Re: [PATCH] Add Jellyfish.

[Ben Woodcroft <b.woodcroft@uq.edu.au>]

Hi Ricardo,

On 19/12/15 04:19, Eric Bavier wrote:
> On 2015-12-18 17:42, Ricardo Wurmus wrote:
>> * gnu/packages/bioinformatics.scm (jellyfish): New variable.
> [...]
>> +    (native-inputs
>> +     `(("bc" ,bc)
>> +       ("time" ,time)
>> +       ("gunzip" ,gzip)))
>
> gzip is an implicit input of gnu-build-system, so could it be left out?
My testing confirms this.

But would it be possible to include the scripting language bindings, 
something along these lines?

+    (arguments
+     `(#:configure-flags '("--enable-ruby-binding"
+                           "--enable-python-binding"
+                           "--enable-perl-binding")
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'set-SHELL-variable
+           (lambda _
+             ;; generator_manager.hpp either uses /bin/sh or $SHELL
+             ;; to run tests.
+             (setenv "SHELL" (which "bash"))
+             #t)))))
+    (native-inputs
+     `(("bc" ,bc)
+       ("time" ,time)
+       ("ruby" ,ruby)
+       ("python" ,python-2)
+       ("perl" ,perl)))

Currently the perl tests fail for reasons I don't have time to 
investigate, and perhaps some search paths need to be exported too.

I did find the time to confirm that the most important part of this 
program works though:

sh-4.3# jellyfish jf
                    .......
           ..........      .....
        ....                   ....
       ..     /-+       +---\     ...
       .     /--|       +----\      ...
      ..                              ...
      .                                 .
      ..      +----------------+         .
       .      |. AAGATGGAGCGC .|         ..
       .      |---.        .--/           .
      ..          \--------/     .        .
      .     .            ..     ..        .
      .    ... .....   .....    ..        ..
      .   .. . .   .  ..   .   ....        .
      .  ..  . ..   . .    ..  .  .         .
      . ..   .  .   ...     . ..  ..        .
     ....    . ..   ..      ...    ..       .
    .. .     ...     .      ..      ..      .
    . ..      .      .       .       ...    ..
    ...       .      .      ..         ...   .
    .         ..     .      ..           .....
   ____  ____  ._    __   _  _  ____  ____  ___  _   _
  (_  _)( ___)(  )  (  ) ( \/ )( ___)(_  _)/ __)( )_( )
.-_)(   )__)  )(__  )(__ \  /  )__)  _)(_ \__ \ ) _ (
\____) (____)(____)(____)(__) (__)  (____)(___/(_) (_)