Re: [PATCH] gnu: Add bioawk.

[Leo Famulari <leo@famulari.name>]

On Tue, Mar 08, 2016 at 09:10:14PM +0100, Roel Janssen wrote:
> From 990eda92a62dc25d0f5792437a82e119c5e3579f Mon Sep 17 00:00:00 2001
> From: Roel Janssen <roel@gnu.org>
> Date: Tue, 8 Mar 2016 21:06:53 +0100
> Subject: [PATCH] gnu: Add bioawk.
> 
> * gnu/packages/bioinformatics.scm (bioawk): New variable.

Thanks for the patch!

[...]

> +    (propagated-inputs
> +     `(("zlib" ,zlib)))

I changed this to a plain input, and then checked the references of the
resulting build, and zlib is referenced. Considering that, does it need
to be propagated into the user's profile? Propagated inputs should be
avoided if possible.

> +    (native-inputs
> +     `(("bison" ,bison)))
> +    (arguments
> +     `(#:parallel-build? #f
> +       #:phases
> +       (modify-phases %standard-phases
> +         (delete 'configure)
> +         (delete 'check)

Can you say why tests are disabled? It can be as simple as "no test
suite" if that is accurate.

> +         (replace
> +          'install
> +          (lambda* (#:key outputs #:allow-other-keys)
> +            (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
> +              (install-file "bioawk" bin)))))))

The git repo includes a manpage 'awk.1'. Can you send an updated patch
that installs that as well?

> +    (home-page "https://github.com/lh3/bioawk")
> +    (synopsis "AWK with bioinformatics extensions")
> +    (description "Bioawk is an extension to Brian Kernighan's awk, adding the
> +support of several common biological data formats, including optionally gzip'ed
> +BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.  It
> +also adds a few built-in functions and an command line option to use TAB as the
> +input/output delimiter.  When the new functionality is not used, bioawk is
> +intended to behave exactly the same as the original BWK awk.")
> +    (license license:x11)))
> +
>  (define-public python2-pybedtools
>    (package
>      (name "python2-pybedtools")
> -- 
> 2.5.0
> 

> Dear Guix,
> 
> Here's a patch to add bioawk -- a version of awk specialized in
> biological data formats.
> 
> Please let me know when something is wrong with the patch.
> 
> Kind regards,
> Roel Janssen