@@ 2974,31 2974,31 @@ sequencing tag position and orientation.")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'enter-dir
- (lambda _ (chdir "core") #t))
+ (lambda _ (chdir "core") #t))
(add-after 'enter-dir 'patch-makefile
- (lambda _
- ;; on advice from the MAFFT authors, there is no need to
- ;; distribute mafft-profile, mafft-distance, or
- ;; mafft-homologs.rb as they are too "specialised".
- (substitute* "Makefile"
- ;; remove mafft-homologs.rb from SCRIPTS
- (("^SCRIPTS = mafft mafft-homologs.rb")
- "SCRIPTS = mafft")
- ;; remove mafft-homologs from MANPAGES
- (("^MANPAGES = mafft.1 mafft-homologs.1")
- "MANPAGES = mafft.1")
- ;; remove mafft-distance from PROGS
- (("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance")
- "PROGS = dvtditr dndfast7 dndblast sextet5")
- ;; remove mafft-profile from PROGS
- (("splittbfast disttbfast tbfast mafft-profile 2cl mccaskillwrap")
- "splittbfast disttbfast tbfast f2cl mccaskillwrap")
- (("^rm -f mafft-profile mafft-profile.exe") "#")
- (("^rm -f mafft-distance mafft-distance.exe") ")#")
- ;; do not install MAN pages in libexec folder
- (("^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES\\) \
+ (lambda _
+ ;; on advice from the MAFFT authors, there is no need to
+ ;; distribute mafft-profile, mafft-distance, or
+ ;; mafft-homologs.rb as they are too "specialised".
+ (substitute* "Makefile"
+ ;; remove mafft-homologs.rb from SCRIPTS
+ (("^SCRIPTS = mafft mafft-homologs.rb")
+ "SCRIPTS = mafft")
+ ;; remove mafft-homologs from MANPAGES
+ (("^MANPAGES = mafft.1 mafft-homologs.1")
+ "MANPAGES = mafft.1")
+ ;; remove mafft-distance from PROGS
+ (("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance")
+ "PROGS = dvtditr dndfast7 dndblast sextet5")
+ ;; remove mafft-profile from PROGS
+ (("splittbfast disttbfast tbfast mafft-profile 2cl mccaskillwrap")
+ "splittbfast disttbfast tbfast f2cl mccaskillwrap")
+ (("^rm -f mafft-profile mafft-profile.exe") "#")
+ (("^rm -f mafft-distance mafft-distance.exe") ")#")
+ ;; do not install MAN pages in libexec folder
+ (("^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES\\) \
\\$\\(DESTDIR\\)\\$\\(LIBDIR\\)") "#"))
- #t))
+ #t))
(add-after 'enter-dir 'patch-paths
(lambda* (#:key inputs #:allow-other-keys)
(substitute* '("pairash.c"
@@ 3008,13 3008,23 @@ sequencing tag position and orientation.")
(string-append prefix (which "awk")))
(("grep") (which "grep")))
#t))
- (delete 'configure))))
+ (delete 'configure)
+ (add-after 'install 'wrap-programs
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (path (string-append
+ (assoc-ref %build-inputs "coreutils") "/bin:")))
+ (for-each (lambda (file)
+ (wrap-program file
+ `("PATH" ":" prefix (,path))))
+ (find-files bin)))
+ #t)))))
(inputs
`(("perl" ,perl)
("gawk" ,gawk)
- ("grep" ,grep)))
- (propagated-inputs
- `(("coreutils" ,coreutils)))
+ ("grep" ,grep)
+ ("coreutils" ,coreutils)))
(home-page "http://mafft.cbrc.jp/alignment/software/")
(synopsis "Multiple sequence alignment program")
(description