Install ans2all utility. Added support for compiling/installing arbitrary NCBI utilit...

Package-Manager: portage-2.1.2.2

diff --git a/sci-biology/ncbi-tools/ChangeLog b/sci-biology/ncbi-tools/ChangeLog
index 189a7475f20283f3890d495b9483bff24f080523..bf9b0254c9f7e64284a5c3b1004aaffbcddd5e20 100644 (file)
--- a/sci-biology/ncbi-tools/ChangeLog
+++ b/sci-biology/ncbi-tools/ChangeLog
@@ -1,6 +1,14 @@
 # ChangeLog for sci-biology/ncbi-tools
-# Copyright 2000-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.50 2006/11/03 02:53:38 ribosome Exp $
+# Copyright 2000-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ChangeLog,v 1.51 2007/03/09 03:55:37 ribosome Exp $
+
+*ncbi-tools-20061015-r1 (09 Mar 2007)
+
+  09 Mar 2007; Olivier Fisette <ribosome@gentoo.org>
+  -ncbi-tools-20061015.ebuild, +ncbi-tools-20061015-r1.ebuild:
+  Install ans2all utility. Added support for compiling/installing arbitrary
+  NCBI utilities. Thanks to José María Fernández González
+  <jmfernandez@cnio.es> for his work (see bug #169822). Pruned old version.
 
   03 Nov 2006; Olivier Fisette <ribosome@gentoo.org>
   -ncbi-tools-20050605-r2.ebuild:

diff --git a/sci-biology/ncbi-tools/Manifest b/sci-biology/ncbi-tools/Manifest
index bef6e2eef9c995071918ddf10f76a57c8edfa2bc..fa9589ac2d3f04c3cc8bebd7a6fa527fc50bf79d 100644 (file)
--- a/sci-biology/ncbi-tools/Manifest
+++ b/sci-biology/ncbi-tools/Manifest
@@ -27,14 +27,14 @@ EBUILD ncbi-tools-20060507.ebuild 6404 RMD160 5b3da85bd685bd72d0e50726afa0814de4
 MD5 b81b36665616d2e18c075acba4c3b289 ncbi-tools-20060507.ebuild 6404
 RMD160 5b3da85bd685bd72d0e50726afa0814de4027c83 ncbi-tools-20060507.ebuild 6404
 SHA256 c583a88edcb81f312927254be5052ee353818ebdadc8faf7f062e2cc50394553 ncbi-tools-20060507.ebuild 6404
-EBUILD ncbi-tools-20061015.ebuild 6412 RMD160 315191efc3ae1cbe17069cda2a6e759734ac800b SHA1 be9079c6baab91128edc9f0d6743f657360c8572 SHA256 d12c8cb1f1b04455c375b4e1416b55af676a35274bbe9028251150964a0bb80c
-MD5 4d1e3aa7575d583fba120b108d351504 ncbi-tools-20061015.ebuild 6412
-RMD160 315191efc3ae1cbe17069cda2a6e759734ac800b ncbi-tools-20061015.ebuild 6412
-SHA256 d12c8cb1f1b04455c375b4e1416b55af676a35274bbe9028251150964a0bb80c ncbi-tools-20061015.ebuild 6412
-MISC ChangeLog 11389 RMD160 694d9fc2d9425cd4432bba07ac4d653bd2d8bc47 SHA1 ae52fb5ecbdd96988f3e4c77766ac5aafeb894ab SHA256 583bfbf4f680bfd52b656ad775bd9610dc4b357e9611af62fc70cd6a3177b765
-MD5 3c3b85d9b57b46cfad1b38adfe441857 ChangeLog 11389
-RMD160 694d9fc2d9425cd4432bba07ac4d653bd2d8bc47 ChangeLog 11389
-SHA256 583bfbf4f680bfd52b656ad775bd9610dc4b357e9611af62fc70cd6a3177b765 ChangeLog 11389
+EBUILD ncbi-tools-20061015-r1.ebuild 6495 RMD160 24ab84b6a4bce25a0571c78a5489d5725e81a01b SHA1 e409498fc64031e0208fb5299d377217670a0759 SHA256 135d19e95452b5662a9751f4101ef17a66a618c3031894bb2aa8f761d64a85ad
+MD5 b87146ee80dd26bf9d65078fafb9bedb ncbi-tools-20061015-r1.ebuild 6495
+RMD160 24ab84b6a4bce25a0571c78a5489d5725e81a01b ncbi-tools-20061015-r1.ebuild 6495
+SHA256 135d19e95452b5662a9751f4101ef17a66a618c3031894bb2aa8f761d64a85ad ncbi-tools-20061015-r1.ebuild 6495
+MISC ChangeLog 11759 RMD160 0d1a2d94263bdc3aa8d2eca5a4db99d3c60e9a39 SHA1 0dcf87831c06d52b6515701f6c540abe236f96a5 SHA256 9a9ed5dfb770082e2ef2ef9f0021dd0ff04cb3523d81a8cdb7d2295ff06f8b9a
+MD5 f581fe846f0938410e0d99f9a7c86570 ChangeLog 11759
+RMD160 0d1a2d94263bdc3aa8d2eca5a4db99d3c60e9a39 ChangeLog 11759
+SHA256 9a9ed5dfb770082e2ef2ef9f0021dd0ff04cb3523d81a8cdb7d2295ff06f8b9a ChangeLog 11759
 MISC metadata.xml 262 RMD160 4eabcbcb990d4d5e3b34db8c27bcd2c0cfcf7501 SHA1 3c024ca60a2b93ed0e0311f6b05ef5ef117bee31 SHA256 89af818a993faf14a4a87e2f254943420156c2a317c385480a9533ba682b650f
 MD5 5f35ae4b4cb1cd144db7c7c093d3fd80 metadata.xml 262
 RMD160 4eabcbcb990d4d5e3b34db8c27bcd2c0cfcf7501 metadata.xml 262
@@ -45,6 +45,6 @@ SHA256 8b4847f987b8741efff3b3db0b1d2856f15c53291362ab0bfba1af21263de19c files/di
 MD5 96f59d6f4dcd072b2744878ce377b23d files/digest-ncbi-tools-20060507 777
 RMD160 d0a656e48f738e1a30061121a7fecf6e5b7ee841 files/digest-ncbi-tools-20060507 777
 SHA256 d20530e140a48cab2fc12df5a0bf0957e956a6ea35a07b5b5ed42a43466ad4d7 files/digest-ncbi-tools-20060507 777
-MD5 4a2b24a25719d45c6a999619053cb37c files/digest-ncbi-tools-20061015 777
-RMD160 82eefb533a71585a5526c9762f9b389341863252 files/digest-ncbi-tools-20061015 777
-SHA256 8dcb338c684c40627c2cfd3a425654b91b29f76804b3c14dde7e4bc4857e3031 files/digest-ncbi-tools-20061015 777
+MD5 4a2b24a25719d45c6a999619053cb37c files/digest-ncbi-tools-20061015-r1 777
+RMD160 82eefb533a71585a5526c9762f9b389341863252 files/digest-ncbi-tools-20061015-r1 777
+SHA256 8dcb338c684c40627c2cfd3a425654b91b29f76804b3c14dde7e4bc4857e3031 files/digest-ncbi-tools-20061015-r1 777

diff --git a/sci-biology/ncbi-tools/files/digest-ncbi-tools-20061015 b/sci-biology/ncbi-tools/files/digest-ncbi-tools-20061015-r1
similarity index 100%
rename from sci-biology/ncbi-tools/files/digest-ncbi-tools-20061015
rename to sci-biology/ncbi-tools/files/digest-ncbi-tools-20061015-r1

diff --git a/sci-biology/ncbi-tools/ncbi-tools-20061015.ebuild b/sci-biology/ncbi-tools/ncbi-tools-20061015-r1.ebuild
similarity index 95%
rename from sci-biology/ncbi-tools/ncbi-tools-20061015.ebuild
rename to sci-biology/ncbi-tools/ncbi-tools-20061015-r1.ebuild
index 9929a10dd286ad0e98254715e53a01af3823f361..377ae81f16c442f9d4542adf45b7847ae5c70cb7 100644 (file)
--- a/sci-biology/ncbi-tools/ncbi-tools-20061015.ebuild
+++ b/sci-biology/ncbi-tools/ncbi-tools-20061015-r1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2006 Gentoo Foundation
+# Copyright 1999-2007 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20061015.ebuild,v 1.1 2006/11/03 02:04:56 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/ncbi-tools/ncbi-tools-20061015-r1.ebuild,v 1.1 2007/03/09 03:55:37 ribosome Exp $
 
 inherit flag-o-matic toolchain-funcs eutils autotools
 
@@ -24,6 +24,8 @@ DEPEND="app-shells/tcsh
 
 S="${WORKDIR}/ncbi"
 
+EXTRA_VIB="asn2all asn2asn"
+
 pkg_setup() {
        echo
        ewarn 'Please note that the NCBI toolkit (and especially the X'
@@ -38,7 +40,7 @@ src_unpack() {
        unpack ${A}
        cd "${S}"
 
-       epatch "${FILESDIR}"/${PN}-asn2all.patch
+       epatch "${FILESDIR}"/${PN}-extra_vib.patch
 
        if use ppc64; then
                epatch "${FILESDIR}"/${PN}-lop.patch
@@ -112,6 +114,7 @@ src_unpack() {
 }
 
 src_compile() {
+       export EXTRA_VIB
        cd "${WORKDIR}"
        ncbi/make/makedis.csh || die
        mkdir "${S}"/cgi
@@ -130,7 +133,9 @@ src_compile() {
 
 src_install() {
        dobin "${S}"/bin/* || die "Failed to install binaries."
-       dobin "${S}"/build/asn2all || 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 || \