Re: [PATCH 2/4] gnu: Add ncbi-tools.

[Ricardo Wurmus]

Hi Ben,

thank you for the patch!

> * gnu/packages/bioinformatics.scm (ncbi-tools): New variable.
> ---
>  gnu/packages/bioinformatics.scm | 62 
> +++++++++++++++++++++++++++++++++++++++++
>  1 file changed, 62 insertions(+)

[…]

> +       #:phases
> +       (modify-phases %standard-phases
> +         (delete 'configure)
> +         (add-after 'unpack 'patch-sources
> +            (lambda _

Indentation here is a little too far.  The opening paren is usually
aligned with the first “d” off “add-after”.

> +              (for-each (lambda (file)
> +                          (substitute* file
> +                            (("NCBI_MAKE_SHELL = .*")
> +                             (string-append
> +                              "NCBI_MAKE_SHELL = "
> +                              (which "sh")
> +                              "\n"))))
> +                        (find-files "platform" ".*mk"))

Here I’d use

    (substitute* (find-files "platform" ".*mk")
      …)

“substitute*” can take a list of files.  That’s nicer than using
“for-each” here.

> +              (substitute* "make/ln-if-absent"
> +                (("set path=\\(/usr/bin /bin\\)") ""))
> +              #t))
> +         (replace 'build
> +            (lambda _

Same as above; it’s a little too far to the right.

> +              (chdir "..")
> +              (zero? (system* "ncbi/make/makedis.csh"))))
> +         (replace 'install
> +           (lambda* (#:key outputs #:allow-other-keys)

And the same here.

> +             (let* ((out (assoc-ref outputs "out"))
> +                    (bin (string-append out "/bin"))
> +                    (man (string-append out "/share/man/man1")))
> +               (for-each (lambda (file)
> +                           (install-file
> +                            (string-append "ncbi/build/" file) bin)
> +                           (install-file
> +                            (string-append "ncbi/doc/man/" file ".1") man))
> +                         ;; XXX: TODO: Install and test other binaries.
> +                         (list "tbl2asn"))
> +               #t))))))
> +    (native-inputs
> +     `(("csh" ,tcsh)
> +       ("pkg-config" ,pkg-config)
> +       ("coreutils" ,coreutils)))
> +    (home-page 
> "https://www.ncbi.nlm.nih.gov/IEB/ToolBox/MainPage/index.html";)
> +    (synopsis "NCBI-related tools")
> +    (description "The United States of America @dfn{National Center for
> +Biotechnology Information} (NCBI) Software Development Toolkit is for the
> +production and distribution of GenBank, Entrez, BLAST and related NCBI
> +services.")
> +    (license license:public-domain)))
> +

Okay with these changes.  Thank you!

-- 
Ricardo

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