sci-chemistry/theseus: Version Bump

Package-Manager: portage-2.2.14/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

3 files changed, 91 insertions, 7 deletions

diff --git a/sci-chemistry/theseus/ChangeLog b/sci-chemistry/theseus/ChangeLog
index e144868e020f..9a2405a8794f 100644
--- a/sci-chemistry/theseus/ChangeLog
+++ b/sci-chemistry/theseus/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/theseus
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/theseus/ChangeLog,v 1.8 2013/06/06 14:17:55 jlec Exp $
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/theseus/ChangeLog,v 1.9 2014/11/13 10:58:13 jlec Exp $
+
+*theseus-3.0.0 (13 Nov 2014)
+
+  13 Nov 2014; Justin Lecher <jlec@gentoo.org> +theseus-3.0.0.ebuild:
+  Version Bump
 
 *theseus-2.0.6 (06 Jun 2013)
 
diff --git a/sci-chemistry/theseus/Manifest b/sci-chemistry/theseus/Manifest
index 61898b39295a..6646a2523d35 100644
--- a/sci-chemistry/theseus/Manifest
+++ b/sci-chemistry/theseus/Manifest
@@ -5,16 +5,30 @@ DIST theseus_1.6.2.tar.gz 1214732 SHA256 2e23f19e8417b3ddf700168c387a9b927b1372f
 DIST theseus_2.0.1.tar.gz 1227936 SHA256 7b726121332223065c8e291a0a527a16ccf7ce57e44adcce2eea742e74336f94 SHA512 fa425b2adfaeae098283f84e4c10d29ad83a580196b41bf2c651f626e05df8fc6025aa4e66ec95b44e0943cf824c1cd4b77391dcadca7062cecdf5ec78d67fac WHIRLPOOL 13de3bd194224a26f36f69d5321fcf31dac79f934844fd2ec79c6bf43b03a0cda07a6e5a7f4ea97857ea1565a3adc26bba9a0c3a118f6b00dc23c53f9ef6e622
 DIST theseus_2.0.3.tar.gz 1256818 SHA256 fa64a7ba5d9675005de745b4750593114dc97c2b855160ac5dff6c58532ea39e SHA512 77ad1378483d87f079d967e15b00274721da3a5930b5b9fe3ba28b1897d52df3fea6a9e82da7d8ab5f46050242521e943ab2a565f6369a47136f54528e5ae562 WHIRLPOOL f4a01714b174ed77e069c8be2719a9b07073715abd53deb59bc8ecc0c852905c2eb764aca4dc1fa364a46d8bb871d1742547601f04cc8df8e6613eaf92ad9f8e
 DIST theseus_2.0.6.tar.gz 1257560 SHA256 f63f4d5fd9ce9d30048312e31807a1a413b433e2bbcfd0cefb3703f455551c23 SHA512 70604c468eb841b92e77a3e91cd57120b96c171512fb1cc31a407b7c4816150dfa31ec123fb9568a842e623f3252c60df0dc53d40fa2a4aece6e3c77039f4696 WHIRLPOOL 01c73e5bec0f4e9a98cd926a15f3213f30d20db10a500e88cfa54e31b92324d3fb741899c30c5c45e8d5a2d31eb68e742113b29a077f70430cf7acda9c02bc54
+DIST theseus_3.0.0.tar.gz 1213574 SHA256 4e474efabf1cfc9a48e96e86ac9e5b0f8035b57677017542e66478759bdc7866 SHA512 251e6273624126406609691e1205d9693c18dcbc8c81e10c77101ac4a1b6bdffcb56a47fd5fdc7ed6ed4fa107c2ed26b03a1780f951f9cc69a25c0722996e7b2 WHIRLPOOL 5a15c0f5270411114ebbca4fc9cad1e4db0449d1e6d8d1693f1e58d6a54f61b401cc6a2df2539d2ca34dd4dc52a09e1c45c0af8b80eb5c8916d8f168bf536ad3
 EBUILD theseus-1.6.2-r1.ebuild 1638 SHA256 5cbd6d5c42d5bc4018c71d3160da8e4e3ceaf01db4b4c69260e188de46b299a6 SHA512 730def30cdd60461616a18b2352afb5f407a1447fd7eac73d088441eed42970a65d5fddeac57786339c090f00f992af723e7428d3a72075d2d67cf032c25cfc4 WHIRLPOOL ffd454a252e75b3b7f68e3104705426b1818a0b9fd0da548fb0174546a1e52ea055cbc58c8f716a4432ab0f605f2e2122f7cacde6a2d0f6691c70cd17ef814af
 EBUILD theseus-2.0.1-r1.ebuild 1575 SHA256 94fe9661149ddb4ea7b4928bc43aec7bf2722b034e5c176399e7f461312aaded SHA512 10967e00447749f560097e6f2d2438d4700ede61e6a2467dcf408642b822520fef3724998378ac5eca526afb600e96e4af9533c4c69363bf62eeff1e7308227d WHIRLPOOL 274827db17d89c9110f79d7da57c5b97b43d8e0d9448efa6331285b929e3beb2cbf06a2d1f1aef938196126db9e71774264fccb3829dd8f3dd5187e0232f051d
 EBUILD theseus-2.0.3.ebuild 1572 SHA256 83402737296e8f3fafffcd3a003dac6b5910dcb87d21c1464204400c30165175 SHA512 10a4f8784ae2a1d59bd3dd33f00a72581109a14c9aa48faaff182bfa7bc19f74c30b920ac7d77a1315743b5c302130ed96396ff19080acfda14715be42e3c33c WHIRLPOOL 0df528c85dcb3ee802b5252f29f0a58c4ad0f8f87395432f2c952abd15ea2fb7bf6ca526dcca628a9a89a6f63f96739c8615a64d2152d1797860212b2e97a681
 EBUILD theseus-2.0.6.ebuild 1562 SHA256 015fbcc7df4ace60cca63336bd41d229ce17a3bdca5fe26dd9f86bd4ed196120 SHA512 cb87e2068a421af8a2ce0311091f7b8a8b31587e27cbdc681209bd4c0764dfb771ee2a9c89c054a90d133ff60f4187777d93aa2f16c87e1ade99195236189f88 WHIRLPOOL 4eafa9aafd96e58c90f47b1c1e86e6799ac0edc5c85868c530873c3f115c1df47ab348750114dab3ce3063c23ea5bdb6176c03d8ce5a77b00a4819a2a646b7d9
-MISC ChangeLog 1323 SHA256 37708f9111336ebdcaa1e882840194a3ae858ec932d78253b0b00b3256aae0de SHA512 583d74e642b2502e4487b3642fface37334299644acf9abb4b235334f88deb88d29d5c4299267d48fdd01b5c91b6e56d41a88a8a27217a1265ca193b451cbcd5 WHIRLPOOL e7d73bb49b6bc7b05f38922bac253fc6b8d1f16f3c831f815f31fd8dc835c0f1e0d7780a40eafb8402cb2a80be3a2ce0d56299c5cc38032ebe31effc0a2adeae
+EBUILD theseus-3.0.0.ebuild 1571 SHA256 80737f10c09bf4b27808aca7690e06dca1688978e11e6fbd03ecfd43a5dea7c7 SHA512 caabe56d37004bf9f89efdc1c39f85e6a1733dc0d8575bf8ec25f8b96962c0232b018813793406263514be1b3232d8cefba40cd82c823e3731033d2ee706d521 WHIRLPOOL 48739be7fd4d092c7752ed7c9f0425e14a4c863fec69d000c3c2a4fa01159794d0b1361e2ec20cf939b6577811267b68292b6492072a38f47f26c286a2aa166b
+MISC ChangeLog 1439 SHA256 dfd7b4523451032c771613d1eff396e7cdc67cc5f435ca398ba56808925dbcf2 SHA512 4c8328a0b8ddefb2809485b26337097e6793591eade6e3a02530d753ba87f9939f7cb025131dad5c5ea66c4f68c2ed33ecc6096e51727cf12ae7de1edb62485f WHIRLPOOL 5e1151af7d7702e12fe9e751a9d19c1a47608347dfad9fe04032221ec0da1b134176993ddf54060a468c59b441189ec378210ff02b8e3ff3ab0dbe9a6a312be9
 MISC metadata.xml 234 SHA256 8297e76ecd2cb828f604e9f138b263179eb84beb640215a0f60d7613eb46bb7f SHA512 0e94c0e6570a9267a39968d81c3b80680ccbc6eebb62199e4830b021a114c94a0de17ef2103cef62b7e27da1f51f225a30abb802aff82140ae6dc43366113d31 WHIRLPOOL fa6d4d90b092953b88ed3ad03e1e8c189296d268b39d13a4b4dcb78f0c4456341e3f1b44eea0860054fee43079179cb7cf7a912acf1fbe693ecdca6d9a65f081
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diff --git a/sci-chemistry/theseus/theseus-3.0.0.ebuild b/sci-chemistry/theseus/theseus-3.0.0.ebuild
new file mode 100644
index 000000000000..2eeca8ab687a
--- /dev/null
+++ b/sci-chemistry/theseus/theseus-3.0.0.ebuild
@@ -0,0 +1,65 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/theseus/theseus-3.0.0.ebuild,v 1.1 2014/11/13 10:58:13 jlec Exp $
+
+EAPI=5
+
+inherit multilib toolchain-funcs
+
+DESCRIPTION="Maximum likelihood superpositioning and analysis of macromolecular structures"
+HOMEPAGE="http://www.theseus3d.org/"
+SRC_URI="http://www.theseus3d.org/src/${PN}_${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples"
+
+RDEPEND="
+	sci-libs/gsl
+	|| (
+		sci-biology/muscle
+		sci-biology/probcons
+		sci-biology/mafft
+		sci-biology/t-coffee
+		sci-biology/kalign
+		sci-biology/clustalw
+		)"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+S="${WORKDIR}"/${PN}_src/
+
+src_prepare() {
+	cat >> make.inc <<- EOF
+	ARCH = $(tc-getAR)
+	ARCHFLAGS = -rvs
+	RANLIB = $(tc-getRANLIB)
+	LOCALLIBDIR = "${EPREFIX}/usr/$(get_libdir)
+	SYSLIBS = $(pkg-config --libs gsl) -lpthread
+	LIBS = -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus
+	LIBDIR = -L./lib
+	INSTALLDIR = "${ED}"/usr/bin
+	OPT =
+	WARN =
+	CFLAGS = ${CFLAGS} -std=c11 \$(WARN)
+	CC = $(tc-getCC)
+	EOF
+
+	sed \
+		-e 's|theseus:|theseus: libs|g' \
+		-e '/-o theseus/s:$(CC):$(CC) ${LDFLAGS}:g' \
+		-i Makefile || die
+
+	sed \
+		-e 's:/usr/bin/sed:sed:g' \
+		-e "s:/usr/local/bin/:/usr/bin/:g" \
+		-e "s:/usr/bin/:${EPREFIX}/usr/bin/:g" \
+		-i theseus_align || die
+}
+
+src_install() {
+	dobin theseus theseus_align
+	dodoc theseus_man.pdf README AUTHORS
+	use examples && insinto /usr/share/${PN} && doins -r examples
+}