Version Bump, #317977; fixed installation of shipped bins

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

5 files changed, 104 insertions, 7 deletions

diff --git a/sci-biology/psipred/ChangeLog b/sci-biology/psipred/ChangeLog
index 340315e55790..970c787dc9e5 100644
--- a/sci-biology/psipred/ChangeLog
+++ b/sci-biology/psipred/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/psipred
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/psipred/ChangeLog,v 1.1 2010/02/28 10:31:18 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/psipred/ChangeLog,v 1.2 2010/05/06 18:27:49 jlec Exp $
+
+*psipred-3.0 (06 May 2010)
+*psipred-2.6.1-r1 (06 May 2010)
+
+  06 May 2010; Justin Lecher <jlec@gentoo.org> +files/3.0-path.patch,
+  -psipred-2.6.1.ebuild, +psipred-2.6.1-r1.ebuild, +psipred-3.0.ebuild:
+  Version Bump, #317977; fixed installation of shipped bins
 
 *psipred-2.6.1 (28 Feb 2010)
 
diff --git a/sci-biology/psipred/Manifest b/sci-biology/psipred/Manifest
index bb42170228b3..02f3379d5b4e 100644
--- a/sci-biology/psipred/Manifest
+++ b/sci-biology/psipred/Manifest
@@ -3,14 +3,17 @@ Hash: SHA1
 
 AUX 2.6.1-Makefile.patch 1295 RMD160 38eb08b77f15db26d60eb9ad5b603df3927f9471 SHA1 4aa02b3f7868e113501538da5cc88b80987029b4 SHA256 f50dc85ad2e630fbe8e3a15315cd7dca0e0349a7e8e83d80b36fb9a4cf7a3d97
 AUX 2.6.1-path.patch 1114 RMD160 b0982bb972daccd9e4d3dbc0668ad80084929a33 SHA1 d0e1f4a20f114312ab8fcf8faa58b5eb29f7fa1d SHA256 0b2c0cf62c9c8b5fc21ac0c6b537aac52dcf617ffd2bd99724f1ac980efce7a5
+AUX 3.0-path.patch 1124 RMD160 985bc8a52db2df5b7ea0529f69e43d440621829d SHA1 db74c92afa9f9b2849fe65a61259bb8cfc5f9ee4 SHA256 2dc3b531f1bc1ab7e2426b0ec95ff67ec93ac8376e017215b3b2dcd5b1c8804d
 DIST psipred261.tar.gz 873613 RMD160 744e984a21145b6caf312f68de66501ba0ac2d39 SHA1 db3af95091ed745fc956153239016d042e44b62d SHA256 0b39c075493d43e63952535dfed5341d0b81a99e4fb72d5431676d657d027126
-EBUILD psipred-2.6.1.ebuild 1188 RMD160 a828327a6186d856ac8b8d02af63ebe323aab6fc SHA1 2c02f74b663f5d58b47a6ace99df02195bd83f86 SHA256 e4d9d7d73bffc6a1f04b99831dd3cfac3b7a707991ad718706ce61d2d19d2ec5
-MISC ChangeLog 432 RMD160 fca8f0897af4499d86638fbbd0245d4113b131ed SHA1 12faf94062d973467919b8ab951821c668371f18 SHA256 be498ed3320370445ba412c78f6a58241af8f142424d11b25780f114cdf01ded
+DIST psipred30.tar.gz 724315 RMD160 6aabe85bff8d3a60d3e80d6646ba391c23716edc SHA1 c7d6c4a5a4cc2fe52acb7b2b24eb3b7780c7afca SHA256 24a70fa859ade37d634f2fa8e047061d107ac96ffba8ea96b5bab186f402e62c
+EBUILD psipred-2.6.1-r1.ebuild 1204 RMD160 e45a3e88e973ae58cd553e7d627f6b684b197d43 SHA1 d814f149f3ea10d36a74d111a2369f57a7823d95 SHA256 d66c6f9d91a47e07ceb00e593579a2d351bdffd7aa7ed7478dfbf6c8ce02a4d6
+EBUILD psipred-3.0.ebuild 1199 RMD160 6e1a35188b15cf3f77053df03445e2470c290f3f SHA1 4a8caf825bafe4e5b092b1d2fc56d59944673951 SHA256 12a8bf0ebe5d37922f87b04ec0820903bec0592dd550ff9b963b85bb89b84b90
+MISC ChangeLog 695 RMD160 64938fae5e94d2cef55a148b9b220a5d9f703e4b SHA1 4a8eaad0ecf488e165af93628dee6f99836080fa SHA256 f207ce434b8078e7b3a7d930a91052345f4f07886aa6c393eb5fa4f47c7aa953
 MISC metadata.xml 216 RMD160 04a6fc4e2160b439296b52aa97d5b7d83af75508 SHA1 9561c9e6eada6aac9b503407917900529ce703e9 SHA256 24f5c205c2655ef27138c8aa087701626f5b4c666229c9ef7fe814e63ea2e776
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.14 (GNU/Linux)
 
-iEYEARECAAYFAkuKRf8ACgkQgAnW8HDreRaOZACghviGuGJ7qzP0Cc182fH1B3uv
-HHgAn227h7ZN9Pu+cCS+BgESvLD5XMnZ
-=3QJ7
+iEYEARECAAYFAkvjCi4ACgkQgAnW8HDreRbS1QCePGNbrzp+jclTNVxTYCKL1BFF
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diff --git a/sci-biology/psipred/files/3.0-path.patch b/sci-biology/psipred/files/3.0-path.patch
new file mode 100644
index 000000000000..ebf9b2a61f4e
--- /dev/null
+++ b/sci-biology/psipred/files/3.0-path.patch
@@ -0,0 +1,38 @@
+diff --git a/runpsipred b/runpsipred
+index e133686..6ad57cc 100755
+--- a/runpsipred
++++ b/runpsipred
+@@ -14,13 +14,13 @@
+ set dbname = uniref90
+ 
+ # Where the NCBI programs have been installed
+-set ncbidir = /usr/local/bin
++set ncbidir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
+ 
+ # Where the PSIPRED V3 programs have been installed
+-set execdir = ./bin
++set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
+ 
+ # Where the PSIPRED V3 data files have been installed
+-set datadir = ./data
++set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data
+ 
+ set basename = $1:r
+ set rootname = $basename:t
+diff --git a/runpsipred_single b/runpsipred_single
+index 1f7680b..7bd5bc3 100755
+--- a/runpsipred_single
++++ b/runpsipred_single
+@@ -10,10 +10,10 @@
+ # NOTE: Script modified to be more cluster friendly (DTJ April 2008)
+ 
+ # Where the PSIPRED V3 programs have been installed
+-set execdir = ./bin
++set execdir = @GENTOO_PORTAGE_EPREFIX@/usr/bin
+ 
+ # Where the PSIPRED V3 data files have been installed
+-set datadir = ./data
++set datadir = @GENTOO_PORTAGE_EPREFIX@/usr/share/psipred/data
+ 
+ set basename = $1:r
+ set rootname = $basename:t
diff --git a/sci-biology/psipred/psipred-2.6.1.ebuild b/sci-biology/psipred/psipred-2.6.1-r1.ebuild
index 2ac04814cdfe..d80c361b20a2 100644
--- a/sci-biology/psipred/psipred-2.6.1.ebuild
+++ b/sci-biology/psipred/psipred-2.6.1-r1.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/psipred/psipred-2.6.1.ebuild,v 1.1 2010/02/28 10:31:18 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/psipred/psipred-2.6.1-r1.ebuild,v 1.1 2010/05/06 18:27:50 jlec Exp $
 
 EAPI="3"
 
@@ -24,6 +24,7 @@ RDEPEND="
 S="${WORKDIR}"
 
 src_prepare() {
+	rm -f bin/*
 	epatch "${FILESDIR}"/${PV}-Makefile.patch
 	epatch "${FILESDIR}"/${PV}-path.patch
 	eprefixify runpsipred*
diff --git a/sci-biology/psipred/psipred-3.0.ebuild b/sci-biology/psipred/psipred-3.0.ebuild
new file mode 100644
index 000000000000..d74553f2952d
--- /dev/null
+++ b/sci-biology/psipred/psipred-3.0.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/psipred/psipred-3.0.ebuild,v 1.1 2010/05/06 18:27:49 jlec Exp $
+
+EAPI="3"
+
+inherit eutils prefix toolchain-funcs versionator
+
+MY_P="${PN}$(delete_all_version_separators)"
+
+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"
+
+LICENSE="psipred"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+	sci-biology/ncbi-tools
+	sci-biology/ncbi-tools++"
+
+S="${WORKDIR}"
+
+src_prepare() {
+	rm -f bin/*
+	epatch "${FILESDIR}"/2.6.1-Makefile.patch
+	epatch "${FILESDIR}"/${PV}-path.patch
+	eprefixify runpsipred*
+}
+
+src_compile() {
+	emake -C src CC=$(tc-getCC) || die "emake failed"
+}
+
+src_install() {
+	emake -C src DESTDIR="${D}" install || die "installation failed"
+	dobin runpsipred* || die
+	insinto /usr/share/${PN}
+	doins -r data || die "failed to install data"
+	dodoc README || die "nothing to read"
+}
+
+pkg_postinst() {
+	elog "Please use the update_blastdb.pl in order to"
+	elog "maintain your own local blastdb"
+}