sci-biology/glimmer: Port to EAPI 7

Closes: https://bugs.gentoo.org/731892
Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: David Seifert <soap@gentoo.org>

sci-biology/glimmer/files/glimmer-3.02b-ldflags.patch

@@ -1,8 +1,6 @@
-diff --git a/src/c_make.gen b/src/c_make.gen
-index 414dead..84c3030 100644
 --- a/src/c_make.gen
 +++ b/src/c_make.gen
-@@ -200,45 +200,12 @@ LOCAL_SYS_INC=$(SEP_PATH)/../SYS/inc
+@@ -200,45 +200,11 @@
  #### Do not redefine if (a) passed in on command line, or (b)
  #### defined in an environment variable.
  
@@ -48,13 +46,12 @@ index 414dead..84c3030 100644
 +CC      ?= cc
 +CXX	?= g++
 +CXXFLAGS ?=
-+CXXDEFS = -D__cplusplus
 +AR      ?= ar
 +ARFLAGS ?= rvs
  
  #### Delete default suffix rules
  .SUFFIXES:
-@@ -359,13 +326,13 @@ $(PROGS):
+@@ -359,13 +325,13 @@
  	  cd $(LOCAL_OBJ); \
  	    if $(CC) -o $(LOCAL_BIN)/$(notdir $@) $(LDFLAGS) \
                 $(LD_DIRS) $(filter-out lib%.a, $+) \
@@ -70,11 +67,9 @@ index 414dead..84c3030 100644
  			true; else rm -f $(LOCAL_BIN)/$(notdir $@); fi; \
  	fi ;
  
-diff --git a/src/c_make.glm b/src/c_make.glm
-index 0decc17..b82131c 100644
 --- a/src/c_make.glm
 +++ b/src/c_make.glm
-@@ -8,10 +8,7 @@ include $(LOCAL_WORK)/src/c_make.gen
+@@ -8,18 +8,14 @@
  
  SUBDIRS = Common ICM Glimmer Util
  
@@ -86,3 +81,12 @@ index 0decc17..b82131c 100644
  
  
  #AS_BUILD_DIR =$(LOCAL_WORK)
+ INC_IMPORT_DIRS += \
+ 		$(patsubst %, $(LOCAL_WORK)/src/%, $(strip $(SUBDIRS))) \
+                 $(LOCAL_WORK)/inc
+-LIB_IMPORT_DIRS += $(LOCAL_WORK)/lib /usr/lib /usr/shlib /usr/X11R6/lib \
+-     $(SYBASE)/lib
++LIB_IMPORT_DIRS += $(LOCAL_WORK)/lib
+ 
+ OBJ_SEARCH_PATH = $(LOCAL_WORK)/obj
+ 

sci-biology/glimmer/glimmer-3.02b.ebuild

@@ -1,28 +1,25 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 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_PV=${PV//./}
 
 DESCRIPTION="An HMM-based microbial gene finding system from TIGR"
 HOMEPAGE="https://ccb.jhu.edu/software/glimmer/index.shtml"
 SRC_URI="https://ccb.jhu.edu/software/${PN}/${PN}${MY_PV}.tar.gz"
+S="${WORKDIR}/${PN}3.02"
 
 LICENSE="Artistic"
 SLOT="0"
-IUSE=""
 KEYWORDS="~amd64 ~x86"
 
-DEPEND=""
-RDEPEND="app-shells/tcsh
+RDEPEND="
+	app-shells/tcsh
 	sci-biology/elph"
 
-#S="${WORKDIR}/${PN}${PV}"
-S="${WORKDIR}/${PN}3.02"
-
 PATCHES=(
 	"${FILESDIR}"/${P}-jobserver-fix.patch
 	"${FILESDIR}"/${P}-ldflags.patch
@@ -37,12 +34,13 @@ src_prepare() {
 	# GCC 4.3 include fix
 	sed -i 's/include  <string>/include  <string.h>/' src/Common/delcher.hh || die
 	#
-	sed -i "s+/fs/szgenefinding/Glimmer3/bin+%${D}/bin/glimmer3+" scripts/g3-* || die
-	sed -i "s+/fs/szgenefinding/Glimmer3/scripts+%${D}/share/glimmer/scripts+" scripts/g3-* || die
-	sed -i "s+/nfshomes/adelcher/bin/elph+%${D}/bin/elph+" scripts/g3-* || die
+	sed -i "s:/fs/szgenefinding/Glimmer3/bin:%${EPREFIX}/usr/bin/glimmer3:" scripts/g3-* || die
+	sed -i "s:/fs/szgenefinding/Glimmer3/scripts:%${EPREFIX}/usr/share/glimmer/scripts:" scripts/g3-* || die
+	sed -i "s:/nfshomes/adelcher/bin/elph:%${EPREFIX}/usr/bin/elph:" scripts/g3-* || die
 	sed -i "s/@ if/if/" src/c_make.gen || die
+
 	# avoid file collision on /usr/bin/extract #247394
-	epatch "${PATCHES[@]}"
+	default
 }
 
 src_compile() {
@@ -60,7 +58,7 @@ src_install() {
 	rm bin/test || die
 	dobin bin/*
 
-	insinto /usr/share/${PN}
+	insinto /usr/share/glimmer
 	doins -r scripts
 
 	dodoc glim302notes.pdf