On 26/07/15 05:26, Ricardo Wurmus wrote:
> Hi Ben,
>
>> +       #:phases
>> +       (modify-phases %standard-phases
>> +         (add-after 'unpack 'enter-dir
>> +                    (lambda _ (chdir "core") #t))
>> +         ;; on advice from the MAFFT authors, do not distribute mafft-profile,
>> +         ;; mafft-distance mafft-homologs.rb
> What does this mean?  Are they non-free software?  If so, they should be
> removed in a snippet.

Sorry for the confusion. MAFFT itself is all free software, but on the 
website it allows you to download a version "with-extensions" which 
includes non-free software.

I contacted the MAFFT authors and they suggested that there was no need 
to distribute these three programs in a mafft package. I've updated the 
comment to clarify.

I'm actually a bit confused as to the difference between a snippet vs. a 
patch stage as above - when is each appropriate? Snippets are only for 
removing non-free software?

>
>> +         (add-after 'enter-dir 'patch-makefile
>> +                    (lambda _
>> +                      (substitute* "Makefile"
>> +                        (("^SCRIPTS = mafft mafft-homologs.rb")
>> +                         "SCRIPTS = mafft")
>> +                        (((string-append "^PROGS = dvtditr dndfast7 dndblast"
>> +                                         " sextet5 mafft-distance"))
>> +                         "PROGS = dvtditr dndfast7 dndblast sextet5")
>> +                        (((string-append "splittbfast disttbfast tbfast "
>> +                                         "mafft-profile f2cl mccaskillwrap"))
>> +                         "splittbfast disttbfast tbfast f2cl mccaskillwrap")
> This line looks particularly unclear.  It took me a little too long to
> find the difference in the replacement.  Is there a nicer regular
> expression that you could use to indicate the removal of
> “mafft-profile”?

I've added comments and alignment.

ben