Re: [PATCH] Add vcflib.

[Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>]

Roel Janssen <roel@gnu.org> writes:
> From c934cee6c84a39de36ecb4c3a85340ff025b1343 Mon Sep 17 00:00:00 2001
> From: Roel Janssen <roel@gnu.org>
> Date: Tue, 22 Mar 2016 15:50:12 +0100
> Subject: [PATCH 6/8] gnu: Add fastahack.

> * gnu/packages/bioinformatics.scm (fastahack): New variable.
> ---
>  gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++++++++++++
>  1 file changed, 34 insertions(+)

> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 261660f..9cbde46 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -4951,3 +4951,37 @@ combinatorial configurations.\" G Ehrlich - Journal of the ACM (JACM),
>        (description "A program to compare version strings.  It intends to be a
>  replacement for strverscmp.")
>        (license license:gpl3+))))
> +
> +(define-public fastahack
> +  (let ((commit "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd"))
> +    (package
> +      (name "fastahack")
> +      (version (string-append "0-1." (string-take commit 7)))
> +      (source (origin
> +        (method url-fetch)
> +        (uri (string-append "https://github.com/ekg/fastahack/archive/"
> +                            commit ".tar.gz"))
> +        (file-name (string-append name "-" version
> "-checkout.tar.gz"))

I don’t think we should add “checkout” here.

> +        (sha256
> +         (base32 "0j25lcl3jk1kls66zzxjfyq5ir6sfcvqrdwfcva61y3ajc9ssay2"))))
> +      (build-system gnu-build-system)
> +      (arguments
> +       `(#:tests? #f ; There are no tests to run.
> +         #:phases
> +         (modify-phases %standard-phases
> +           (delete 'configure) ; There is no configure phase.
> +           (replace 'install
> +             (lambda* (#:key outputs #:allow-other-keys)
> +               (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
> +                 (install-file "fastahack" bin)))))))
> +      (home-page "https://github.com/ekg/fastahack")
> +      (synopsis "Program for indexing and sequence extraction from
> FASTA files")

This sounds a bit off.  It’s “indexing of ... FASTA files” (not “from”)
but “sequence extraction from FASTA files”.  Maybe dropping “Program
for” would help here:

  “Index and extract sequences from FASTA files”

What do you think?

> +      (description "Fastahack is a small application for indexing and extracting
> +sequences and subsequences from FASTA files.  The included Fasta.cpp library
> +provides a FASTA reader and indexer that can be embeddedinto applications which
> +would benefit from directly reading subsequences from FASTA files.  The library
> +automatically handles index file generation and use.")

“embeddedinto” should be split.
I would drop mention of “Fasta.cpp” – or is this really the name of the library?

> +      ;; libdisorder is licensed GPLv2.  The parent project (vcflib), of which
> +      ;; this program is a submodule, is licensed MIT, which is the same as
> +      ;; the Expat license.
> +      (license (list license:gpl2 license:expat)))))

As before we use the license of this code and ignore the parent
project’s license.

Here’s a license problem, though.  The files “Fasta.h” and “Fasta.cpp”
contain notices like this:

> // ***************************************************************************
> // FastaIndex.h (c) 2010 Erik Garrison <erik.garrison@bc.edu>
> // Marth Lab, Department of Biology, Boston College
> // All rights reserved.
> // ---------------------------------------------------------------------------
> // Last modified: 5 February 2010 (EG)
> // ---------------------------------------------------------------------------

“disorder.c” has license GPLv2+.

There’s a bug report mentioning this problem here:

   https://github.com/ekg/fastahack/issues/8

As it is now we cannot include this in Guix upstream unless the non-free
files are removed in a snippet.

~~ Ricardo