Updating liguros repo

15 files changed, 452 insertions, 237 deletions

diff --git a/sci-biology/muscle/files/3.8.31-make.patch b/sci-biology/muscle/files/3.8.31-make.patch
index 7c0e7308df54..fa3f5c3a014b 100644
--- a/sci-biology/muscle/files/3.8.31-make.patch
+++ b/sci-biology/muscle/files/3.8.31-make.patch
@@ -1,7 +1,5 @@
-diff --git a/src/mk b/src/mk
-index 475d25a..d4b7e83 100755
---- a/src/mk
-+++ b/src/mk
+--- a/mk
++++ b/mk
 @@ -5,17 +5,14 @@ ObjNames='aligngivenpath.o aligngivenpathsw.o aligntwomsas.o aligntwoprofs.o aln
  rm -f *.o muscle.make.stdout.txt muscle.make.stderr.txt
  for CPPName in $CPPNames
diff --git a/sci-biology/muscle/muscle-3.8.31.ebuild b/sci-biology/muscle/muscle-3.8.31.ebuild
index ab08d868936d..4534f220869a 100644
--- a/sci-biology/muscle/muscle-3.8.31.ebuild
+++ b/sci-biology/muscle/muscle-3.8.31.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
 
 MY_P="${PN}${PV}_src"
 
@@ -14,19 +14,18 @@ SRC_URI="http://www.drive5.com/muscle/downloads${PV}/${MY_P}.tar.gz"
 LICENSE="public-domain"
 SLOT="0"
 KEYWORDS="amd64 ppc x86"
-IUSE=""
 
 RDEPEND="!sci-libs/libmuscle"
-DEPEND=""
 
 S="${WORKDIR}"/${PN}${PV}/src
 
-src_prepare() {
-	epatch "${FILESDIR}"/${PV}-make.patch
+PATCHES=( "${FILESDIR}"/${PV}-make.patch )
+
+src_configure() {
 	tc-export CXX
 }
 
 src_install() {
-	dobin "${PN}"
+	dobin muscle
 	dodoc *.txt
 }
diff --git a/sci-biology/phylip/Manifest b/sci-biology/phylip/Manifest
index 5a714766bc16..444e3d45e356 100644
--- a/sci-biology/phylip/Manifest
+++ b/sci-biology/phylip/Manifest
@@ -1,2 +1 @@
-DIST phylip-3.69.tar.gz 1511935 BLAKE2B 76aa5a79d2553c6f269c011f633d1101ee4d85ac398a36dd463e5605d90833ecb1e5f6c21edba3e142e2d4ab5ef034fa739e52e0ab3f941a7987915ae352be0b SHA512 e36d12bfe597896b4298c1d0e3b0b7bd783573dc03e861b9472d8284391b2339cb3fb58eb6580298724bbd516127b68925815455514f939da9272fcfed7e229d
-DIST phylip-3.696.tar.gz 3955721 BLAKE2B dc75fc442eb63e44bc2e68e5dc97b3ff8f741bfa53740ed57ca114b53dcb71db9baeb9a96c3e693f7fae92afbaa71c7b5acfb39e7770bacb6aafa8c33b355be6 SHA512 711a9a34be72b0f63c746733cd1384f091b7cc597dbd9a40c130e074efbf0a0ecc30e5a6b3452bb73dc69cddbdae2fc07d1c0a68f0be207471eab73ab876c6be
+DIST phylip-3.698.zip 9675991 BLAKE2B 8d020cf17b3245b9827af4bdd1d17167c3e1a41ae805766c4b72f09de107775314a2a296c00f84f928487403cc02741fd46ae73585d0dba143f4b926777e9add SHA512 7f822dabd1ffdb6a689e0c308f5a3ae129bd86e305086a18c0c755ac3c6ca28a4337d52ced76b280706926370e23f19f304851ef82e32833d1945ed277f7d70d
diff --git a/sci-biology/phylip/files/phylip-3.698-fno-common.patch b/sci-biology/phylip/files/phylip-3.698-fno-common.patch
new file mode 100644
index 000000000000..986b1d9650ab
--- /dev/null
+++ b/sci-biology/phylip/files/phylip-3.698-fno-common.patch
@@ -0,0 +1,70 @@
+--- 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

+ 

diff --git a/sci-biology/phylip/files/phylip-3.698-makefile.patch b/sci-biology/phylip/files/phylip-3.698-makefile.patch
new file mode 100644
index 000000000000..f55ab98dd9cb
--- /dev/null
+++ b/sci-biology/phylip/files/phylip-3.698-makefile.patch
@@ -0,0 +1,266 @@
+--- a/src/Makefile.unx
++++ b/src/Makefile.unx
+@@ -81,7 +81,6 @@
+ #CC        = cc
+ #
+ #  To use GCC instead:
+-CC        = gcc
+ #
+ # ----------------------------------------------------------------------------
+ #
+@@ -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 $(LIBS) -o treedist
+ 
+ 
+ # ----------------------------------------------------------------------------
diff --git a/sci-biology/phylip/phylip-3.69-r1.ebuild b/sci-biology/phylip/phylip-3.69-r1.ebuild
deleted file mode 100644
index 4e4a0113ecfb..000000000000
--- a/sci-biology/phylip/phylip-3.69-r1.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs
-
-DESCRIPTION=" The PHYLogeny Inference Package"
-HOMEPAGE="https://evolution.genetics.washington.edu/phylip.html"
-SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="free-noncomm"
-IUSE=""
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos"
-
-RDEPEND="x11-libs/libXaw"
-DEPEND="${RDEPEND}
-	x11-base/xorg-proto"
-
-S="${WORKDIR}/${P}/src"
-
-src_prepare() {
-	sed \
-		-e "s/CFLAGS  = -O3 -fomit-frame-pointer/CFLAGS = ${CFLAGS}/" \
-		-e "s/CC        = cc/CC        = $(tc-getCC)/" \
-		-e "s/DC        = cc/DC        = $(tc-getCC)/" \
-		-e "/ -o /s:\(\$(CC)\):\1 ${LDFLAGS}:g" \
-		-i Makefile || die "Patching Makefile failed."
-	mkdir ../fonts || die
-}
-
-src_compile() {
-	emake -j1 all put
-}
-
-src_install() {
-	cd "${WORKDIR}/${P}" || die
-
-	mv exe/font* fonts || die "Font move failed."
-	mv exe/factor exe/factor-${PN} || die "Renaming factor failed."
-
-	dobin exe/*
-
-	dodoc "${FILESDIR}"/README.Gentoo
-
-	dohtml -r phylip.html doc
-
-	insinto /usr/share/${PN}/
-	doins -r fonts
-}
diff --git a/sci-biology/phylip/phylip-3.696-r1.ebuild b/sci-biology/phylip/phylip-3.696-r1.ebuild
deleted file mode 100644
index dfed75bd24ff..000000000000
--- a/sci-biology/phylip/phylip-3.696-r1.ebuild
+++ /dev/null
@@ -1,54 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs
-
-DESCRIPTION=" The PHYLogeny Inference Package"
-HOMEPAGE="https://evolution.genetics.washington.edu/phylip.html"
-SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD-2"
-IUSE=""
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
-
-RDEPEND="x11-libs/libXaw"
-DEPEND="${RDEPEND}
-	x11-base/xorg-proto"
-
-S="${WORKDIR}/${P}/src"
-
-src_prepare() {
-	mv Makefile.unx Makefile || die
-	sed \
-		-e "/ -o /s:\(\$(CC)\):\1 ${LDFLAGS}:g" \
-		-i Makefile || die "Patching Makefile failed."
-	mkdir ../fonts || die
-}
-
-src_compile() {
-	emake -j1 \
-		CC="$(tc-getCC)" \
-		DC="$(tc-getCC)" \
-		CFLAGS="${CFLAGS} -Wno-unused-result" \
-		all put
-}
-
-src_install() {
-	cd "${WORKDIR}/${P}" || die
-
-	mv exe/font* fonts || die "Font move failed."
-	mv exe/factor exe/factor-${PN} || die "Renaming factor failed."
-
-	dolib.so exe/*so && rm exe/*so
-	dobin exe/*
-
-	dodoc "${FILESDIR}"/README.Gentoo
-
-	dohtml -r phylip.html doc
-
-	insinto /usr/share/${PN}/
-	doins -r fonts
-}
diff --git a/sci-biology/phylip/phylip-3.696-r2.ebuild b/sci-biology/phylip/phylip-3.696-r2.ebuild
deleted file mode 100644
index aaf786336939..000000000000
--- a/sci-biology/phylip/phylip-3.696-r2.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs
-
-DESCRIPTION=" The PHYLogeny Inference Package"
-HOMEPAGE="https://evolution.genetics.washington.edu/phylip.html"
-SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="BSD-2"
-IUSE=""
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
-# 'mix' tool collides with dev-lang/elixir, bug #537514
-RDEPEND="x11-libs/libXaw
-	!!dev-lang/elixir"
-DEPEND="${RDEPEND}
-	x11-base/xorg-proto"
-
-S="${WORKDIR}/${P}/src"
-
-src_prepare() {
-	mv Makefile.unx Makefile || die
-	sed \
-		-e "/ -o /s:\(\$(CC)\):\1 ${LDFLAGS}:g" \
-		-i Makefile || die "Patching Makefile failed."
-	mkdir ../fonts || die
-}
-
-src_compile() {
-	emake -j1 \
-		CC="$(tc-getCC)" \
-		DC="$(tc-getCC)" \
-		CFLAGS="${CFLAGS} -Wno-unused-result" \
-		all put
-}
-
-src_install() {
-	cd "${WORKDIR}/${P}" || die
-
-	mv exe/font* fonts || die "Font move failed."
-	mv exe/factor exe/factor-${PN} || die "Renaming factor failed."
-
-	dolib.so exe/*so && rm exe/*so
-	dobin exe/*
-
-	dodoc "${FILESDIR}"/README.Gentoo
-
-	dohtml -r phylip.html doc
-
-	insinto /usr/share/${PN}/
-	doins -r fonts
-}
diff --git a/sci-biology/phylip/phylip-3.698.ebuild b/sci-biology/phylip/phylip-3.698.ebuild
new file mode 100644
index 000000000000..552a4c47ab1f
--- /dev/null
+++ b/sci-biology/phylip/phylip-3.698.ebuild
@@ -0,0 +1,60 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit flag-o-matic toolchain-funcs
+
+DESCRIPTION=" The PHYLogeny Inference Package"
+HOMEPAGE="https://evolution.genetics.washington.edu/phylip.html"
+SRC_URI="http://evolution.gs.washington.edu/${PN}/download/${P}.zip"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+
+# 'mix' tool collides with dev-lang/elixir, bug #537514
+RDEPEND="
+	x11-libs/libXaw
+	!dev-lang/elixir"
+DEPEND="${RDEPEND}
+	x11-base/xorg-proto"
+BDEPEND="app-arch/unzip"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-makefile.patch
+	"${FILESDIR}"/${P}-fno-common.patch
+)
+
+src_prepare() {
+	default
+
+	mkdir fonts || die
+	# clear out old binaries
+	rm -r exe || die
+}
+
+src_configure() {
+	tc-export CC
+	append-cflags -Wno-unused-result
+}
+
+src_compile() {
+	emake -C src -f Makefile.unx all put
+}
+
+src_install() {
+	mv exe/font* fonts || die "Font move failed"
+	mv exe/factor exe/factor-${PN} || die "Renaming factor failed"
+
+	dolib.so exe/*so
+	rm exe/*so || die
+	dobin exe/*
+
+	dodoc "${FILESDIR}"/README.Gentoo
+	docinto html
+	dodoc -r phylip.html doc
+
+	insinto /usr/share/phylip
+	doins -r fonts
+}
diff --git a/sci-biology/profphd/Manifest b/sci-biology/profphd/Manifest
index bcdb5a4a9ca3..9aa5af5a04db 100644
--- a/sci-biology/profphd/Manifest
+++ b/sci-biology/profphd/Manifest
@@ -1,2 +1 @@
-DIST profphd-1.0.39.tar.xz 4406776 BLAKE2B 9ac4bccd1fedf04f9556ff6953452879fc8cf9deb92853214b2c8b5c0b1c4daf3e5e0044d10ded9540e9dd3f40a6fee3a25ae808fd1e94b90e0db23f3af7b6df SHA512 0ea6a34a8dad8fcd0d8b23e7a7d476e211587bf580389e9f43ed857bab7853cbe5ce698d2a610e9344e9bc95661cf074355310ea02c1a03e6378058ba169b15b
 DIST profphd-1.0.40.tar.xz 4491592 BLAKE2B 2aa1e091c0674fa5318a075148a63b15354ecb6d8d6f7ac41d1d05f8bea17c47b6f37be707cc1c738e22342c26ae9be59cabf919610e5bffd5028fc587b2995b SHA512 287f1a548030e7978119788dffdf2529e0018cd772bc820e116f79ed10cefd440645424b56415333362098a1ed32f4841d3fd4069adede2a95968f81c63956e3
diff --git a/sci-biology/profphd/files/profphd-1.0.40-symlink.patch b/sci-biology/profphd/files/profphd-1.0.40-symlink.patch
new file mode 100644
index 000000000000..7733d55af4a6
--- /dev/null
+++ b/sci-biology/profphd/files/profphd-1.0.40-symlink.patch
@@ -0,0 +1,11 @@
+--- a/src/prof/Makefile
++++ b/src/prof/Makefile
+@@ -40,7 +40,7 @@
+ 		./. $(DESTDIR)$(prefix)/share/profphd/prof/.
+ 	find $(DESTDIR)$(prefix)/share/profphd/prof/embl/phd.pl $(DESTDIR)$(prefix)/share/profphd/prof/scr/CONFprof.pl $(DESTDIR)$(prefix)/share/profphd/prof/prof $(DESTDIR)$(prefix)/share/profphd/prof/scr/lib/prof.pm \
+ 		-type f -exec sed -i -e 's|__PREFIX__|$(prefix)|g;s|__VERSION__|$(VERSION)|;' {} \;
+-	rm -rf $(DESTDIR)$(prefix)/bin/prof && mkdir -p $(DESTDIR)$(prefix)/bin && ln -s ../share/profphd/prof/prof $(DESTDIR)$(prefix)/bin/prof
++	rm -rf $(DESTDIR)$(prefix)/bin/prof && mkdir -p $(DESTDIR)$(prefix)/bin && ln -s ../share/profphd/prof/prof $(DESTDIR)$(prefix)/bin/profphd
+ 
+ install-neuralnet:
+ 	mkdir -p $(DESTDIR)$(prefix)/share/profphd/prof/embl/para && rsync -aC \
diff --git a/sci-biology/profphd/profphd-1.0.39.ebuild b/sci-biology/profphd/profphd-1.0.39.ebuild
deleted file mode 100644
index cacbc13cbdf2..000000000000
--- a/sci-biology/profphd/profphd-1.0.39.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="Secondary structure and solvent accessibility predictor"
-HOMEPAGE="https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction"
-SRC_URI="ftp://rostlab.org/profphd/${P}.tar.xz"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-DEPEND="dev-lang/perl"
-RDEPEND="${DEPEND}
-	dev-perl/librg-utils-perl
-	sci-libs/profnet
-	sci-libs/profphd-utils
-"
-
-src_prepare() {
-	sed \
-		-e '/ln -s/s:prof$:profphd:g' \
-		-i src/prof/Makefile || die
-	epatch "${FILESDIR}"/${P}-perl.patch
-}
-
-src_compile() {
-	emake prefix="${EPREFIX}/usr"
-}
-
-src_install() {
-	emake prefix="${EPREFIX}/usr" DESTDIR="${D}" install
-}
diff --git a/sci-biology/profphd/profphd-1.0.40.ebuild b/sci-biology/profphd/profphd-1.0.40.ebuild
index 8e24cebeb5f3..4f9a16a9fe9d 100644
--- a/sci-biology/profphd/profphd-1.0.40.ebuild
+++ b/sci-biology/profphd/profphd-1.0.40.ebuild
@@ -1,37 +1,33 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
-
-inherit eutils
+EAPI=7
 
 DESCRIPTION="Secondary structure and solvent accessibility predictor"
 HOMEPAGE="https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction"
 SRC_URI="ftp://rostlab.org/profphd/${P}.tar.xz"
 
-SLOT="0"
 LICENSE="GPL-2"
+SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
 
 DEPEND="dev-lang/perl"
-RDEPEND="${DEPEND}
+RDEPEND="
+	${DEPEND}
 	dev-perl/librg-utils-perl
 	sci-libs/profnet
-	sci-libs/profphd-utils
-"
+	sci-libs/profphd-utils"
 
-src_prepare() {
-	sed \
-		-e '/ln -s/s:prof$:profphd:g' \
-		-i src/prof/Makefile || die
-	epatch "${FILESDIR}"/${PN}-1.0.39-perl.patch
-}
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.0.39-perl.patch
+	"${FILESDIR}"/${PN}-1.0.40-symlink.patch
+)
 
 src_compile() {
-	emake prefix="${EPREFIX}/usr"
+	emake prefix="${EPREFIX}"/usr
 }
 
 src_install() {
-	emake prefix="${EPREFIX}/usr" DESTDIR="${D}" install
+	emake prefix="${EPREFIX}"/usr DESTDIR="${D}" install
+	einstalldocs
 }
diff --git a/sci-biology/unafold/files/unafold-3.8-doc-version.patch b/sci-biology/unafold/files/unafold-3.8-doc-version.patch
new file mode 100644
index 000000000000..b15858fd69e6
--- /dev/null
+++ b/sci-biology/unafold/files/unafold-3.8-doc-version.patch
@@ -0,0 +1,11 @@
+--- a/tests/hybrid.tml
++++ b/tests/hybrid.tml
+@@ -10,7 +10,7 @@
+   </test>
+   <test command="hybrid --version" return="0">
+     <stdin></stdin>
+-    <stdout>hybrid (UNAFold) 3.7
++    <stdout>hybrid (UNAFold) 3.8
+ By Nicholas R. Markham and Michael Zuker
+ Copyright (C) 2006
+ Rensselaer Polytechnic Institute
diff --git a/sci-biology/unafold/unafold-3.8-r1.ebuild b/sci-biology/unafold/unafold-3.8-r1.ebuild
index 8c96bff34b67..ff3e7ed1ef66 100644
--- a/sci-biology/unafold/unafold-3.8-r1.ebuild
+++ b/sci-biology/unafold/unafold-3.8-r1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 inherit flag-o-matic
 
@@ -14,14 +14,17 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="custom-cflags"
 
-DEPEND=""
-RDEPEND="${DEPEND}"
+RDEPEND="
+	media-libs/freeglut
+	media-libs/gd
+	virtual/opengl"
+DEPEND="${RDEPEND}"
 
-src_prepare() {
+PATCHES=( "${FILESDIR}"/${P}-doc-version.patch )
+
+src_configure() {
 	# recommended in README
 	use custom-cflags || append-flags -O3
 
-	sed \
-		-e 's:hybrid (UNAFold) 3.7:hybrid (UNAFold) 3.8:g' \
-		-i tests/hybrid.tml || die
+	default
 }