[bug#27376] [PATCH] gnu: Add kentutils.

[Kei Kebreau]

Ricardo Wurmus <address@hidden> writes:

> * gnu/packages/bioinformatics.scm (kentutils): New variable.
> ---
>  gnu/packages/bioinformatics.scm | 115 
> ++++++++++++++++++++++++++++++++++++++++
>  1 file changed, 115 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 22a81f160..1f71f80ae 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -50,6 +50,7 @@
>    #:use-module (gnu packages cpio)
>    #:use-module (gnu packages curl)
>    #:use-module (gnu packages documentation)
> +  #:use-module (gnu packages databases)
>    #:use-module (gnu packages datastructures)
>    #:use-module (gnu packages file)
>    #:use-module (gnu packages flex)
> @@ -84,6 +85,7 @@
>    #:use-module (gnu packages readline)
>    #:use-module (gnu packages ruby)
>    #:use-module (gnu packages serialization)
> +  #:use-module (gnu packages shells)
>    #:use-module (gnu packages statistics)
>    #:use-module (gnu packages swig)
>    #:use-module (gnu packages tbb)
> @@ -9496,3 +9498,116 @@ correct interaction matrices, identify adn compare 
> the so-called
>  interaction matrices, and finally, extract structural properties from the
>  models.  TADbit is complemented by TADkit for visualizing 3D models.")
>      (license license:gpl3+)))
> +
> +(define-public kentutils
> +  (package
> +    (name "kentutils")
> +    ;; 302.1.0 is out, but the only difference is the inclusion of
> +    ;; pre-built binaries.
> +    (version "302.0.0")
> +    (source
> +     (origin
> +       (method url-fetch)
> +       (uri (string-append "https://github.com/ENCODE-DCC/kentUtils/";
> +                           "archive/v" version ".tar.gz"))
> +       (file-name (string-append name "-" version ".tar.gz"))
> +       (sha256
> +        (base32
> +         "134aja3k1cj32kbk1nnw0q9gxjb2krr15q6sga8qldzvc0585rmm"))
> +       (modules '((guix build utils)
> +                  (srfi srfi-26)
> +                  (ice-9 ftw)))
> +       (snippet
> +        '(begin
> +           ;; Only the contents of the specified directories are free
> +           ;; for all uses, so we remove the rest.  "hg/autoSql" and
> +           ;; "hg/autoXml" are nominally free, but they depend on a
> +           ;; library that is built from the sources in "hg/lib",
> +           ;; which is nonfree.
> +           (let ((free (list "." ".."
> +                             "utils" "lib" "inc" "tagStorm"
> +                             "parasol" "htslib"))
> +                 (directory? (lambda (file)
> +                               (eq? 'directory (stat:type (stat file))))))
> +             (for-each (lambda (file)
> +                         (and (directory? file)
> +                              (delete-file-recursively file)))
> +                       (map (cut string-append "src/" <>)
> +                            (scandir "src"
> +                                     (lambda (file)
> +                                       (not (member file free)))))))
> +           ;; Only make the utils target, not the userApps target,
> +           ;; because that requires libraries we won't build.
> +           (substitute* "Makefile"
> +             ((" userApps") " utils"))
> +           ;; Only build libraries that are free.
> +           (substitute* "src/makefile"
> +             (("DIRS =.*") "DIRS =\n")
> +             (("cd jkOwnLib.*") "")
> +             ((" hgLib") "")
> +             (("cd hg.*") ""))
> +           (substitute* "src/utils/makefile"
> +             ;; These tools depend on "jkhgap.a", which is part of the
> +             ;; nonfree "src/hg/lib" directory.
> +             (("raSqlQuery") "")
> +             (("pslLiftSubrangeBlat") "")
> +
> +             ;; Do not build UCSC tools, which may require nonfree
> +             ;; components.
> +             (("ALL_APPS =.*") "ALL_APPS = $(UTILS_APPLIST)\n"))
> +           #t))))
> +    (build-system gnu-build-system)
> +    (arguments
> +     `( ;; There is no global test target and the test target for
> +       ;; individual tools depends on input files that are not
> +       ;; included.
> +       #:tests? #f
> +       #:phases
> +       (modify-phases %standard-phases
> +         (add-after 'unpack 'fix-paths
> +           (lambda _
> +             (substitute* "Makefile"
> +               (("/bin/echo") (which "echo")))
> +             #t))
> +         (add-after 'unpack 'prepare-samtabix
> +           (lambda* (#:key inputs #:allow-other-keys)
> +             (copy-recursively (assoc-ref inputs "samtabix")
> +                               "samtabix")
> +             #t))
> +         (delete 'configure)
> +         (replace 'install
> +           (lambda* (#:key outputs #:allow-other-keys)
> +             (let ((bin (string-append (assoc-ref outputs "out")
> +                                       "/bin")))
> +               (copy-recursively "bin" bin))
> +             #t)))))
> +    (native-inputs
> +     `(("samtabix"
> +        ,(origin
> +           (method git-fetch)
> +           (uri (git-reference
> +                 (url "http://genome-source.cse.ucsc.edu/samtabix.git";)
> +                 (commit "10fd107909c1ac4d679299908be4262a012965ba")))
> +           (sha256
> +            (base32
> +             "0c1nj64l42v395sa84n7az43xiap4i6f9n9dfz4058aqiwkhkmma"))))))
> +    (inputs
> +     `(("zlib" ,zlib)
> +       ("tcsh" ,tcsh)
> +       ("perl" ,perl)
> +       ("libpng" ,libpng)
> +       ("mysql" ,mysql)
> +       ("openssl" ,openssl)))
> +    (home-page "http://genome.cse.ucsc.edu/index.html";)
> +    (synopsis "Assorted bioinformatics utilities")
> +    (description "This package provides the kentUtils, a selection of
> +bioinformatics utilities used in combination with the UCSC genome
> +browser.")
> +    ;; Only a subset of the sources are released under a non-copyleft
> +    ;; free software license.  All other sources are removed in a
> +    ;; snippet.  See this bug report for an explanation of how the
> +    ;; license statements apply:
> +    ;; https://github.com/ENCODE-DCC/kentUtils/issues/12
> +    (license (license:non-copyleft
> +              "http://genome.ucsc.edu/license/";
> +              "The contents of this package are free for all uses."))))

LGTM.

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