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