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 .| ..
. |---. .--/ .
.. \--------/ . .
. . .. .. .
. ... ..... ..... .. ..
. .. . . . .. . .... .
. .. . .. . . .. . . .
. .. . . ... . .. .. .
.... . .. .. ... .. .
.. . ... . .. .. .
. .. . . . ... ..
... . . .. ... .
. .. . .. .....
____ ____ ._ __ _ _ ____ ____ ___ _ _
(_ _)( ___)( ) ( ) ( \/ )( ___)(_ _)/ __)( )_( )
.-_)( )__) )(__ )(__ \ / )__) _)(_ \__ \ ) _ (
\____) (____)(____)(____)(__) (__) (____)(___/(_) (_)
