sci-chemistry/shiftx2: Respect FLAGS

Package-Manager: portage-2.2.0_alpha180

3 files changed, 28 insertions, 12 deletions

diff --git a/sci-chemistry/shiftx2/ChangeLog b/sci-chemistry/shiftx2/ChangeLog
new file mode 100644
index 000000000..5aafaf3ca
--- /dev/null
+++ b/sci-chemistry/shiftx2/ChangeLog
@@ -0,0 +1,8 @@
+# ChangeLog for sci-chemistry/shiftx2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  16 Jun 2013; Justin Lecher <jlec@gentoo.org> shiftx2-1.07_p20120106.ebuild,
+  metadata.xml:
+  Respect FLAGS
+
diff --git a/sci-chemistry/shiftx2/metadata.xml b/sci-chemistry/shiftx2/metadata.xml
index 947e3461e..80444f44b 100644
--- a/sci-chemistry/shiftx2/metadata.xml
+++ b/sci-chemistry/shiftx2/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<herd>sci</herd>
-	<longdescription>
+  <herd>sci</herd>
+  <longdescription>
 		SHIFTX2 predicts both the backbone and side chain 1H, 13C and 15N chemical
 		shifts for proteins using their structural (PDB) coordinates as input.
 		SHIFTX2 combines ensemble machine learning methods with sequence
@@ -33,7 +33,7 @@
 		prediction. Journal of Biomolecular NMR, Volume 50, Number 1, 43-57.
 		doi: 10.1007/s10858-011-9478-4.
 	</longdescription>
-	<use>
-		<flag name='debug'>Enables debug output in the shiftx2 java part</flag>
-	</use>
+  <use>
+    <flag name="debug">Enables debug output in the shiftx2 java part</flag>
+  </use>
 </pkgmetadata>
diff --git a/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild b/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild
index e9cb4c73a..5a19e4b0b 100644
--- a/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild
+++ b/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild
@@ -25,12 +25,15 @@ CDEPEND="dev-util/weka"
 
 RDEPEND="${CDEPEND}
 	dev-lang/R
+	sci-chemistry/reduce
 	>=virtual/jre-1.5"
 DEPEND="${CDEPEND}
 	>=virtual/jdk-1.5"
 
 S="${WORKDIR}"/${MY_P}
 
+QA_PREBUILT="/opt/.*"
+
 src_prepare() {
 	epatch "${FILESDIR}/gentoo-fixes.patch"
 	rm "${S}"/src/FeatureRanges.java || die
@@ -43,7 +46,12 @@ src_prepare() {
 	fi
 
 	# hack alert!
-	sed '/-o/s:$: -lm:g' -i "${S}/modules/resmf/Makefile" || die
+	sed \
+		-e '/-o/s:$(GCC):$(GCC) $(LDFLAGS):g' \
+		-e '/-o/s:$(CC):$(CC) $(LDFLAGS):g' \
+		-i modules/*/Makefile || die
+
+	sed -e '/-o/s:$: -lm:g' -i "${S}/modules/resmf/Makefile" || die
 }
 
 src_compile() {
@@ -65,7 +73,7 @@ src_compile() {
 	einfo "Building module effects"
 	cd "${S}"/modules/effects || die
 	emake clean
-	emake CFLAGS="${CFLAGS}" GCC=$(tc-getCC) LINK="${LDFLAGS}" all
+	emake CFLAGS="${CFLAGS}" CC=$(tc-getCC) LINK="${LDFLAGS}" all
 }
 
 src_install() {
@@ -83,12 +91,11 @@ src_install() {
 	dodoc README 1UBQ.pdb
 	python_parallel_foreach_impl python_doscript "${S}"/*py
 
-	# modules/angles
-	cd "${S}"/modules/angles || die
-	dobin get_angles phipsi
-
 	# other modules
-	dobin "${S}"/modules/resmf/resmf "${S}"/modules/effects/caleffect
+	dobin \
+		"${S}"/modules/angles/{get_angles,phipsi} \
+		"${S}"/modules/resmf/resmf \
+		"${S}"/modules/effects/caleffect
 
 	# script
 	python_scriptinto ${instdir}/script
@@ -101,4 +108,5 @@ src_install() {
 	python_parallel_foreach_impl python_doscript "${S}"/shifty3/*py
 	exeinto ${instdir}/shifty3
 	doexe "${S}"/shifty3/xalign_x
+	dosym ../${PN}/shifty3/xalign_x /opt/bin/xalign_x
 }