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add phylip

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starsareintherose 2021-11-02 08:41:22 +00:00
parent 45208dbbe0
commit 21671d7759
5 changed files with 388 additions and 0 deletions
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42
phylip/PKGBUILD Normal file
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@ -0,0 +1,42 @@
# Maintainer: Michael Schubert <mschu.dev at gmail>
# Contributor: Abhishek Dasgupta <abhidg@gmail.com>
# Contributor: Damir Perisa <damir.perisa@bluewin.ch>
pkgname=phylip
pkgver=3.698
pkgrel=1
pkgdesc="A collection of programmes for evolutive genetics and inferring phylogenies"
arch=('i686' 'x86_64')
url="http://evolution.genetics.washington.edu/phylip.html"
source=(http://evolution.gs.washington.edu/phylip/download/phylip-$pkgver.zip
phylip-3.698-makefile.patch
phylip-3.698-fno-common.patch)
optdepends=('java-runtime')
license=('custom')
sha256sums=('cb12e5105d25872eed705d243ca32b400e180d38c3437d58335f11a431df0e46'
'91779c722959b7e08f4e3e03e9c1cc14c4a81d152e46d4a6b30d0dd09e276637'
'd2638f99a6cb1e893aa6c362f906d5fca94700e0e4d50392abba853be8f0fff3')
prepare() {
cd "$srcdir"/$pkgname-$pkgver
# patches from gentoo ebuild: https://gitweb.gentoo.org/repo/gentoo.git/plain/sci-biology/phylip/files
patch -p1 < ../phylip-3.698-makefile.patch
patch -p1 < ../phylip-3.698-fno-common.patch
}
build() {
cd "$srcdir"/$pkgname-$pkgver/src
make -f Makefile.unx all
}
package() {
cd "$srcdir"/$pkgname-$pkgver/src
make -f Makefile.unx put
cd "$srcdir"/$pkgname-$pkgver
mkdir -p "$pkgdir"/usr/{lib,bin,share/phylip}
rm -rf exe/testdata
mv exe/factor{,-phylip}
mv exe/*.so "$pkgdir"/usr/lib/
mv exe/font* "$pkgdir"/usr/share/phylip/
mv exe/* "$pkgdir"/usr/bin
}

10
phylip/lilac.py Executable file
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#!/usr/bin/env python3
from lilaclib import *
def pre_build():
update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
run_cmd(['updpkgsums'])
def post_build():
git_add_files('PKGBUILD')
git_commit()

8
phylip/lilac.yaml Executable file
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maintainers:
- github: starsareintherose
email: starsareintherose@outlook.com
build_prefix: extra-x86_64
update_on:
- source: regex
url: "https://evolution.gs.washington.edu/phylip/download/"
regex: "phylip-(\d+.\d+).zip"

70
phylip/phylip-3.698-fno-common.patch Normal file
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--- a/src/draw.c
+++ b/src/draw.c
@@ -34,6 +34,11 @@
char fontname[LARGE_BUF_LENGTH];
+long treecolor, namecolor, backcolor, bottomcolor, vrmlskycolornear, vrmlskycolorfar,
+ vrmlgroundcolornear, vrmlgroundcolorfar, vrmlplotcolor;
+
+char afmfile[FNMLNGTH];
+
/* format of matrix: capheight, length[32],length[33],..length[256]*/
byte *full_pic ;
--- a/src/draw.h
+++ b/src/draw.h
@@ -52,10 +52,10 @@
double intensity, x, y, z;
} vrmllighttype;
-long treecolor, namecolor, backcolor, bottomcolor, vrmlskycolornear, vrmlskycolorfar,
+extern long treecolor, namecolor, backcolor, bottomcolor, vrmlskycolornear, vrmlskycolorfar,
vrmlgroundcolornear, vrmlgroundcolorfar, vrmlplotcolor;
-char afmfile[FNMLNGTH];
+extern char afmfile[FNMLNGTH];
double lengthtext(char *, long, char *, fonttype);
double heighttext(fonttype, char *);
--- a/src/drawtree.c
+++ b/src/drawtree.c
@@ -69,7 +69,7 @@
uselengths, regular, rotate, empty, rescaled,
notfirst, improve, nbody, firstscreens, labelavoid;
boolean pictbold,pictitalic,pictshadow,pictoutline;
-boolean javarun;
+extern boolean javarun;
striptype stripe;
plottertype plotter, oldplotter;
--- a/src/phylip.c
+++ b/src/phylip.c
@@ -34,6 +34,8 @@
#include "phylip.h"
+boolean javarun;
+
#ifdef WIN32
#include <windows.h>
/* for console code (clear screen, text color settings) */
--- a/src/phylip.h
+++ b/src/phylip.h
@@ -331,7 +331,7 @@
/* Lower-triangular format. */
#define MAT_LOWERTRI (MAT_LOWER | MAT_MACHINE)
-boolean javarun;
+extern boolean javarun;
typedef long *steptr;
typedef long longer[6];
@@ -351,7 +351,6 @@
extern long spp, words, bits;
extern boolean ibmpc, ansi, tranvsp;
extern naym *nayme; /* names of species */
-boolean firstplotblock; // for debugging BMP output
#define ebcdic EBCDIC

258
phylip/phylip-3.698-makefile.patch Normal file
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@ -0,0 +1,258 @@
--- a/src/Makefile.unx
+++ b/src/Makefile.unx
@@ -91,7 +90,6 @@
#
#
#A minimal one
-CFLAGS =
#
# A basic one for debugging
#CFLAGS = -g
@@ -220,7 +218,7 @@
@echo "Done."
@echo ""
-put:
+put: all
@echo "Installing PHYLIP v3.6 binaries in $(EXEDIR)"
@mkdir -p $(EXEDIR)
@cp $(PROGS) $(EXEDIR)
@@ -270,195 +268,195 @@
clique.o: clique.c disc.h phylip.h
clique: clique.o disc.o phylip.o
- $(CC) $(CFLAGS) clique.o disc.o phylip.o $(LIBS) -o clique
+ $(CC) $(LDFLAGS) clique.o disc.o phylip.o $(LIBS) -o clique
cons.o: cons.c cons.h phylip.h
consense.o: consense.c cons.h phylip.h
consense: consense.o phylip.o cons.o
- $(CC) $(CFLAGS) consense.o phylip.o cons.o $(LIBS) -o consense
+ $(CC) $(LDFLAGS) consense.o phylip.o cons.o $(LIBS) -o consense
contml.o: contml.c cont.h phylip.h
contml: contml.o cont.o phylip.o
- $(CC) $(CFLAGS) contml.o cont.o phylip.o $(LIBS) -o contml
+ $(CC) $(LDFLAGS) contml.o cont.o phylip.o $(LIBS) -o contml
contrast.o: contrast.c cont.h phylip.h
contrast: contrast.o cont.o phylip.o
- $(CC) $(CFLAGS) contrast.o cont.o phylip.o $(LIBS) -o contrast
+ $(CC) $(LDFLAGS) contrast.o cont.o phylip.o $(LIBS) -o contrast
dnacomp.o: dnacomp.c seq.h phylip.h
dnacomp: dnacomp.o seq.o phylip.o
- $(CC) $(CFLAGS) dnacomp.o seq.o phylip.o $(LIBS) -o dnacomp
+ $(CC) $(LDFLAGS) dnacomp.o seq.o phylip.o $(LIBS) -o dnacomp
dnadist.o: dnadist.c seq.h phylip.h
dnadist: dnadist.o seq.o phylip.o
- $(CC) $(CFLAGS) dnadist.o seq.o phylip.o $(LIBS) -o dnadist
+ $(CC) $(LDFLAGS) dnadist.o seq.o phylip.o $(LIBS) -o dnadist
dnainvar.o: dnainvar.c seq.h phylip.h
dnainvar: dnainvar.o seq.o phylip.o
- $(CC) $(CFLAGS) dnainvar.o seq.o phylip.o $(LIBS) -o dnainvar
+ $(CC) $(LDFLAGS) dnainvar.o seq.o phylip.o $(LIBS) -o dnainvar
dnaml.o: dnaml.c seq.h phylip.h
dnaml: dnaml.o seq.o phylip.o
- $(CC) $(CFLAGS) dnaml.o seq.o phylip.o $(LIBS) -o dnaml
+ $(CC) $(LDFLAGS) dnaml.o seq.o phylip.o $(LIBS) -o dnaml
dnamlk.o: dnamlk.c seq.h phylip.h mlclock.h printree.h
dnamlk: dnamlk.o seq.o phylip.o mlclock.o printree.o
- $(CC) $(CFLAGS) dnamlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o dnamlk
+ $(CC) $(LDFLAGS) dnamlk.o seq.o phylip.o mlclock.o printree.o $(LIBS) -o dnamlk
dnamove.o: dnamove.c seq.h moves.h phylip.h
dnamove: dnamove.o seq.o moves.o phylip.o
- $(CC) $(CFLAGS) dnamove.o seq.o moves.o phylip.o $(LIBS) -o dnamove
+ $(CC) $(LDFLAGS) dnamove.o seq.o moves.o phylip.o $(LIBS) -o dnamove
dnapenny.o: dnapenny.c seq.h phylip.h
dnapenny: dnapenny.o seq.o phylip.o
- $(CC) $(CFLAGS) dnapenny.o seq.o phylip.o $(LIBS) -o dnapenny
+ $(CC) $(LDFLAGS) dnapenny.o seq.o phylip.o $(LIBS) -o dnapenny
dnapars.o: dnapars.c seq.h phylip.h
dnapars: dnapars.o seq.o phylip.o
- $(CC) $(CFLAGS) dnapars.o seq.o phylip.o $(LIBS) -o dnapars
+ $(CC) $(LDFLAGS) dnapars.o seq.o phylip.o $(LIBS) -o dnapars
dolmove.o: dolmove.c disc.h moves.h dollo.h phylip.h
dolmove: dolmove.o disc.o moves.o dollo.o phylip.o
- $(CC) $(CFLAGS) dolmove.o disc.o moves.o dollo.o phylip.o $(LIBS) -o dolmove
+ $(CC) $(LDFLAGS) dolmove.o disc.o moves.o dollo.o phylip.o $(LIBS) -o dolmove
dollop.o: dollop.c disc.h dollo.h phylip.h
dollop: dollop.o disc.o dollo.o phylip.o
- $(CC) $(CFLAGS) dollop.o disc.o dollo.o phylip.o $(LIBS) -o dollop
+ $(CC) $(LDFLAGS) dollop.o disc.o dollo.o phylip.o $(LIBS) -o dollop
dolpenny.o: dolpenny.c disc.h dollo.h phylip.h
dolpenny: dolpenny.o disc.o dollo.o phylip.o
- $(CC) $(CFLAGS) dolpenny.o disc.o dollo.o phylip.o $(LIBS) -o dolpenny
+ $(CC) $(LDFLAGS) dolpenny.o disc.o dollo.o phylip.o $(LIBS) -o dolpenny
draw.o: draw.c draw.h phylip.h
- $(CC) $(DFLAGS) -c draw.c
+ $(CC) $(DFLAGS) $(CPPFLAGS) -c draw.c
draw2.o: draw2.c draw.h phylip.h
- $(CC) $(DFLAGS) -c draw2.c
+ $(CC) $(DFLAGS) $(CPPFLAGS) -c draw2.c
drawgram.o: drawgram.c draw.h phylip.h
- $(CC) $(DFLAGS) -c drawgram.c
+ $(CC) $(DFLAGS) $(CPPFLAGS) -c drawgram.c
drawgram: drawgram.o draw.o draw2.o phylip.o
- $(CC) $(DFLAGS) draw.o draw2.o drawgram.o phylip.o $(DLIBS) -o drawgram
+ $(CC) $(LDFLAGS) draw.o draw2.o drawgram.o phylip.o $(DLIBS) -o drawgram
# needed by java
-libdrawgram.so: drawgram.o draw.o draw2.o phylip.o
- $(CC) $(CFLAGS) -o libdrawgram.so -shared -fPIC drawgram.c draw.c draw2.c phylip.c $(CLIBS)
+libdrawgram.so:
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o libdrawgram.so -Wl,-soname,libdrawgram.so -shared -fPIC drawgram.c draw.c draw2.c phylip.c $(CLIBS)
drawtree.o: drawtree.c draw.h phylip.h
- $(CC) $(DFLAGS) -shared -fPIC -c drawtree.c
+ $(CC) $(DFLAGS) $(CPPFLAGS) -c drawtree.c
drawtree: drawtree.o draw.o draw2.o phylip.o
- $(CC) $(DFLAGS) draw.o draw2.o drawtree.o phylip.o $(DLIBS) -o drawtree
+ $(CC) $(LDFLAGS) draw.o draw2.o drawtree.o phylip.o $(DLIBS) -o drawtree
# needed by java
-libdrawtree.so: drawtree.o draw.o draw2.o phylip.o
- $(CC) $(CFLAGS) -o libdrawtree.so -shared -fPIC drawtree.c draw.c draw2.c phylip.c $(CLIBS)
+libdrawtree.so:
+ $(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -o libdrawtree.so -Wl,-soname,libdrawtree.so -shared -fPIC drawtree.c draw.c draw2.c phylip.c $(CLIBS)
factor.o: factor.c phylip.h
factor: factor.o phylip.o
- $(CC) $(CFLAGS) factor.o phylip.o $(LIBS) -o factor
+ $(CC) $(LDFLAGS) factor.o phylip.o $(LIBS) -o factor
fitch.o: fitch.c dist.h phylip.h
fitch: fitch.o dist.o phylip.o
- $(CC) $(CFLAGS) fitch.o dist.o phylip.o $(LIBS) -o fitch
+ $(CC) $(LDFLAGS) fitch.o dist.o phylip.o $(LIBS) -o fitch
gendist.o: gendist.c phylip.h
gendist: gendist.o phylip.o
- $(CC) $(CFLAGS) gendist.o phylip.o $(LIBS) -o gendist
+ $(CC) $(LDFLAGS) gendist.o phylip.o $(LIBS) -o gendist
kitsch.o: kitsch.c dist.h phylip.h
kitsch: kitsch.o dist.o phylip.o
- $(CC) $(CFLAGS) kitsch.o dist.o phylip.o $(LIBS) -o kitsch
+ $(CC) $(LDFLAGS) kitsch.o dist.o phylip.o $(LIBS) -o kitsch
mix.o: mix.c disc.h wagner.h phylip.h
mix: mix.o disc.o wagner.o phylip.o
- $(CC) $(CFLAGS) mix.o disc.o wagner.o phylip.o $(LIBS) -o mix
+ $(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
# ----------------------------------------------------------------------------