(define-public gatk
  (package
    (name "gatk")
    (version "4.4.0.0")
    (source (origin
             (method url-fetch)
             (uri 
	       (string-append "https://github.com/broadinstitute/gatk/releases/download/" version "/gatk-" version ".zip"))
             (sha256
              (base32
               "1453l72cfwqw5y3na0d520czzq11x46d9dq66q5ssilbngvh0ij4"))))
    (build-system gnu-build-system)
    (arguments
    `(#:tests? #f ; This is a binary package only, so no tests.
      #:phases
      (modify-phases %standard-phases
        (delete 'configure) ; Nothing to configure.
        (delete 'build) ; This is a binary package only.
        (replace 'install
          (lambda _
            (let ((out (string-append (assoc-ref %outputs "out")
                                      "/share/java/" ,name "/")))
              (mkdir-p out)
	      (copy-recursively (assoc-ref %build-inputs "source")
				(string-append out "/"))))))))
    (native-inputs
      (list
	unzip))
    (propagated-inputs
     (list
       r-gsalib
       r-ggplot2
       r-gplots
       r-reshape
       r-optparse
       r-dnacopy
       r-naturalsort
       r-dplyr
       r-data-table
       r-hmm
       ))
    (home-page "https://www.broadinstitute.org/gatk/")
    (synopsis "Package for analysis of high-throughput sequencing")
    (description "The Genome Analysis Toolkit or GATK is a software package for
analysis of high-throughput sequencing data, developed by the Data Science and
Data Engineering group at the Broad Institute.  The toolkit offers a wide
variety of tools, with a primary focus on variant discovery and genotyping as
well as strong emphasis on data quality assurance.  Its robust architecture,
powerful processing engine and high-performance computing features make it
capable of taking on projects of any size.")
    ;; There are additional restrictions that make it nonfree.
    (license license:expat)))

error: in phase 'install': uncaught exception:
system-error "copy-file" "~A" ("Is a directory") (21) 
phase `install' failed after 0.0 seconds

$ guix build cuda-toolkit@11 -v10
guix build: warning: ambiguous package specification `cuda-toolkit@11'
guix build: warning: choosing [email protected] from guix-science-nonfree/packages/cuda.scm:226:2
substitute: updating substitutes from 'https://substitutes.nonguix.org'... 100.0%
substitute: updating substitutes from 'https://bordeaux.guix.gnu.org'... 100.0%
substitute: updating substitutes from 'https://ci.guix.gnu.org'... 100.0%
The following derivations will be built:
  /gnu/store/8b5g9iq27a0vpzhzjgc1p11gklpr9a92-cuda-toolkit-11.8.0.drv
  /gnu/store/hrz73h3pm608vfqxmkizjm1v0hiv3cr2-cuda_11.8.0_520.61.05_linux.run.drv
building /gnu/store/hrz73h3pm608vfqxmkizjm1v0hiv3cr2-cuda_11.8.0_520.61.05_linux.run.drv...

Starting download of /gnu/store/sg1kpnwh07acn8n1zy86rl48fnggk5ap-cuda_11.8.0_520.61.05_linux.run
From https://developer.download.nvidia.com/compute/cuda/11.8.0/local_installers/cuda_11.8.0_520.61.05_linux.run...
downloading from https://developer.download.nvidia.com/compute/cuda/11.8.0/local_installers/cuda_11.8.0_520.61.05_linux.run ...
 cuda_11.8.0_520.61.05_linux.run  4.04GiB                                                     3.4MiB/s 20:23 ▕██████████████████▏ 100.0%
guix build: error: short write in copy_file_range `15' to `16': No such file or directory