Re: [PATCH] gnu: Add SEEK.

[Alex Kost]

Ricardo Wurmus (2016-06-15 16:31 +0300) wrote:

> * gnu/packages/bioinformatics.scm (seek): New variable.
> ---
>  gnu/packages/bioinformatics.scm | 74 
> +++++++++++++++++++++++++++++++++++++++++
>  1 file changed, 74 insertions(+)
[...]
> +(define-public seek
> +  ;; There are no release tarballs.  According to the installation
> +  ;; instructions at http://seek.princeton.edu/installation.jsp, the latest
> +  ;; stable release is identified by this changeset ID.
> +  (let ((changeset "2329130")
> +        (revision "1"))
> +    (package
> +      (name "seek")
> +      (version (string-append "0-" revision "." changeset))
> +      (source (origin
> +                (method hg-fetch)
> +                (uri (hg-reference
> +                      (url "https://bitbucket.org/libsleipnir/sleipnir";)
> +                      (changeset changeset)))
> +                (sha256
> +                 (base32
> +                  "0qrvilwh18dpbhkf92qvxbmay0j75ra3jg2wrhz67gf538zzphsx"))))
> +      (build-system gnu-build-system)
> +      (arguments
> +       `(#:modules ((srfi srfi-1)
> +                    (guix build gnu-build-system)
> +                    (guix build utils))
> +         #:phases
> +         (let ((dirs '("SeekMiner"
> +                       "SeekEvaluator"
> +                       "SeekPrep"
> +                       "Distancer"
> +                       "Data2DB"
> +                       "PCL2Bin")))
> +           (modify-phases %standard-phases
> +             (add-before 'configure 'bootstrap
> +               (lambda _
> +                 (zero? (system* "bash" "gen_auto"))))
> +             (add-after 'build 'build-additional-tools
> +               (lambda* (#:key make-flags #:allow-other-keys)
> +                 (fold (lambda (dir result)
> +                         (with-directory-excursion (string-append "tools/" 
> dir)
> +                           (and result
> +                                (zero? (apply system*
> +                                              `("make" ,@make-flags))))))

or just: (zero? (apply system* "make" make-flags))

Is 'fold' really needed here?  What about:

  (every (lambda (dir)
           (with-directory-excursion (string-append "tools/" dir)
             (zero? (apply system* "make" make-flags))))
         dirs)

> +                       #t dirs)))
> +             (add-after 'install 'install-additional-tools
> +               (lambda* (#:key make-flags #:allow-other-keys)
> +                 (fold (lambda (dir result)
> +                         (with-directory-excursion (string-append "tools/" 
> dir)
> +                           (and result
> +                                (zero? (apply system*
> +                                              `("make" ,@make-flags 
> "install"))))))
> +                       #t dirs)))))))
> +      (inputs
> +       `(("gsl" ,gsl)
> +         ("boost" ,boost)
> +         ("libsvm" ,libsvm)
> +         ("readline" ,readline)
> +         ("gengetopt" ,gengetopt)
> +         ("log4cpp" ,log4cpp)))
> +      (native-inputs
> +       `(("autoconf" ,autoconf)
> +         ("automake" ,automake)
> +         ("perl" ,perl)))
> +      (home-page "http://seek.princeton.edu";)
> +      (synopsis "Gene co-expression search engine")
> +      (description
> +       "SEEK is a computational gene co-expression search engine.  SEEK 
> provides
> +biologists with a way to navigate the massive human expression compendium 
> that
> +now contains thousands of expression datasets.  SEEK returns a robust ranking
> +of co-expressed genes in the biological area of interest defined by the 
> user's
> +query genes.  It also prioritizes thousands of expression datasets according
> +to the user's query of interest.")
> +      (license license:cc-by3.0))))
> +
>  (define-public samtools
>    (package
>      (name "samtools")

-- 
Alex