sci-biology/phrap: Revbump to EAPI=6

Package-Manager: portage-2.3.1

3 files changed, 112 insertions, 6 deletions

diff --git a/sci-biology/phrap/Manifest b/sci-biology/phrap/Manifest
index 1275fda8b314..c3bf6b3d1fb5 100644
--- a/sci-biology/phrap/Manifest
+++ b/sci-biology/phrap/Manifest
@@ -1 +1 @@
-DIST phrap-1.080812-distrib.tar.gz 317350 SHA256 7025f3cb30e5a3305a13d150f39a85580ade0bbf8169b25db65cbe396e201052
+DIST phrap-1.080812-distrib.tar.gz 317350 SHA256 7025f3cb30e5a3305a13d150f39a85580ade0bbf8169b25db65cbe396e201052 SHA512 6b125b9a99b6180eb5de16bccfe068abefdb59237fd3295924c418749f2f2d6e39cdbcecc6786e42738846975334c4d8a645eae8fd0fcbda6b0e99241deb15ca WHIRLPOOL e516561804620ba8c96ed0e5c5d791f3fe1e7984e08f646e6fd7c30042f2550f5d1c9b2f800e8a853e42b049b92418ed9d0121e77bf4e9aa895974bce5e73717
diff --git a/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch b/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch
new file mode 100644
index 000000000000..6d30c2ce326a
--- /dev/null
+++ b/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch
@@ -0,0 +1,100 @@
+* Fix perl shebang to be portable
+* Make build system honour LDFLAGS
+
+--- a/makefile
++++ b/makefile
+@@ -25,9 +25,8 @@
+ # Makefile for swat, phrap, cross_match, phrapview; also swprobs (currently inactivated)
+ #CC= icc
+ #CFLAGS= -O2 -wd266,880
+-CC= cc
+-CFLAGS= -O2
+-LFLAGS= -lm
++CC ?= cc
++LIBS = -lm
+ 
+ SWATOBJS= swat.o weibull.o
+ 
+@@ -96,46 +95,46 @@
+ 	chmod a+x phrapview
+ 
+ swat: makefile $(SWATOBJS) $(SWOBJS)
+-	$(CC) $(CFLAGS) -o $@ $(SWATOBJS) $(SWOBJS) $(LFLAGS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(SWATOBJS) $(SWOBJS) $(LIBS)
+ 	chmod o-r swat
+ 
+ alpha_swat: makefile $(ALPHOBJS) $(SWOBJS) 
+-	$(CC) $(CFLAGS) -o $@ $(ALPHOBJS) $(SWOBJS) $(LFLAGS) 
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(ALPHOBJS) $(SWOBJS) $(LIBS) 
+ 	chmod o-r alpha_swat
+ 
+ swat_counts: makefile $(COUNOBJS) $(SWOBJS) 
+-	$(CC) $(CFLAGS) -o $@ $(COUNOBJS) $(SWOBJS) $(LFLAGS) 
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(COUNOBJS) $(SWOBJS) $(LIBS) 
+ 	chmod o-r swat_counts
+ 
+ swprobs: makefile $(PROBOBJS)
+-	$(CC) $(CFLAGS) -o $@ $(PROBOBJS) $(LFLAGS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(PROBOBJS) $(LIBS)
+ 
+ phrap: makefile phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS)
+-	$(CC) $(CFLAGS) -o $@ phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(LFLAGS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(LIBS)
+ 	chmod o-r phrap
+ 
+ gcphrap: makefile gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS)
+-	$(CC) $(CFLAGS) -o $@ gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LFLAGS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LIBS)
+ 	chmod o-r gcphrap
+ 
+ cross_match: makefile cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS)
+-	$(CC) $(CFLAGS) -o $@ cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(LFLAGS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(LIBS)
+ 	chmod o-r cross_match
+ 
+ gccross_match: makefile gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS)
+-	$(CC) $(CFLAGS) -o $@ gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LFLAGS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LIBS)
+ 	chmod o-r gccross_match
+ 
+ cluster: makefile $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS)
+-	$(CC) $(CFLAGS) -o $@ $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) $(LFLAGS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) $(LIBS)
+ 	chmod o-r cluster
+ 
+ loco: makefile $(LOCOOBJS) $(SWOBJS)
+-	$(CC) $(CFLAGS) -o $@ $(LOCOOBJS) $(SWOBJS) $(LFLAGS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(LOCOOBJS) $(SWOBJS) $(LIBS)
+ 	chmod o-r loco
+ 
+ erf_test: $(ERFOBJS)
+-	$(CC) $(CFLAGS) -o $@ $(ERFOBJS) $(LFLAGS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(ERFOBJS) $(LIBS)
+ 
+ loco.o: swat.h
+ 
+@@ -228,7 +227,7 @@
+ anomalies.o: swat.h 
+ 
+ fast_smith_wat.s: fast_smith_wat.c
+-	cc -S -machine_code -source_listing -O3 fast_smith_wat.c
++	$(CC) $(CFLAGS) -S -machine_code -source_listing fast_smith_wat.c
+ #N.B. fast_smith_wat.s MUST BE EDITTED BEFORE USE!!!
+ 
+ tig_node.o: swat.h
+--- a/phrapview
++++ b/phrapview
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/env perl
+ 
+ 
+ #/*****************************************************************************
+@@ -25,6 +25,7 @@
+ #                                                                         
+ #*****************************************************************************/
+ 
++use warnings;
+ use strict;
+ use Tk;
+ #phrapview version 0.960731
diff --git a/sci-biology/phrap/phrap-1.080812-r1.ebuild b/sci-biology/phrap/phrap-1.080812-r2.ebuild
index e3a3f9ebf591..3ae24453e453 100644
--- a/sci-biology/phrap/phrap-1.080812-r1.ebuild
+++ b/sci-biology/phrap/phrap-1.080812-r2.ebuild
@@ -2,7 +2,9 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=5
+EAPI=6
+
+inherit toolchain-funcs
 
 DESCRIPTION="Shotgun assembly and alignment utilities"
 HOMEPAGE="http://www.phrap.org/"
@@ -21,6 +23,7 @@ RDEPEND="
 S="${WORKDIR}"
 
 RESTRICT="fetch"
+PATCHES=( "${FILESDIR}/${PN}-1.080812-fix-build-system.patch" )
 
 pkg_nofetch() {
 	einfo "Please visit http://www.phrap.org/phredphrapconsed.html and obtain the file"
@@ -28,15 +31,18 @@ pkg_nofetch() {
 	einfo "and put it in ${DISTDIR}"
 }
 
-src_prepare() {
-	sed -i 's/CFLAGS=/#CFLAGS=/' makefile || die
-	sed -i 's|#!/usr/local/bin/perl|#!/usr/bin/env perl|' phrapview || die
+src_compile() {
+	emake CC="$(tc-getCC)" \
+		CFLAGS="${CFLAGS}" \
+		LDFLAGS="${LDFLAGS}"
 }
 
 src_install() {
 	dobin cross_match loco phrap phrapview swat
 	newbin cluster cluster_phrap
-	for i in {general,phrap,swat}.doc ; do
+
+	local i
+	for i in {general,phrap,swat}.doc; do
 		newdoc ${i} ${i}.txt
 	done
 }