sci-chemistry/pdb-tools: Fix double prefix installation

Package-Manager: portage-2.2.0_alpha174/cvs/Linux x86_64
Manifest-Sign-Key: 0x8009D6F070EB7916

3 files changed, 89 insertions, 5 deletions

diff --git a/sci-chemistry/pdb-tools/ChangeLog b/sci-chemistry/pdb-tools/ChangeLog
index ad360d17a127..107d9894de74 100644
--- a/sci-chemistry/pdb-tools/ChangeLog
+++ b/sci-chemistry/pdb-tools/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/pdb-tools
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-tools/ChangeLog,v 1.11 2013/04/26 10:20:16 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-tools/ChangeLog,v 1.12 2013/05/10 19:57:31 jlec Exp $
+
+*pdb-tools-0.2.1-r1 (10 May 2013)
+
+  10 May 2013; Justin Lecher <jlec@gentoo.org> +pdb-tools-0.2.1-r1.ebuild:
+  Fix double prefix installation
 
 *pdb-tools-0.2.1 (26 Apr 2013)
 
diff --git a/sci-chemistry/pdb-tools/Manifest b/sci-chemistry/pdb-tools/Manifest
index 2932cf9f3fa6..77307a9beaa5 100644
--- a/sci-chemistry/pdb-tools/Manifest
+++ b/sci-chemistry/pdb-tools/Manifest
@@ -5,13 +5,14 @@ DIST pdb-tools_0.1.4.tar.gz 101510 SHA256 6aeb9e76747147f840ac76e29b7a9494304e4a
 DIST pdbTools_0.2.1.tar.gz 103835 SHA256 317a5246e806a2b3d0425d080d679646fc77388e3e855412527603f945fa37ae SHA512 9c43c10e8739f8a34dbb1a3bba710cc727f7d8392ff979681371bd4460c67203253fb01852438eb93b214c4a009789608d200ca551f30399652fb76d702cf724 WHIRLPOOL 36d8cf71ba9f9b28e3ad59828539f4e94bbb8bc4514f050ddcbec63857b154ecdc7c32c2945c0d15f4d718c4fe5ab3adcb2e62a4368bfd819b80e9641a9dfd88
 EBUILD pdb-tools-0.1.4-r3.ebuild 1900 SHA256 95336505ac3b41c3ba72895043dd32f577843a817bcacc63d11990b0c04cfef1 SHA512 2a5057cfe9140fb796e9abadd2c1c7b83ae13081acb9c38217c2c18069b659970a258b97c90950a99c8ec34b7d87e0f2d716152a4db6cb49c27e5e8d93bf018e WHIRLPOOL 58a963038c563730287bed24611494ede28c14d605480ca4b5c067eb4fe5336b2c9314237c256a575db0c03ee055afb78a0425b3054607f23268cd084399eed7
 EBUILD pdb-tools-0.1.4-r4.ebuild 1701 SHA256 5322f83830eb523308e72bbda7e97732ce7bfd503644577a364bc4450a7b59d8 SHA512 5c15ffbc6876d770bc058c39b15ac8e228aee053049eeeb06ceb2d2f3a6593fabf3b2eca04852402a3da5c5059d9f15fa7eb40c95b2bab84bbd418559060248e WHIRLPOOL 0c472e75d2010796740eb8c21066d2e282c0d0a666b1c6712d86ed185cd1b4df329e4d4ca21aa8dffa43c2d076ffeef804c83be43c5e73b26d31abed3b71e98f
+EBUILD pdb-tools-0.2.1-r1.ebuild 1747 SHA256 52c77af33d965762915b1f3e4146f4666d01e5947b1ed40d163802093701c955 SHA512 7b62fb03a6aeb8127c719f46bc7fc7e601f2208395cb4700091cee96e1bc244412033c5dfb58cf3d64dc53ccabbafcb33bcdc17ad6fbcf2416cc4f564d60c0e9 WHIRLPOOL 92990c0648e2a998a43ef766251b37ec5fda590d0d90d6f88205d520812de1cd77acee9230ce6684905ff11a2690b0a57575e66eab7df39ac949ffb7f3298011
 EBUILD pdb-tools-0.2.1.ebuild 1754 SHA256 334d2cbdc9d1eaba354511ccc3f9ae75864baab80258c21c25a4ef4f18eefdb2 SHA512 562f99dc6bab6ffde1335bb4c1a55c8a8278ba9fd7f7a7bc4ea8267af129e55ecc5087397f65a1a008640795cf71f8ece9b57b34209b55e8cc57997f860e1eee WHIRLPOOL 86c330cb79620364b35c3679fe1b93699819b24380a703596c44fc9d6545afc7847104c267a0cdf225ce5fe165f326d1ca7ff84d42bc27b8e25689b024ebca3b
-MISC ChangeLog 1807 SHA256 902771454a774656d59732b869f8bcc74e72cdad8edbcd8925af578d51833392 SHA512 7f4a30c700a8e7edfb3d7c229afdc1ae551bcc302e157f8182b5da05d569e070565e6483007665d4d1c22b92dcce18ffefc6858eca35fdf188c594c49aec9f4c WHIRLPOOL 4693f5e9e3cd9f46640bd83b76acc95d493b8a8175dca853ce12ef9ae8ff57d48223a7105b3f123f7171c0a20787f294eb22351f8281f21c57f8450158eeedbe
+MISC ChangeLog 1951 SHA256 996fcaa02a30ab73a22a21756e3c9c84b14e85d84d2ea5ce24afcc87a3c58f6e SHA512 5a4ee736a094ce09fa56548a2f958847ac885374e0abf0aabbb3081da973bd10b574ee2b30f5adbbce0f581a35a9bcf748df29ab151816bfbb360c33ff859946 WHIRLPOOL 7e9e35bd8fc721f7a0ab09737b7eff5587329520283efafd0d6db4bc10645b51f583b6063f4eac91ceaee41834cc48d020093a99804f6a89fdeb86250292fd90
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diff --git a/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild
new file mode 100644
index 000000000000..4a2e2c3b1fe9
--- /dev/null
+++ b/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild
@@ -0,0 +1,78 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pdb-tools/pdb-tools-0.2.1-r1.ebuild,v 1.1 2013/05/10 19:57:31 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} pypy{1_8,1_9} )
+
+inherit fortran-2 python-single-r1 toolchain-funcs
+
+MY_PN="pdbTools"
+
+DESCRIPTION="Tools for manipulating and doing calculations on wwPDB macromolecule structure files"
+HOMEPAGE="http://code.google.com/p/pdb-tools/"
+SRC_URI="http://${PN}.googlecode.com/files/${MY_PN}_${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND=""
+DEPEND=""
+
+S="${WORKDIR}"/${MY_PN}_${PV}
+
+pkg_setup() {
+	python-single-r1_pkg_setup
+	fortran-2_pkg_setup
+}
+
+src_prepare() {
+	sed \
+		-e "s:script_dir,\"pdb_data\":\"${EPREFIX}/usr/share/${PN}\",\"pdb_data\":g" \
+		-i pdb_sasa.py || die
+	sed \
+		-e "/satk_path =/s:^.*$:satk_path = \"${EPREFIX}/usr/bin\":g" \
+		-i pdb_satk.py || die
+	sed \
+		-e 's:> %:>%:g' \
+		-i pdb_seq.py || die
+}
+
+src_compile() {
+	mkdir bin
+	cd satk
+	for i in *.f; do
+		einfo "$(tc-getFC) ${FFLAGS} ${LDFLAGS} ${i} -o ${i/.f}"
+		$(tc-getFC) ${FFLAGS} -c ${i} -o ${i/.f/.o} || die
+		$(tc-getFC) ${LDFLAGS} -o ../bin/${i/.f} ${i/.f/.o} || die
+		sed \
+			-e "s:${i/.f}.out:${i/.f}:g" \
+			-i ../pdb_satk.py || die
+	done
+}
+
+src_install() {
+	local script
+	insinto /usr/share/${PN}
+	doins -r pdb_data/peptides
+	rm -rf pdb_data/peptides || die
+
+	python_domodule helper pdb_data
+
+	python_moduleinto ${PN/-/_}
+	python_domodule *.py
+
+	for i in pdb_*.py; do
+		cat > ${i/.py} <<- EOF
+		#!${EPREFIX}/bin/bash
+		${PYTHON} -O "$(python_get_sitedir)/${PN/-/_}/${i}" \$@
+		EOF
+		dobin ${i/.py}
+	done
+
+	dobin bin/*
+	dodoc README
+}