Version bump

Package-Manager: portage-2.2_rc86/cvs/Linux x86_64

3 files changed, 24 insertions, 22 deletions

diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog
index 65f815c36cf6..de99bb217865 100644
--- a/sci-biology/ncbi-tools/ChangeLog
+++ b/sci-biology/ncbi-tools/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/ncbi-tools
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.78 2010/06/24 20:41:40 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.79 2010/09/30 17:41:44 weaver Exp $
+
+*ncbi-tools-20100808 (30 Sep 2010)
+
+  30 Sep 2010; Andrey Kislyuk <weaver@gentoo.org>
+  -ncbi-tools-20090809-r1.ebuild, +ncbi-tools-20100808.ebuild:
+  Version bump
 
   24 Jun 2010; Justin Lecher <jlec@gentoo.org> -ncbi-tools-20060507.ebuild,
   -ncbi-tools-20061015-r1.ebuild, -ncbi-tools-20070826.ebuild,
diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest
index 384cde4e4ecb..92c061aeb23f 100644
--- a/sci-biology/ncbi-tools/Manifest
+++ b/sci-biology/ncbi-tools/Manifest
@@ -1,6 +1,3 @@
------BEGIN PGP SIGNED MESSAGE-----
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-
 AUX 21ncbi-r1 232 RMD160 ba65fe937c9a29f4cc185d99db18522343bbb28b SHA1 5674f379f7a70e71394bca272fedd72a1622a7da SHA256 55d5d53c177200d4a9369102d3e2d8ef232f09dd8559aab6c6e4d2173e8bb411
 AUX ncbi-tools-asn2all.patch 1190 RMD160 3aaccc677bd8b9bad6c6424f5080c71cdac553d7 SHA1 ae22c77cfcd7d416a89ea3fe1e0331264473669d SHA256 e2fd71fdaa07b9e1c9cf646b2d3aa02c2ec822d41dcd45cadfced4164f458bed
 AUX ncbi-tools-extra_vib.patch 1393 RMD160 05e2dcf17b6af9475625eb0aa0be6bc96071a923 SHA1 bb92aeada6786d4573f9ad98e3d50b4a4201ba10 SHA256 b7639937d59c8bd636c6b02a65a4469d188645b9a10fffd0c8680fb861a7a8e1
@@ -8,17 +5,11 @@ AUX ncbi-tools-lop.patch 701 RMD160 1b9d8d196b1d4f27b090e616c9ac03cb9b4e6a09 SHA
 AUX ncbirc 33 RMD160 3bfa36288b608b4e29252ad1972bb8c06cded3e1 SHA1 eb14976d464f4fa0e14085c8dd58886b0c684a56 SHA256 8687909c83658049cbad656b6d99c8e6143365286e2fa981fbdddc87b178ab8e
 DIST ncbi-tools-20080302.tar.gz 17294669 RMD160 e269bcadc9e498163252e348a314bab8d0ece8f6 SHA1 d91a66bafac62dd07cc2e524874492388e5a780d SHA256 93a30ec0a6e408858c6364039a4eb240d9fadaf8ce670a14151e03c5169a12c1
 DIST ncbi-tools-20090809.tar.gz 64646971 RMD160 a1482a252647b2ea878ac9b08093cfd48bfaa82a SHA1 9727c13d94cc06cfe2f70148fa6bc5dfe011af50 SHA256 0c874961baf1bbfde9c209cc65fdcc5fe07f6f644b69674a89703b6726b66b15
+DIST ncbi-tools-20100808.tar.gz 65119702 RMD160 24d5f9f09869eacd01db2ff793f29a7c938e64ed SHA1 ae1e1e780c52ba9da539f1d3d50418d36e9fd1e2 SHA256 5302481373b86e5d9fc41cc6b405f63000d56cc2ee9fc0ffa5aeb9e611c45ff0
 DIST ncbi-tools-sdk-doc.tar.bz2 263568 RMD160 f9c4d610c2535ec2b4afae6ecef065fd5746910b SHA1 6fd259b1fc75684db43bd817fc4720e92f56e81c SHA256 352ec02e527f24d03bafb7d40b31c98e0a6f931bed34c4933c5f7153b8034cb2
 EBUILD ncbi-tools-20080302.ebuild 7142 RMD160 e3075bab7683b75cf57d6d05649d439a4c97889a SHA1 cbf189eb91175135b765d532eed3569a1b254900 SHA256 c68218365e73bb1cc38bf7e7003d52789e39bd23e5a77a6ed94a75441cff5b33
-EBUILD ncbi-tools-20090809-r1.ebuild 6369 RMD160 53e310cb8c26e3c558ce5b05e1983cdff8ecfd1b SHA1 a6cc52cedd9c150d3357c302d41fbea9632146d1 SHA256 25fb0726fd7c7a31622037dea83f14af0dbb640eb61a66c5ebd11d8a8f8289a1
 EBUILD ncbi-tools-20090809-r2.ebuild 6408 RMD160 25d7b53e5f3981d42a6debb3c8c942161757e705 SHA1 f78e56fad65e993c634e429b3c4aed146a5aa616 SHA256 ff41f9b663414314d0418d8eededc3a8fb59d31cde7d0e927114eff3c4161d1f
 EBUILD ncbi-tools-20090809.ebuild 6126 RMD160 e26c8ebfd87e22517b735b4dff8b448bd1600c6a SHA1 d965066318a5376a4beb4165c16a01f2dd678943 SHA256 9cf86f497256a35108c7779a02b433bde2532ada28584cbf56a8d1b40c548e0b
-MISC ChangeLog 15838 RMD160 27310e1db7d7c37bbb3775c65cef8389380a6adc SHA1 bf9359b4f5934e46c6e7a4cddb95ea3d5a2094ae SHA256 c9f7e2fa2f1e747f5034cfe6c8e67f41369201f73e31d8d8858aab0874576469
+EBUILD ncbi-tools-20100808.ebuild 6730 RMD160 5413f33c701b036d2e8d0c5c545160f6de527b03 SHA1 de80d953b7967b011cb6e5ab0c4c9117f24a3fce SHA256 43dd072152a25a90241cc0672a568ce070158eecb79c7feeed4dabddbc6dea50
+MISC ChangeLog 16005 RMD160 369cbd65c47b16dc8fead8377c24b3d1f1eb808c SHA1 a19e04ab4d58d02fa379accaedf82455b1b16f1e SHA256 b5f5e50f5f5d2f760048c24784194abf494f02ca90eafaddbc58a91ba730a4fb
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
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diff --git a/sci-biology/ncbi-tools/ncbi-tools-20090809-r1.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20100808.ebuild
index 780ce6fff16c..ba49d26b2eff 100644
--- a/sci-biology/ncbi-tools/ncbi-tools-20090809-r1.ebuild
+++ b/sci-biology/ncbi-tools/ncbi-tools-20100808.ebuild
@@ -1,8 +1,8 @@
 # Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20090809-r1.ebuild,v 1.1 2010/02/13 10:49:43 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20100808.ebuild,v 1.1 2010/09/30 17:41:44 weaver Exp $
 
-EAPI="2"
+EAPI="3"
 
 inherit flag-o-matic toolchain-funcs eutils
 
@@ -12,7 +12,7 @@ HOMEPAGE="http://www.ncbi.nlm.nih.gov/"
 SRC_URI="ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${PV}/ncbi.tar.gz -> ${P}.tar.gz"
 
 SLOT="0"
-KEYWORDS="~alpha ~amd64 ~ppc64 ~x86"
+KEYWORDS="~alpha ~amd64 ~ppc64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
 
 # IUSE=mpi deprecated, use sci-biology/mpiblast separately
 IUSE="doc X"
@@ -128,13 +128,14 @@ src_compile() {
 }
 
 src_install() {
+	mv "${S}"/bin/cdscan "${S}"/bin/cdscan-ncbi #sci-geosciences/cdat-lite
 	dobin "${S}"/bin/* || die "Failed to install binaries."
 	for i in ${EXTRA_VIB}; do
 		dobin "${S}"/build/${i} || die "Failed to install binaries."
 	done
 	dolib "${S}"/lib/* || die "Failed to install libraries."
-	mkdir -p "${D}"/usr/include/ncbi
-	cp -RL "${S}"/include/* "${D}"/usr/include/ncbi || \
+	mkdir -p "${ED}"/usr/include/ncbi
+	cp -RL "${S}"/include/* "${ED}"/usr/include/ncbi || \
 		die "Failed to install headers."
 
 	# TODO: wwwblast with webapps
@@ -144,7 +145,7 @@ src_install() {
 	#doins ${S}/real/*
 
 	# Basic documentation
-	dodoc "${S}"/{README,VERSION,doc/{*.txt,README.asn2xml}} || \
+	dodoc "${S}"/{README,VERSION,doc/{*.txt,README.*}} || \
 		die "Failed to install basic documentation."
 	newdoc "${S}"/doc/fa2htgs/README README.fa2htgs || \
 		die "Failed renaming fa2htgs documentation."
@@ -160,16 +161,20 @@ src_install() {
 		die "Failed to install man pages."
 
 	# Hypertext user documentation
-	dohtml "${S}"/{README.htm,doc/{*.html,*.gif}} || \
+	dohtml "${S}"/{README.htm,doc/{*.html,*.htm,*.gif}} || \
 		die "Failed to install HTML documentation."
 	insinto /usr/share/doc/${PF}/html/blast
 	doins "${S}"/doc/blast/* || die "Failed to install blast HTML documentation."
+	insinto /usr/share/doc/${PF}/html/images
+	doins "${S}"/doc/images/* || die "Failed to install documentation images."
+	insinto /usr/share/doc/${PF}/html/seq_install
+	doins "${S}"/doc/seq_install/* || die "Failed to install seq_install documentation."
 
 	# Developer documentation
 	if use doc; then
 		# Demo programs
-		mkdir "${D}"/usr/share/ncbi
-		mv "${S}"/demo "${D}"/usr/share/ncbi/demo || die
+		mkdir "${ED}"/usr/share/ncbi
+		mv "${S}"/demo "${ED}"/usr/share/ncbi/demo || die
 	fi
 
 	# Shared data (similarity matrices and such) and database directory.