sci-biology/psipred: Version BUmp

Package-Manager: portage-2.2.7/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

4 files changed, 86 insertions, 12 deletions

diff --git a/sci-biology/psipred/ChangeLog b/sci-biology/psipred/ChangeLog
index 5f023bb90b4a..8d6b125f2e7b 100644
--- a/sci-biology/psipred/ChangeLog
+++ b/sci-biology/psipred/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/psipred
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/psipred/ChangeLog,v 1.9 2013/06/19 03:42:49 bicatali Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/psipred/ChangeLog,v 1.10 2013/11/05 19:34:55 jlec Exp $
+
+*psipred-3.4 (05 Nov 2013)
+
+  05 Nov 2013; Justin Lecher <jlec@gentoo.org> +psipred-3.4.ebuild,
+  metadata.xml:
+  Version BUmp
 
   19 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> metadata.xml:
   herd is now sci-biology
diff --git a/sci-biology/psipred/Manifest b/sci-biology/psipred/Manifest
index 2af33c25b14a..4ca192d24d01 100644
--- a/sci-biology/psipred/Manifest
+++ b/sci-biology/psipred/Manifest
@@ -1,5 +1,5 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
 AUX 2.6.1-Makefile.patch 1295 SHA256 f50dc85ad2e630fbe8e3a15315cd7dca0e0349a7e8e83d80b36fb9a4cf7a3d97 SHA512 bb6b01795ee4842f4020e05111d1653d17f11d28defc8f02fef7c3169773286bf5040404b4289ec31dcf5b4b723263a8f8456ef41e9b360aae0a432f2876c2a4 WHIRLPOOL b84b15b28c5c45de3f8c1a02e4265e3802779ded9e191336e6959ea6174699208f08a8b3490dc96df18ecb260f930df5db317dd6b0db994edc83f5e17570eed4
 AUX 2.6.1-path.patch 1114 SHA256 0b2c0cf62c9c8b5fc21ac0c6b537aac52dcf617ffd2bd99724f1ac980efce7a5 SHA512 1b85bbb080f01b83aa64c291c31cccf55d376f712b1939d9c785e8400edd9756618f156343b73c67563a44c5d7c8ee5a01bec43ee67556980de59e8e78403b83 WHIRLPOOL 257fbb076e51f9729dba4cb7d486950ef0540485f2a92eb4fecffa4402c4e5f14461b4caa114e11c4cb61ca6aff0cd3812aa98fbb3c5217fa2bc5431269fba7e
@@ -9,6 +9,7 @@ AUX 3.1-fgets.patch 427 SHA256 a1f52692ad3593278718a8d2cc95d176e8bcd773305a6f676
 AUX 3.1-path.patch 1128 SHA256 0b91a360760bd27f4ba43639d32e891d5576595451e1f7285632fc9ad38a80fa SHA512 e6201669db910f074bb13d1b781416d8d99300f328147cccd7755d5d6595b25aa45353f6da6566f225a067e94ab8ee41ea89bfd75cf2cdf2c076481707acf88c WHIRLPOOL 33802ea504dea3445c8024b9c13eb351a009f13ee4b4a1d126392e5d807006d08dc0c582972eac2d13975d9acc9f6b5ccbf1bdc09115810abcc63dcae5e393cd
 AUX 3.2-fgets.patch 427 SHA256 95d68881c502c567025eb5e74fcd545bf012ded48ab2731aa70827f0ff449696 SHA512 a8a59a765057e20b9c606b8e4d76b5657a9a06150247b426d939805547148ddc8a1cb4282e04bcdcd756bfa6df7bebffcc77b84f62c86be2f643069d2ff913bb WHIRLPOOL 92b0c8af14387db54eef5ea171ffd0c096658f6922729a6a1a1836eeb14b21b1feb3cd330dfb564eb3aaa8435d18b55f4559da96fb32f666f88349a1af3fb191
 DIST psipred3.3.tar.gz 1239746 SHA256 133eef16ba4ac6ff5e10a757290ef794552833f42ed8251ff866ae56d9527c40 SHA512 38f5dd0f6eb6fc38888f9a850604b95904a8626d6862eb0b2a389caaf49af8f81436aa78a087da22281113d8afad2d28e5109ddade7d17718c1028eed8325b7e WHIRLPOOL d3883df88bde12a0f5ba6e195dc37b7104db36d16b5846b978fb045def6c4452edce4361dcced27ed36937bbd8d0e8dd4391b8592dca390941b3450e49cc5d34
+DIST psipred3.4.tar.gz 1102416 SHA256 c0eb8877313eb0564d34fc4d0e2d8d22e09d84d245e41008227560a10e64da9d SHA512 1bc7ac41a213766139324540ba6952538f2890749ecf217d771b4ce59e25231857d38c237ea573674f11a82300750e9a3ff628ec0156864863a9528a144cd919 WHIRLPOOL bdb47f296db1172df08f84b8cf18782e8585a8bc49f190b9783192db0e9d632bd6660437e8a35c24bb5970ca7a556b368c5a93373772f20d4be9a98ef963b902
 DIST psipred31.tar.gz 746797 SHA256 2150696cae281bc942a18fc5f1e2057ed70cb6ee7b492c9594cbd99b8f6987dd SHA512 a04482fc5a08de03b2c1ac3eafbc289d476906811ef2557681f00e3ba865488c6061a194c5e12fe3ff38d31f42f13f4e783de1ca4a04508dd38a93c3ad848710 WHIRLPOOL 288d161698726a944b40acb3e2c355e61bad3644bf5edca40fd5e478f9d37e3acc9a91ee199fbadea680ab3a8c974eb8f80dd700dfe790e84d8a862148538dff
 DIST psipred32.tar.gz 747120 SHA256 0775b0f07df87b2afd4989a378fc9b47f462507a264aaf2d56dd0243d9d00343 SHA512 49660d1c3cb9aa4c3ab13e721e23b83d70d0b6ecb772b08bd1058d3293dbcc9642d63092dd9746aa2a3a9085a13ba91e9849172d36954228a4f7a16e6e81050d WHIRLPOOL 24413200771fcee89c123fad25033b3230de3fdd82016ad7d084ddb096c081c46537f35c06578dad84a79a62c493e03b8f7b51be296b04d9568ea00b94293360
 DIST psipred321.tar.gz 747151 SHA256 5e88f2402e333be401b3022937b0167a33203f6289a84dd344941546f550f1f8 SHA512 b742f5fd3151bd624452bf37761fa66d364ea5b28d9d005ae6ce6f52fc6f2b17df31d6f1e600bd6c57776a1812f22b1eafbca781b430811a010d74f157a75cd1 WHIRLPOOL bb7111851ffe533b30fd6b77fb1ae396f0dd6506ce941944974c3b5c73c41d1a5b04c5af3d7e697aeb0640c03168b78d8832747940ed0de087df784d2d27e9f1
@@ -17,12 +18,23 @@ EBUILD psipred-3.1.ebuild 1268 SHA256 939a6841f67a59a17585381a930973ac57e17c234a
 EBUILD psipred-3.2.1.ebuild 1188 SHA256 567ce93f012cf97380fbc27c90c12a7eaf214d22433d660dcda10a4c11ba4a54 SHA512 57be1511fb56a4d26aa075b73256fcaa457a78c86127ff602666173b3cfbc4d7ccaabfc42c7f8c822746a654357ff63e33c4be394e90c764fbca836b487a81e5 WHIRLPOOL 3fea1d283d6bc044b5937f95e5d3b69fbb1756168d1ed8aaa24e20807982ff4159cd4e2d08ef46b2db0e5c02813a4dac16792ef60c1e0342cc42e46ee1d3afc3
 EBUILD psipred-3.2.ebuild 1264 SHA256 02205a927aedd70a33350ecfb155a387651ddebd6322d3755c8fbdc00ece4d94 SHA512 a35f5b4650dd68daada6b896ea85287cd05e22a8faa8427a5ebe4491b439d5541fff20243a2acd7272c9503e39ef365e3d6b64b01ec6f6442f8cfd8d7f526263 WHIRLPOOL 29053ecffd8f6f26497bf9b9f5a7187c05603855bc0f0037729864f035f3318c25d5bd68af4b36781f57aecf3612de17ed5f8efe5eaa5e9b6abc0a0f648ef0fe
 EBUILD psipred-3.3.ebuild 1288 SHA256 d15386d5725261fdecc8ddab63da3d5db0edeea4d4109fec4e7817a81fd4f6bb SHA512 295e44aecd808d6749f6923a137aa3b4e463431e4374b50d66f6bd0f3e3f63d70cdff2eacd8b786ed989cc78016208321544bc4ab66f78f3afd3f3fc22d7960f WHIRLPOOL ad4fdc2c300437df1aab80f498c103e0c670dc9bef1915cc07bfbbf7bcf2d488ea3a82501583d74ce4f681956cfd854f8cae57ce7a4c04269740cb161fba1d2c
-MISC ChangeLog 1740 SHA256 04ee9628886ad1c5a9400fa9782d0982f0b065f40d8b822f2bf01f1790e0e730 SHA512 9f5d6f62dcd7d46f1530bb283fc66f401a271818249977ed4c686d6cc24d1f16c117b16b9cbb6bed42329106953832a462b6700d49a34bba5d4259bfa06ebd2c WHIRLPOOL 4e33129476ad317ef71fe895941b88ad49893f7702a6f766b9635c5bde18d822103061428c20da3775d4b2e1e656c1716ae7f83c3a1a0d3bbc7c8502c0c2aea1
-MISC metadata.xml 224 SHA256 481c4b7590f1dad773f231e4f2e906a51fb7bacdb87e7dace4aec255ae78bced SHA512 27d7ae0f4be9c65e8a9fdb3999dd9e2e86f606b6742f36b2a2aebdff3a7d0604c4696622a3893b2b4164c40ab94913eecafd64e297e517816f5531c266c848f3 WHIRLPOOL 8c1aa84076c1d2af539fe0e245a1c14be98c516b4964ef16e8aaf72b814b9dfaba7debcc03fdc35a5a4cb27bff98b1818602127a70e11c1eca52f819006ec1a3
+EBUILD psipred-3.4.ebuild 1300 SHA256 074c4e97221af17e9cf25b73833082d7693c0fc96a8fac6a4578536ee8b6ba8a SHA512 39ee438b476b824fab7505f2cab1363bdb2aa7e1403c4a0713f27e1ae398f22ee121f95d112d0514bf164ec0ac0b360b953854890ca78de19690555f3b8d6ee4 WHIRLPOOL 93adcc77d9ff27caa57dfc110f935427f6e53af1171a4ee6d2905456c3abccc11886ce67c97f9a59718a77d42d7c4a246c6696acd3cb1c6ee08eedb89bd0dd90
+MISC ChangeLog 1865 SHA256 d893c3fdff57c6ee130588bb245568a2b78e2e4f5a523864e3a6e7056ccc2ca6 SHA512 08cf76d3748d8a8d15f9b37ed4278acd73e8fb7cb7d09094437b075032d65836b1b010928e960c65c2b2b2edf0d4e7dba459df2b3c19b0b69d86b8f61e5fd65f WHIRLPOOL 156f647b5c605b42f33898cadedb75af1fdd13b5716e13f2adaac5ea66756fb9ec2e7fcc5f2b384a89375f7f70b197229020281e897757c66bdee388b52b7c28
+MISC metadata.xml 232 SHA256 b47c46d4e7fca734d775e015a144a25f079048297e96acb5e9ea46f41bc8cebf SHA512 49ca8eac296332df2bf730e2eabef6c0281b2d3d76792868fe091366d3eb2aef83dd8ed8df377270c2d8437ddddee0fa03fbe0d7a0692aded6cee1af416cd846 WHIRLPOOL 54aa42b7394c7da49d2fe0e0b697516b19b2749066e2a89ccea7bc0111d5deb67662954056d83c30938ec0c768c8c8135957c775ee8fe2101e9c5b1b10b73b47
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.20 (GNU/Linux)
+Version: GnuPG v2.0.22 (GNU/Linux)
 
-iEYEAREIAAYFAlHBKLoACgkQ1ycZbhPLE2BivQCeKGHg4fpdXd98sKGHB4jQX3w1
-s3MAn2Vip+QnnJ6E/EfpRTvO/KbIadhO
-=4gAg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+=CBy8
 -----END PGP SIGNATURE-----
diff --git a/sci-biology/psipred/metadata.xml b/sci-biology/psipred/metadata.xml
index 3dc75947cefe..655b161c218d 100644
--- a/sci-biology/psipred/metadata.xml
+++ b/sci-biology/psipred/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-biology</herd>
-<maintainer>
-  <email>jlec@gentoo.org</email>
-</maintainer>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>jlec@gentoo.org</email>
+  </maintainer>
 </pkgmetadata>
diff --git a/sci-biology/psipred/psipred-3.4.ebuild b/sci-biology/psipred/psipred-3.4.ebuild
new file mode 100644
index 000000000000..9a20b4ec3568
--- /dev/null
+++ b/sci-biology/psipred/psipred-3.4.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/psipred/psipred-3.4.ebuild,v 1.1 2013/11/05 19:34:55 jlec Exp $
+
+EAPI=5
+
+inherit eutils prefix toolchain-funcs versionator
+
+#MY_P="${PN}$(delete_all_version_separators)"
+MY_P="${PN}${PV}"
+
+DESCRIPTION="Protein Secondary Structure Prediction"
+HOMEPAGE="http://bioinf.cs.ucl.ac.uk/psipred/"
+SRC_URI="
+	http://bioinf.cs.ucl.ac.uk/downloads/${PN}/${MY_P}.tar.gz
+	test? ( http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/old/data/tdbdata.tar.gz )"
+
+LICENSE="psipred"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="test"
+
+RDEPEND="
+	app-shells/tcsh
+	sci-biology/ncbi-tools
+	sci-biology/ncbi-tools++"
+DEPEND=""
+
+S="${WORKDIR}"/${PN}
+
+src_prepare() {
+	rm -f bin/*
+	epatch \
+		"${FILESDIR}"/3.1-Makefile.patch \
+		"${FILESDIR}"/3.1-path.patch \
+		"${FILESDIR}"/3.2-fgets.patch
+	eprefixify runpsipred*
+	emake -C src clean
+}
+
+src_compile() {
+	emake -C src CC=$(tc-getCC)
+}
+
+src_install() {
+	emake -C src DESTDIR="${D}" install
+	dobin runpsipred* bin/* BLAST+/runpsipred*
+	insinto /usr/share/${PN}
+	doins -r data
+	dodoc README
+}
+
+pkg_postinst() {
+	elog "Please use the update_blastdb.pl in order to"
+	elog "maintain your own local blastdb"
+}