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commit: db6617fcd21401115d88ef59b233ae5430650d18 |
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Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Sun Feb 26 22:13:52 2017 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Sun Feb 26 22:13:52 2017 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=db6617fc |
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|
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sci-biology/gbench and sci-biology/ncbi-tools++: do not download ncbi-vdb |
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|
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Do not download sources from github during configure phase. This disables |
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the feature completely. Somehow it does not find vdb binaries provided |
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by our sci-biology/ncbi-tools++ package? |
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|
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sci-biology/gbench/gbench-2.10.7.ebuild | 20 +++++++++++++++++--- |
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sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 5 +++++ |
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2 files changed, 22 insertions(+), 3 deletions(-) |
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|
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diff --git a/sci-biology/gbench/gbench-2.10.7.ebuild b/sci-biology/gbench/gbench-2.10.7.ebuild |
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index 4c57d1656..48e7f9d68 100644 |
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--- a/sci-biology/gbench/gbench-2.10.7.ebuild |
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+++ b/sci-biology/gbench/gbench-2.10.7.ebuild |
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@@ -1,4 +1,4 @@ |
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-# Copyright 1999-2016 Gentoo Foundation |
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+# Copyright 1999-2017 Gentoo Foundation |
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# Distributed under the terms of the GNU General Public License v2 |
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|
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EAPI=5 |
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@@ -34,6 +34,7 @@ RDEPEND="${PYTHON_DEPS} |
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media-libs/freetype |
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media-libs/giflib |
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media-libs/tiff:0= |
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+ || ( sci-biology/ncbi-tools++ sci-biology/sra_sdk ) |
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gnutls? ( net-libs/gnutls ) |
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hdf5? ( sci-libs/hdf5 ) |
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sys-fs/fuse |
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@@ -70,6 +71,19 @@ src_configure(){ |
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# configure: error: --datadir=/usr/share: unknown option; use --help to show usage |
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# configure: error: --sysconfdir=/etc: unknown option; use --help to show usage |
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# configure: error: --localstatedir=/var/lib: unknown option; use --help to show usage |
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- ./configure --prefix="${DESTDIR}"/"${EPREFIX}/usr" --libdir="${EPREFIX}/usr/$(get_libdir)" CC="$(tc-getCC)" \ |
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- CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}" || die |
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+ ./configure --prefix="${DESTDIR}"/"${EPREFIX}/usr" --libdir="${EPREFIX}/usr/$(get_libdir)" \ |
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+ --without-downloaded-vdb \ |
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+ CC="$(tc-getCC)" CFLAGS="${CFLAGS}" CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}" || die |
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} |
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+ |
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+# Doh, it runs git during configure phase if it could not find NCBI SRA VDB |
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+# by executing ./scripts/common/add_vdb.sh which points to https://github.com/ncbi/ncbi-vdb |
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+# But, we already have sci-biology/sra_sdk which blocks sci-biology/ncbi-tools++ |
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+# as some file overlap. Seems ncbi-vdb is yet another smaller subset of either |
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+# of the two? |
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+# |
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+# Same come checking out ncbi-vdb should be in ncbi-tools++-18.0.0 . |
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+# |
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+# That behavior is entirely optional; you can suppress it by |
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+# configuring the Toolkit --without-downloaded-vdb, --with-vdb=PATH (e.g., |
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+# --with-vdb=/usr), or --without-vdb altogether. |
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|
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diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild |
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index 179baeaea..5c91c1b0c 100644 |
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--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild |
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+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild |
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@@ -220,6 +220,11 @@ src_configure() { |
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--without-sybase |
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--with-autodep |
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# --with-3psw=std:netopt favor standard (system) builds of the above pkgs |
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+ # preventing executing git to checkout during configure phase ncbi-vdb sources |
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+ # resulting in 'checking for ncbi-vdb... no' and |
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+ # '^PACKAGES:' |
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+ # '^ disabled: ... VDB' |
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+ --without-downloaded-vdb |
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$(use_with debug) |
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$(use_with debug max-debug) |
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$(use_with debug symbols) |
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