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Re: [PATCH] Add MAFFT.
From: |
Ben Woodcroft |
Subject: |
Re: [PATCH] Add MAFFT. |
Date: |
Sun, 26 Jul 2015 13:10:14 +1000 |
User-agent: |
Mozilla/5.0 (X11; Linux x86_64; rv:31.0) Gecko/20100101 Thunderbird/31.7.0 |
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
0001-gnu-Add-mafft.patch
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