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Re: [PATCH] Add MAFFT.
From: |
Ricardo Wurmus |
Subject: |
Re: [PATCH] Add MAFFT. |
Date: |
Sat, 25 Jul 2015 21:26:50 +0200 |
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.
> + (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”?
> + (("^rm -f mafft-profile mafft-profile.exe") "#")
> + (("^rm -f mafft-distance mafft-distance.exe") ")#")
> + ;; do not install MAN pages in libexec folder
> + (((string-append "^\t\\$\\(INSTALL\\) -m 644 \\$\\("
> + "MANPAGES\\) \\$\\(DESTDIR\\)\\$"
> + "\\(LIBDIR\\)")) "#"))
> + #t))
> + (delete 'configure))))
> + (inputs
> + `(("perl" ,perl)))
> + (home-page "http://mafft.cbrc.jp/alignment/software/")
> + (synopsis
> + "Multiple sequence alignment program for unix-like operating systems")
Please remove “for unix-like operating systems”.
> + (description
> + "MAFFT offers a range of multiple alignment methods for nucleotide and
> +protein sequences. For instance, it offers L-INS-i (accurate; for alignment
> +of <∼200 sequences) and FFT-NS-2 (fast; for alignment of <∼30,000
> +sequences).")
> + (license (license:non-copyleft "file://license"
> + "See license in the distribution."))))
~~ Ricardo