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add phylip
This commit is contained in:
starsareintherose
parent
45208dbbe0
commit
21671d7759
5 changed files with 388 additions and 0 deletions
42
phylip/PKGBUILD
Normal file
42
phylip/PKGBUILD
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@ -0,0 +1,42 @@
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# Maintainer: Michael Schubert <mschu.dev at gmail>
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# Contributor: Abhishek Dasgupta <abhidg@gmail.com>
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# Contributor: Damir Perisa <damir.perisa@bluewin.ch>
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pkgname=phylip
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pkgver=3.698
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pkgrel=1
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pkgdesc="A collection of programmes for evolutive genetics and inferring phylogenies"
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arch=('i686' 'x86_64')
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url="http://evolution.genetics.washington.edu/phylip.html"
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source=(http://evolution.gs.washington.edu/phylip/download/phylip-$pkgver.zip
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phylip-3.698-makefile.patch
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phylip-3.698-fno-common.patch)
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optdepends=('java-runtime')
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license=('custom')
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sha256sums=('cb12e5105d25872eed705d243ca32b400e180d38c3437d58335f11a431df0e46'
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'91779c722959b7e08f4e3e03e9c1cc14c4a81d152e46d4a6b30d0dd09e276637'
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'd2638f99a6cb1e893aa6c362f906d5fca94700e0e4d50392abba853be8f0fff3')
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prepare() {
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cd "$srcdir"/$pkgname-$pkgver
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# patches from gentoo ebuild: https://gitweb.gentoo.org/repo/gentoo.git/plain/sci-biology/phylip/files
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patch -p1 < ../phylip-3.698-makefile.patch
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patch -p1 < ../phylip-3.698-fno-common.patch
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}
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build() {
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cd "$srcdir"/$pkgname-$pkgver/src
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make -f Makefile.unx all
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}
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package() {
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cd "$srcdir"/$pkgname-$pkgver/src
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make -f Makefile.unx put
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cd "$srcdir"/$pkgname-$pkgver
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mkdir -p "$pkgdir"/usr/{lib,bin,share/phylip}
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rm -rf exe/testdata
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mv exe/factor{,-phylip}
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mv exe/*.so "$pkgdir"/usr/lib/
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mv exe/font* "$pkgdir"/usr/share/phylip/
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mv exe/* "$pkgdir"/usr/bin
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}
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10
phylip/lilac.py
Executable file
10
phylip/lilac.py
Executable file
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@ -0,0 +1,10 @@
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#!/usr/bin/env python3
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from lilaclib import *
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def pre_build():
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update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
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run_cmd(['updpkgsums'])
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def post_build():
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git_add_files('PKGBUILD')
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git_commit()
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8
phylip/lilac.yaml
Executable file
8
phylip/lilac.yaml
Executable file
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@ -0,0 +1,8 @@
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maintainers:
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- github: starsareintherose
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email: starsareintherose@outlook.com
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build_prefix: extra-x86_64
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update_on:
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- source: regex
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url: "https://evolution.gs.washington.edu/phylip/download/"
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regex: "phylip-(\d+.\d+).zip"
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70
phylip/phylip-3.698-fno-common.patch
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70
phylip/phylip-3.698-fno-common.patch
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@ -0,0 +1,70 @@
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--- a/src/draw.c
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+++ b/src/draw.c
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@@ -34,6 +34,11 @@
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char fontname[LARGE_BUF_LENGTH];
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+long treecolor, namecolor, backcolor, bottomcolor, vrmlskycolornear, vrmlskycolorfar,
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+ vrmlgroundcolornear, vrmlgroundcolorfar, vrmlplotcolor;
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+
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+char afmfile[FNMLNGTH];
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+
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/* format of matrix: capheight, length[32],length[33],..length[256]*/
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byte *full_pic ;
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--- a/src/draw.h
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+++ b/src/draw.h
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@@ -52,10 +52,10 @@
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double intensity, x, y, z;
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} vrmllighttype;
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-long treecolor, namecolor, backcolor, bottomcolor, vrmlskycolornear, vrmlskycolorfar,
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+extern long treecolor, namecolor, backcolor, bottomcolor, vrmlskycolornear, vrmlskycolorfar,
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vrmlgroundcolornear, vrmlgroundcolorfar, vrmlplotcolor;
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-char afmfile[FNMLNGTH];
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+extern char afmfile[FNMLNGTH];
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double lengthtext(char *, long, char *, fonttype);
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double heighttext(fonttype, char *);
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--- a/src/drawtree.c
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+++ b/src/drawtree.c
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@@ -69,7 +69,7 @@
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uselengths, regular, rotate, empty, rescaled,
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notfirst, improve, nbody, firstscreens, labelavoid;
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boolean pictbold,pictitalic,pictshadow,pictoutline;
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-boolean javarun;
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+extern boolean javarun;
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striptype stripe;
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plottertype plotter, oldplotter;
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--- a/src/phylip.c
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+++ b/src/phylip.c
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@@ -34,6 +34,8 @@
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#include "phylip.h"
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+boolean javarun;
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+
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#ifdef WIN32
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#include <windows.h>
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/* for console code (clear screen, text color settings) */
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--- a/src/phylip.h
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+++ b/src/phylip.h
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@@ -331,7 +331,7 @@
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/* Lower-triangular format. */
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#define MAT_LOWERTRI (MAT_LOWER | MAT_MACHINE)
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-boolean javarun;
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+extern boolean javarun;
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typedef long *steptr;
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typedef long longer[6];
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@@ -351,7 +351,6 @@
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extern long spp, words, bits;
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extern boolean ibmpc, ansi, tranvsp;
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extern naym *nayme; /* names of species */
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-boolean firstplotblock; // for debugging BMP output
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#define ebcdic EBCDIC
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258
phylip/phylip-3.698-makefile.patch
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258
phylip/phylip-3.698-makefile.patch
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@ -0,0 +1,258 @@
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--- a/src/Makefile.unx
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+++ b/src/Makefile.unx
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@@ -91,7 +90,6 @@
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#
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#
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#A minimal one
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-CFLAGS =
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#
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# A basic one for debugging
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#CFLAGS = -g
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@@ -220,7 +218,7 @@
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@echo "Done."
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@echo ""
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-put:
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+put: all
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@echo "Installing PHYLIP v3.6 binaries in $(EXEDIR)"
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@mkdir -p $(EXEDIR)
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@cp $(PROGS) $(EXEDIR)
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@@ -270,195 +268,195 @@
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clique.o: clique.c disc.h phylip.h
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clique: clique.o disc.o phylip.o
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- $(CC) $(CFLAGS) clique.o disc.o phylip.o $(LIBS) -o clique
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+ $(CC) $(LDFLAGS) clique.o disc.o phylip.o $(LIBS) -o clique
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cons.o: cons.c cons.h phylip.h
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consense.o: consense.c cons.h phylip.h
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consense: consense.o phylip.o cons.o
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- $(CC) $(CFLAGS) consense.o phylip.o cons.o $(LIBS) -o consense
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+ $(CC) $(LDFLAGS) consense.o phylip.o cons.o $(LIBS) -o consense
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contml.o: contml.c cont.h phylip.h
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contml: contml.o cont.o phylip.o
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- $(CC) $(CFLAGS) contml.o cont.o phylip.o $(LIBS) -o contml
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+ $(CC) $(LDFLAGS) contml.o cont.o phylip.o $(LIBS) -o contml
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contrast.o: contrast.c cont.h phylip.h
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contrast: contrast.o cont.o phylip.o
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- $(CC) $(CFLAGS) contrast.o cont.o phylip.o $(LIBS) -o contrast
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+ $(CC) $(LDFLAGS) contrast.o cont.o phylip.o $(LIBS) -o contrast
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dnacomp.o: dnacomp.c seq.h phylip.h
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dnacomp: dnacomp.o seq.o phylip.o
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- $(CC) $(CFLAGS) dnacomp.o seq.o phylip.o $(LIBS) -o dnacomp
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+ $(CC) $(LDFLAGS) dnacomp.o seq.o phylip.o $(LIBS) -o dnacomp
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dnadist.o: dnadist.c seq.h phylip.h
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dnadist: dnadist.o seq.o phylip.o
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- $(CC) $(CFLAGS) dnadist.o seq.o phylip.o $(LIBS) -o dnadist
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+ $(CC) $(LDFLAGS) dnadist.o seq.o phylip.o $(LIBS) -o dnadist
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dnainvar.o: dnainvar.c seq.h phylip.h
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dnainvar: dnainvar.o seq.o phylip.o
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- $(CC) $(CFLAGS) dnainvar.o seq.o phylip.o $(LIBS) -o dnainvar
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+ $(CC) $(LDFLAGS) dnainvar.o seq.o phylip.o $(LIBS) -o dnainvar
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dnaml.o: dnaml.c seq.h phylip.h
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dnaml: dnaml.o seq.o phylip.o
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- $(CC) $(CFLAGS) dnaml.o seq.o phylip.o $(LIBS) -o dnaml
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+ $(CC) $(LDFLAGS) dnaml.o seq.o phylip.o $(LIBS) -o dnaml
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dnamlk.o: dnamlk.c seq.h phylip.h mlclock.h printree.h
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dnamlk: dnamlk.o seq.o phylip.o mlclock.o printree.o
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- $(CC) $(CFLAGS) dnamlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o dnamlk
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+ $(CC) $(LDFLAGS) dnamlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o dnamlk
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dnamove.o: dnamove.c seq.h moves.h phylip.h
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dnamove: dnamove.o seq.o moves.o phylip.o
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- $(CC) $(CFLAGS) dnamove.o seq.o moves.o phylip.o $(LIBS) -o dnamove
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+ $(CC) $(LDFLAGS) dnamove.o seq.o moves.o phylip.o $(LIBS) -o dnamove
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dnapenny.o: dnapenny.c seq.h phylip.h
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dnapenny: dnapenny.o seq.o phylip.o
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- $(CC) $(CFLAGS) dnapenny.o seq.o phylip.o $(LIBS) -o dnapenny
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+ $(CC) $(LDFLAGS) dnapenny.o seq.o phylip.o $(LIBS) -o dnapenny
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dnapars.o: dnapars.c seq.h phylip.h
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dnapars: dnapars.o seq.o phylip.o
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- $(CC) $(CFLAGS) dnapars.o seq.o phylip.o $(LIBS) -o dnapars
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+ $(CC) $(LDFLAGS) dnapars.o seq.o phylip.o $(LIBS) -o dnapars
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dolmove.o: dolmove.c disc.h moves.h dollo.h phylip.h
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dolmove: dolmove.o disc.o moves.o dollo.o phylip.o
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- $(CC) $(CFLAGS) dolmove.o disc.o moves.o dollo.o phylip.o $(LIBS) -o dolmove
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+ $(CC) $(LDFLAGS) dolmove.o disc.o moves.o dollo.o phylip.o $(LIBS) -o dolmove
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dollop.o: dollop.c disc.h dollo.h phylip.h
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dollop: dollop.o disc.o dollo.o phylip.o
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- $(CC) $(CFLAGS) dollop.o disc.o dollo.o phylip.o $(LIBS) -o dollop
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+ $(CC) $(LDFLAGS) dollop.o disc.o dollo.o phylip.o $(LIBS) -o dollop
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dolpenny.o: dolpenny.c disc.h dollo.h phylip.h
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dolpenny: dolpenny.o disc.o dollo.o phylip.o
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- $(CC) $(CFLAGS) dolpenny.o disc.o dollo.o phylip.o $(LIBS) -o dolpenny
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+ $(CC) $(LDFLAGS) dolpenny.o disc.o dollo.o phylip.o $(LIBS) -o dolpenny
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draw.o: draw.c draw.h phylip.h
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- $(CC) $(DFLAGS) -c draw.c
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+ $(CC) $(DFLAGS) $(CPPFLAGS) -c draw.c
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draw2.o: draw2.c draw.h phylip.h
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- $(CC) $(DFLAGS) -c draw2.c
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+ $(CC) $(DFLAGS) $(CPPFLAGS) -c draw2.c
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drawgram.o: drawgram.c draw.h phylip.h
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- $(CC) $(DFLAGS) -c drawgram.c
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+ $(CC) $(DFLAGS) $(CPPFLAGS) -c drawgram.c
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drawgram: drawgram.o draw.o draw2.o phylip.o
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- $(CC) $(DFLAGS) draw.o draw2.o drawgram.o phylip.o $(DLIBS) -o drawgram
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+ $(CC) $(LDFLAGS) draw.o draw2.o drawgram.o phylip.o $(DLIBS) -o drawgram
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# needed by java
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-libdrawgram.so: drawgram.o draw.o draw2.o phylip.o
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- $(CC) $(CFLAGS) -o libdrawgram.so -shared -fPIC drawgram.c draw.c draw2.c phylip.c $(CLIBS)
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+libdrawgram.so:
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o libdrawgram.so -Wl,-soname,libdrawgram.so -shared -fPIC drawgram.c draw.c draw2.c phylip.c $(CLIBS)
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drawtree.o: drawtree.c draw.h phylip.h
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- $(CC) $(DFLAGS) -shared -fPIC -c drawtree.c
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+ $(CC) $(DFLAGS) $(CPPFLAGS) -c drawtree.c
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drawtree: drawtree.o draw.o draw2.o phylip.o
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- $(CC) $(DFLAGS) draw.o draw2.o drawtree.o phylip.o $(DLIBS) -o drawtree
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+ $(CC) $(LDFLAGS) draw.o draw2.o drawtree.o phylip.o $(DLIBS) -o drawtree
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# needed by java
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-libdrawtree.so: drawtree.o draw.o draw2.o phylip.o
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- $(CC) $(CFLAGS) -o libdrawtree.so -shared -fPIC drawtree.c draw.c draw2.c phylip.c $(CLIBS)
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+libdrawtree.so:
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+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o libdrawtree.so -Wl,-soname,libdrawtree.so -shared -fPIC drawtree.c draw.c draw2.c phylip.c $(CLIBS)
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factor.o: factor.c phylip.h
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factor: factor.o phylip.o
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- $(CC) $(CFLAGS) factor.o phylip.o $(LIBS) -o factor
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+ $(CC) $(LDFLAGS) factor.o phylip.o $(LIBS) -o factor
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fitch.o: fitch.c dist.h phylip.h
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fitch: fitch.o dist.o phylip.o
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- $(CC) $(CFLAGS) fitch.o dist.o phylip.o $(LIBS) -o fitch
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+ $(CC) $(LDFLAGS) fitch.o dist.o phylip.o $(LIBS) -o fitch
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gendist.o: gendist.c phylip.h
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gendist: gendist.o phylip.o
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- $(CC) $(CFLAGS) gendist.o phylip.o $(LIBS) -o gendist
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+ $(CC) $(LDFLAGS) gendist.o phylip.o $(LIBS) -o gendist
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kitsch.o: kitsch.c dist.h phylip.h
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kitsch: kitsch.o dist.o phylip.o
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- $(CC) $(CFLAGS) kitsch.o dist.o phylip.o $(LIBS) -o kitsch
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+ $(CC) $(LDFLAGS) kitsch.o dist.o phylip.o $(LIBS) -o kitsch
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mix.o: mix.c disc.h wagner.h phylip.h
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mix: mix.o disc.o wagner.o phylip.o
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- $(CC) $(CFLAGS) mix.o disc.o wagner.o phylip.o $(LIBS) -o mix
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||||||
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+ $(CC) $(LDFLAGS) mix.o disc.o wagner.o phylip.o $(LIBS) -o mix
|
||||||
|
|
||||||
|
move.o: move.c disc.h moves.h wagner.h phylip.h
|
||||||
|
|
||||||
|
move: move.o disc.o moves.o wagner.o phylip.o
|
||||||
|
- $(CC) $(CFLAGS) move.o disc.o moves.o wagner.o phylip.o $(LIBS) -o move
|
||||||
|
+ $(CC) $(LDFLAGS) move.o disc.o moves.o wagner.o phylip.o $(LIBS) -o move
|
||||||
|
|
||||||
|
neighbor.o: neighbor.c dist.h phylip.h
|
||||||
|
|
||||||
|
neighbor: neighbor.o dist.o phylip.o
|
||||||
|
- $(CC) $(CFLAGS) neighbor.o dist.o phylip.o $(LIBS) -o neighbor
|
||||||
|
+ $(CC) $(LDFLAGS) neighbor.o dist.o phylip.o $(LIBS) -o neighbor
|
||||||
|
|
||||||
|
pars.o: pars.c discrete.h phylip.h
|
||||||
|
|
||||||
|
pars: pars.o discrete.o phylip.o
|
||||||
|
- $(CC) $(CFLAGS) pars.o discrete.o phylip.o $(LIBS) -o pars
|
||||||
|
+ $(CC) $(LDFLAGS) pars.o discrete.o phylip.o $(LIBS) -o pars
|
||||||
|
|
||||||
|
penny.o: penny.c disc.h wagner.h phylip.h
|
||||||
|
|
||||||
|
penny: penny.o disc.o wagner.o phylip.o
|
||||||
|
- $(CC) $(CFLAGS) penny.o disc.o wagner.o phylip.o $(LIBS) -o penny
|
||||||
|
+ $(CC) $(LDFLAGS) penny.o disc.o wagner.o phylip.o $(LIBS) -o penny
|
||||||
|
|
||||||
|
proml.o: proml.c seq.h phylip.h
|
||||||
|
|
||||||
|
proml: proml.o seq.o phylip.o
|
||||||
|
- $(CC) $(CFLAGS) proml.o seq.o phylip.o $(LIBS) -o proml
|
||||||
|
+ $(CC) $(LDFLAGS) proml.o seq.o phylip.o $(LIBS) -o proml
|
||||||
|
|
||||||
|
promlk.o: promlk.c seq.h phylip.h mlclock.h printree.h
|
||||||
|
|
||||||
|
promlk: promlk.o seq.o phylip.o mlclock.o printree.o
|
||||||
|
- $(CC) $(CFLAGS) promlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o promlk
|
||||||
|
+ $(CC) $(LDFLAGS) promlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o promlk
|
||||||
|
|
||||||
|
protdist.o: protdist.c seq.h phylip.h
|
||||||
|
|
||||||
|
protdist: protdist.o seq.o phylip.o
|
||||||
|
- $(CC) $(CFLAGS) protdist.o seq.o phylip.o $(LIBS) -o protdist
|
||||||
|
+ $(CC) $(LDFLAGS) protdist.o seq.o phylip.o $(LIBS) -o protdist
|
||||||
|
|
||||||
|
protpars.o: protpars.c seq.h phylip.h
|
||||||
|
|
||||||
|
protpars: protpars.o seq.o phylip.o
|
||||||
|
- $(CC) $(CFLAGS) protpars.o seq.o phylip.o $(LIBS) -o protpars
|
||||||
|
+ $(CC) $(LDFLAGS) protpars.o seq.o phylip.o $(LIBS) -o protpars
|
||||||
|
|
||||||
|
restdist.o: restdist.c seq.h phylip.h
|
||||||
|
|
||||||
|
restdist: restdist.o seq.o phylip.o
|
||||||
|
- $(CC) $(CFLAGS) restdist.o seq.o phylip.o $(LIBS) -o restdist
|
||||||
|
+ $(CC) $(LDFLAGS) restdist.o seq.o phylip.o $(LIBS) -o restdist
|
||||||
|
|
||||||
|
restml.o: restml.c seq.h phylip.h
|
||||||
|
|
||||||
|
restml: restml.o seq.o phylip.o
|
||||||
|
- $(CC) $(CFLAGS) restml.o seq.o phylip.o $(LIBS) -o restml
|
||||||
|
+ $(CC) $(LDFLAGS) restml.o seq.o phylip.o $(LIBS) -o restml
|
||||||
|
|
||||||
|
retree.o: retree.c moves.h phylip.h
|
||||||
|
|
||||||
|
retree: retree.o moves.o phylip.o
|
||||||
|
- $(CC) $(CFLAGS) retree.o moves.o phylip.o $(LIBS) -o retree
|
||||||
|
+ $(CC) $(LDFLAGS) retree.o moves.o phylip.o $(LIBS) -o retree
|
||||||
|
|
||||||
|
seqboot.o: seqboot.c phylip.h
|
||||||
|
|
||||||
|
seqboot: seqboot.o seq.o phylip.o
|
||||||
|
- $(CC) $(CFLAGS) seqboot.o seq.o phylip.o $(LIBS) -o seqboot
|
||||||
|
+ $(CC) $(LDFLAGS) seqboot.o seq.o phylip.o $(LIBS) -o seqboot
|
||||||
|
|
||||||
|
treedist.o: treedist.c cons.h phylip.h
|
||||||
|
|
||||||
|
treedist: treedist.o phylip.o cons.o
|
||||||
|
- $(CC) $(CFLAGS) treedist.o cons.o phylip.o $(LIBS) -o treedist
|
||||||
|
+ $(CC) $(LDFLAGS) treedist.o cons.o phylip.o $(LIBS) -o treedist
|
||||||
|
|
||||||
|
|
||||||
|
# ----------------------------------------------------------------------------
|
||||||
Loading…
Add table
Reference in a new issue