwl") + `("GUILE_LOAD_PATH" prefix + (,(string-append out "/share/guile/site/" effective-version) + ,(getenv "GUILE_LOAD_PATH"))) + `("GUILE_LOAD_COMPILED_PATH" prefix + (,(string-append out "/lib/guile/" effective-version "/site-ccache") + ,(getenv "GUILE_LOAD_COMPILED_PATH")))))))))) + (inputs + `(("bash" ,bash-minimal) + ("guile" ,guile-3.0) + ("guile-libyaml" ,guile-libyaml))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("lzip" ,lzip) + ;; To build documentation + ("cwltool" ,cwltool) + ("graphviz" ,graphviz) + ("skribilo" ,skribilo))) + (home-page "https://ccwl.systemreboot.net") + (synopsis "Concise common workflow language") + (description "The @acronym{ccwl, Concise Common Workflow Language} is a +concise syntax to express CWL workflows. ccwl is a compiler to generate CWL +workflows from concise descriptions in ccwl. It is implemented as an +@acronym{EDSL, Embedded Domain Specific Language} in the Scheme programming +language.") + (license license:gpl3+))) |