[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/

[Martin Mokrejs]

commit:     cb2f6200cc1de77fcdb6b3ac1b5b1d835ab4225f
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jun  2 12:06:58 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jun  2 12:06:58 2014 +0000
URL:        
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cb2f6200

sci-biology/ncbi-tools++: added a note about a taxonomy database add-on not yet 
installed by Gentoo

---
 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild   | 3 +++
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild | 4 ++++
 sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild    | 5 +++++
 3 files changed, 12 insertions(+)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild 
b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index d4a5085..3b19a93 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -18,6 +18,8 @@ SRC_URI="
        
ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz";
 #      http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz";
 
+# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
+# see http://www.biostars.org/p/76551/ and 
http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
 LICENSE="public-domain"
 SLOT="0"
 IUSE="
@@ -271,6 +273,7 @@ src_configure() {
 #              --without-static \
 #              --with-dll \
 #              --with-mt \
+#              --with-openmp \
 #              --with-lfs \
 #              --prefix="${ED}"/usr \
 #              --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild 
b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
index 7b3ba9e..89ae176 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0-r1.ebuild
@@ -18,6 +18,9 @@ SRC_URI="
        
ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz";
 #      http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz";
 
+# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
+# see http://www.biostars.org/p/76551/ and 
http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
+
 LICENSE="public-domain"
 SLOT="0"
 IUSE="
@@ -281,6 +284,7 @@ src_configure() {
 #              --without-static \
 #              --with-dll \
 #              --with-mt \
+#              --with-openmp \
 #              --with-lfs \
 #              --prefix="${ED}"/usr \
 #              --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild 
b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
index 2824e09..8020276 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-9.0.0.ebuild
@@ -18,6 +18,9 @@ SRC_URI="
        
ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz";
 #      http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz";
 
+# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
+# see http://www.biostars.org/p/76551/ and 
http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
+
 LICENSE="public-domain"
 SLOT="0"
 IUSE="berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype ftds gif 
glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python 
sablotron sqlite sqlite3 ssl tiff xerces xalan xml xpm xslt X"
@@ -283,6 +286,8 @@ src_configure() {
                --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \
                ${myconf} LDFLAGS="-Wl,--no-as-needed" \
                || die
+
+       # --with-openmp
 }
 
 src_compile() {