diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 64 |
1 files changed, 37 insertions, 27 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b29ee0bf2f..5ee881f372 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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 |