CVS: dists/10.2/unstable/main/finkinfo/sci phylip-3.6a3-1.info,NONE,1.1 phylip-3.6a3-1.patch,NONE,1.1

[David R. M. <dm...@us...>]

Update of /cvsroot/fink/dists/10.2/unstable/main/finkinfo/sci
In directory sc8-pr-cvs1:/tmp/cvs-serv28995

Added Files:
	phylip-3.6a3-1.info phylip-3.6a3-1.patch 
Log Message:
new package from tracker


--- NEW FILE: phylip-3.6a3-1.info ---
Package: phylip
Version: 3.6a3
Revision: 1
Source: ftp://evolution.genetics.washington.edu/pub/%n/%n36/%n.tar.Z
Source-MD5: d2fcb9c5f6cbe90a30f45548d584e914
PatchScript: sed 's|@PREFIX@|%p|g' <%a/%f.patch | patch -p1 
Depends: x11
#cd %p/src/%f/%n/src/ && make install
CompileScript: <<
head -7 src/phylip.c > Copyright
cd src && make install
<<
InstallScript: <<
install -d -m 755 %i/bin
install -d -m 755 %i/share/%n
install -m 644 exe/font* %i/share/%n
ln -s font1 %i/share/%n/fontfile
rm -f exe/font*
install -m 755 exe/* %i/bin
install -d -m 755 %i/share/doc/%n
install -d -m 755 %i/share/doc/%n/doc
install -m 644 %n.html Copyright %i/share/doc/%n
install -m 644 doc/* %i/share/doc/%n/doc
<<
Description: Package of programs for inferring phylogenies
DescDetail: <<
PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). It is available free over the Internet, and written to work on as many different kinds of computer systems as possible.  The source code is distributed (in C), and for some particular systems executables are also distributed.  In particular, already-compiled executables are available for Windows95/98/NT, Windows 3.x, DOS, PowerMac, and 68k Macintosh systems.  Complete documentation is available on documentation files that come with the package. 

Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites, distance matrices, and 0/1 discrete characters. 

The programs are controlled through a menu , which asks the users which options they want to set, and allows them to start the computation.  The data are read into the program from a text file, which the user can prepare using any word processor or text editor (but it is important that this text file not be in the special format of that word processor -- it should instead be in "flat ASCII" or "Text Only" format).  Some sequence analysis programs such as alignment programs can write data files in the PHYLIP format.  Most of the programs look for the data in a file called "infile" -- if they do not find this file they then ask the user to type in the file name of the data file. 

Output is written onto special files with names like "outfile" and "treefile". Trees written onto "treefile" are in the Newick format, an informal standard agreed to in 1986 by authors of a number of major phylogeny packages. 
<<

License: Restrictive
Maintainer: Cyril Gallut <ga...@cc...>
Homepage: http://evolution.genetics.washington.edu/phylip.html

--- NEW FILE: phylip-3.6a3-1.patch ---
--- phylip/src/Makefile~        2002-07-27 00:17:20.000000000 +0200
+++ phylip/src/Makefile 2003-02-28 15:53:13.000000000 +0100
@@ -62,13 +62,13 @@
 #
 #
 #A minimal one
-CFLAGS =
+#CFLAGS =
 #
 # A basic one for debugging
 #CFLAGS  = -g 
 #
 # An optimized one for gcc
-#CFLAGS  = -O3 -fomit-frame-pointer
+CFLAGS  = -O3 -fomit-frame-pointer
 #
 # For some serious debugging using Gnu gcc
 #
@@ -84,14 +84,14 @@
 # and here are some possible DFLAGS statements:
 #
 # A minimal one
-DFLAGS  = -DX $(CFLAGS)
+#DFLAGS  = -DX $(CFLAGS)
 DLIBS= -lX11 -lXaw -lXt
 #
 # A basic one for debugging
 #DFLAGS  = -g -DX
 #
 # For Gnu C++ for runs
-#DFLAGS  = -O3 -DX -fomit-frame-pointer
+DFLAGS  = -O3 -DX -fomit-frame-pointer -I/usr/X11R6/include
 #
 # For Digital Alpha systems with Compaq Tru64 Unix
 #DFLAGS = -DX -fast 
@@ -115,16 +115,16 @@
 # ordinary compiles and the tree-drawing programs, CC and DC
 #
 # This one specifies the "cc" C compiler
-CC        = cc $(CFLAGS)
+#CC        = cc $(CFLAGS)
 #
 #  To use GCC instead, if it is not the compiler that "cc" invokes
-#CC        = gcc $(CFLAGS)
+CC        = gcc $(CFLAGS)
 #
 # This one specifies the "cc" C compiler for the Draw programs
-DC        = cc $(DFLAGS)
+#DC        = cc $(DFLAGS)
 #
 # To use GCC instead, if it is not the compiler that "cc" invokes
-#DC        = gcc $(DFLAGS)
+DC        = gcc $(DFLAGS)
 #
 # ----------------------------------------------------------------------------
 #  (After this point there should not be any reason to change anything)

--- phylip/src/phylip.h~   2003-02-28 17:50:55.000000000 +0100
+++ phylip/src/phylip.h    2003-02-28 17:51:00.000000000 +0100
@@ -67,7 +67,7 @@
 #define EBCDIC false
 #define INFILE "infile"
 #define OUTFILE "outfile"
-#define FONTFILE "fontfile" /* on unix this might be /usr/local/lib/fontfile */
+#define FONTFILE "@PREFIX@/share/phylip/fontfile" /* on unix this might be /usr/local/lib/fontfile */
 #define PLOTFILE "plotfile"
 #define INTREE "intree"
 #define INTREE2 "intree2"