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
GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC
http://elephly.net
