Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv14667
Added Files:
mafft.info mafft.patch
Log Message:
new package mafft 7.058
--- NEW FILE: mafft.patch ---
--- a/core/Makefile.orig 2013-08-16 13:17:08.000000000 -0400
+++ b/core/Makefile 2013-08-16 13:25:36.000000000 -0400
@@ -1,7 +1,8 @@
-PREFIX = /usr/local
-LIBDIR = $(PREFIX)/libexec/mafft
+PREFIX = @FINK_PREFIX@
+LIBDIR = $(PREFIX)/lib/mafft
BINDIR = $(PREFIX)/bin
MANDIR = $(PREFIX)/share/man/man1
+DESTDIR =
#MNO_CYGWIN = -mno-cygwin
@@ -511,17 +512,17 @@
# rm -f ../binaries/* ../scripts/*
install : all
- mkdir -p $(LIBDIR)
- chmod 755 $(LIBDIR)
- mkdir -p $(BINDIR)
- chmod 755 $(BINDIR)
+ mkdir -p $(DESTDIR)$(LIBDIR)
+ chmod 755 $(DESTDIR)$(LIBDIR)
+ mkdir -p $(DESTDIR)$(BINDIR)
+ chmod 755 $(DESTDIR)$(BINDIR)
chmod 755 $(SCRIPTS)
- $(INSTALL) $(SCRIPTS) $(BINDIR)
+ $(INSTALL) $(SCRIPTS) $(DESTDIR)$(BINDIR)
chmod 755 $(PROGS)
- $(INSTALL) -s $(PROGS) $(LIBDIR)
- $(INSTALL) -m 644 $(MANPAGES) $(LIBDIR)
+ $(INSTALL) -s $(PROGS) $(DESTDIR)$(LIBDIR)
+ $(INSTALL) -m 644 $(MANPAGES) $(DESTDIR)$(LIBDIR)
- ( cd $(BINDIR); \
+ ( cd $(DESTDIR)$(BINDIR); \
rm -f linsi ginsi einsi fftns fftnsi nwns nwnsi xinsi qinsi; \
rm -f mafft-linsi mafft-ginsi mafft-einsi mafft-fftns mafft-fftnsi mafft-nwns
mafft-nwnsi mafft-xinsi mafft-qinsi; \
ln -s mafft linsi; ln -s mafft ginsi; ln -s mafft fftns; \
@@ -533,8 +534,8 @@
rm -f mafft-profile mafft-profile.exe; ln -s $(LIBDIR)/mafft-profile .; \
rm -f mafft-distance mafft-distance.exe; ln -s $(LIBDIR)/mafft-distance . )
- mkdir -p $(MANDIR)
- chmod 755 $(MANDIR)
- $(INSTALL) -m 644 $(MANPAGES) $(MANDIR)
+ mkdir -p $(DESTDIR)$(MANDIR)
+ chmod 755 $(DESTDIR)$(MANDIR)
+ $(INSTALL) -m 644 $(MANPAGES) $(DESTDIR)$(MANDIR)
# remove incorrectly installed manpages by previous versions
# rm -f /usr/local/man/man1/mafft.1 /usr/local/man/man1/mafft-homologs.1
--- NEW FILE: mafft.info ---
Package: mafft
Version: 7.058
Revision: 1
Description: Multiple sequenc alignment program
License: BSD
Maintainer: Hanspeter Niederstrasser <nie...@users.sourceforge.net>
Source: http://mafft.cbrc.jp/alignment/software/%n-%v-without-extensions-src.tgz
Source-MD5: ecb72d3194ac25af2d8b4adfb65aa09e
Source-Checksum: SHA1(549c3588e3d2890628eff75bda2facfff131ad33)
SourceDirectory: %n-%v-without-extensions
PatchFile: %n.patch
PatchFile-MD5: f923a089eec295edc3a766f63a178a2e
PatchScript:<<
sed 's|@FINK_PREFIX@|%p|g' < %{PatchFile} | patch -p1
<<
CompileScript: <<
cd core; make PREFIX=%p
<<
InfoTest: <<
TestScript: <<
#!/bin/sh -ev
cd test
export MAFFT_BINARIES=%b/binaries
export PATH=%b/binaries:%b/scripts:$PATH
mafft --progress %b/core/progressfile sample > test.fftns2 ||
exit 2
mafft --progress %b/core/progressfile --maxiterate 100 sample
> test.fftnsi || exit 2
mafft --progress %b/core/progressfile --globalpair sample >
test.gins1 || exit 2
mafft --progress %b/core/progressfile --globalpair --maxiterate
100 sample > test.ginsi || exit 2
mafft --progress %b/core/progressfile --localpair sample >
test.lins1 || exit 2
mafft --progress %b/core/progressfile --localpair --maxiterate
100 sample > test.linsi || exit 2
diff test.fftns2 sample.fftns2 || exit 2
diff test.fftnsi sample.fftnsi || exit 2
diff test.gins1 sample.gins1 || exit 2
diff test.ginsi sample.ginsi || exit 2
diff test.lins1 sample.lins1 || exit 2
<<
<<
InstallScript: <<
cd core; make install PREFIX=%p DESTDIR=%d
<<
DocFiles: license
Homepage: http://mafft.cbrc.jp/alignment/software/
DescDetail: <<
MAFFT is a multiple sequence alignment program for unix-like operating
systems. It offers a range of multiple alignment methods, L-INS-i
(accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; for
alignment of <~10,000 sequences), etc.
Katoh, Misawa, Kuma, Miyata 2002 (Nucleic Acids Res. 30:3059-3066)
MAFFT: a novel method for rapid multiple sequence alignment based
on fast Fourier transform.
<<
DescPort: <<
Add DESTDIR to Makefile. Reported upstream.
<<
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