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authorJustin Lecher <jlec@gentoo.org>2015-08-09 11:48:20 +0200
committerJustin Lecher <jlec@gentoo.org>2015-08-09 11:48:20 +0200
commit732af598693d9c7fcc4047f5c0bc1cad6fb9ec71 (patch)
tree45b76f744e7268b072992d094b110b518b6fecac
parentImport from tree (diff)
parentsci-biology/inGAP-bin: Fix CAT move and many more things (diff)
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Merge remote-tracking branch 'github/master'
* github/master: sci-biology/inGAP-bin: Fix CAT move and many more things sci-biology/staden: Fix SLOT operators, bug #556946 sys-cluster/openmpi: bump 1.8.8 and sync with gx86 (java support) sci-chemistry/phenix-bin: Prefix love
-rw-r--r--sci-biology/inGAP-bin/ChangeLog5
-rw-r--r--sci-biology/inGAP-bin/inGAP-bin-3.0.1.ebuild22
-rw-r--r--sci-biology/staden/ChangeLog4
-rw-r--r--sci-biology/staden/staden-2.0.0_beta9.ebuild2
-rw-r--r--sci-biology/staden/staden-9999.ebuild2
-rw-r--r--sci-chemistry/phenix-bin/ChangeLog3
-rw-r--r--sci-chemistry/phenix-bin/phenix-bin-1.9.1692.ebuild2
-rw-r--r--sys-cluster/openmpi/ChangeLog6
-rw-r--r--sys-cluster/openmpi/Manifest2
-rw-r--r--sys-cluster/openmpi/openmpi-1.8.8.ebuild (renamed from sys-cluster/openmpi/openmpi-1.8.7.ebuild)26
10 files changed, 56 insertions, 18 deletions
diff --git a/sci-biology/inGAP-bin/ChangeLog b/sci-biology/inGAP-bin/ChangeLog
index c573f62fc..7d0b57b53 100644
--- a/sci-biology/inGAP-bin/ChangeLog
+++ b/sci-biology/inGAP-bin/ChangeLog
@@ -1,7 +1,10 @@
# ChangeLog for sci-biology/inGAP-bin
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 07 Aug 2015; Justin Lecher <jlec@gentoo.org> inGAP-bin-3.0.1.ebuild:
+ sci-biology/inGAP-bin: Fix CAT move and many more things
+
*inGAP-bin-3.0.1 (23 Mar 2014)
23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/inGAP-bin/inGAP-bin-3.0.1.ebuild b/sci-biology/inGAP-bin/inGAP-bin-3.0.1.ebuild
index 0c7903c13..ebe1350ba 100644
--- a/sci-biology/inGAP-bin/inGAP-bin-3.0.1.ebuild
+++ b/sci-biology/inGAP-bin/inGAP-bin-3.0.1.ebuild
@@ -1,14 +1,17 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=3
+EAPI=5
MY_PV="3_0_1"
S="${WORKDIR}"/inGAP_"${MY_PV}"
+inherit java-utils-2
+
DESCRIPTION="Detect SNPs and indels from Next-gen sequences using a Bayesian algorithm"
-HOMEPAGE="http://sites.google.com/site/nextgengenomics/ingap
+HOMEPAGE="
+ http://sites.google.com/site/nextgengenomics/ingap
http://sourceforge.net/projects/ingap/"
SRC_URI="http://sourceforge.net/projects/ingap/files/ingap/v"${PV}"/inGAP_"${MY_PV}".tgz"
@@ -17,23 +20,22 @@ SLOT="0"
KEYWORDS="~amd64"
IUSE=""
-DEPEND=""
+DEPEND=">=virtual/jre-1.7"
RDEPEND="${DEPEND}
dev-java/jfreechart
dev-java/swing-layout
dev-java/jcommon
dev-java/itext
dev-java/bytecode
- dev-java/biojava
+ sci-biology/biojava
dev-java/absolutelayout" # gnujaxp ?
src_install(){
- dobin inGAP.jar || die
+ java-pkg_dojar inGAP.jar
+ java-pkg_dolauncher inGAP --jar inGAP.jar
# dobin external/bin/{primer3_core, run_cpp, trf}
- mv manual.pdf inGAP_Manual.pdf || die
- dodoc inGAP_Manual.pdf || die
- insinto /usr/share/inGAP
- doins doc/manual.htm
+ newdoc manual.pdf inGAP_Manual.pdf
+ dodoc doc/manual.htm
insinto /usr/share/inGAP/manual_files
doins doc/manual_files/*.png
}
diff --git a/sci-biology/staden/ChangeLog b/sci-biology/staden/ChangeLog
index e874d2958..9dd6b53dc 100644
--- a/sci-biology/staden/ChangeLog
+++ b/sci-biology/staden/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 07 Aug 2015; Justin Lecher <jlec@gentoo.org> staden-2.0.0_beta9.ebuild,
+ staden-9999.ebuild:
+ sci-biology/staden: Fix SLOT operators, bug #556946
+
02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
staden-2.0.0_beta9.ebuild, staden-9999.ebuild:
sci-biology/staden: added SLOT operator
diff --git a/sci-biology/staden/staden-2.0.0_beta9.ebuild b/sci-biology/staden/staden-2.0.0_beta9.ebuild
index 152ee6ca7..fa64a7465 100644
--- a/sci-biology/staden/staden-2.0.0_beta9.ebuild
+++ b/sci-biology/staden/staden-2.0.0_beta9.ebuild
@@ -28,7 +28,7 @@ IUSE="curl debug fortran png tcl tk X zlib"
#
DEPEND="
app-arch/xz-utils
- dev-lang/tk:*
+ dev-lang/tk:0=
dev-tcltk/tklib
media-libs/libpng:0
sci-biology/samtools
diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild
index af64ca007..84082e977 100644
--- a/sci-biology/staden/staden-9999.ebuild
+++ b/sci-biology/staden/staden-9999.ebuild
@@ -27,7 +27,7 @@ IUSE="curl debug fortran png tcl tk X zlib"
#
DEPEND="
app-arch/xz-utils
- dev-lang/tk:*
+ dev-lang/tk:0=
dev-tcltk/tklib
media-libs/libpng:0
sci-biology/samtools
diff --git a/sci-chemistry/phenix-bin/ChangeLog b/sci-chemistry/phenix-bin/ChangeLog
index bd837b5be..25a800118 100644
--- a/sci-chemistry/phenix-bin/ChangeLog
+++ b/sci-chemistry/phenix-bin/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 05 Aug 2015; Justin Lecher <jlec@gentoo.org> phenix-bin-1.9.1692.ebuild:
+ sci-chemistry/phenix-bin: Prefix love
+
03 Aug 2015; Justin Lecher <jlec@gentoo.org> phenix-bin-1.9.1692.ebuild:
sci-chemistry/phenix-bin: Fix for latest linux kernel
diff --git a/sci-chemistry/phenix-bin/phenix-bin-1.9.1692.ebuild b/sci-chemistry/phenix-bin/phenix-bin-1.9.1692.ebuild
index bb4237185..be1a24f61 100644
--- a/sci-chemistry/phenix-bin/phenix-bin-1.9.1692.ebuild
+++ b/sci-chemistry/phenix-bin/phenix-bin-1.9.1692.ebuild
@@ -90,7 +90,7 @@ src_prepare() {
}
src_compile() {
- ./install --prefix="${S}/foo" || die
+ LD_LIBRARY_PATH="${EPREFIX}/usr/$(get_libdir)" ./install --prefix="${S}/foo" || die
}
src_install() {
diff --git a/sys-cluster/openmpi/ChangeLog b/sys-cluster/openmpi/ChangeLog
index 2e3f10e4e..29e768208 100644
--- a/sys-cluster/openmpi/ChangeLog
+++ b/sys-cluster/openmpi/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*openmpi-1.8.8-r1 (06 Aug 2015)
+
+ 06 Aug 2015; Justin Bronder <jsbronder@gentoo.org> +openmpi-1.8.8-r1.ebuild,
+ -openmpi-1.8.7.ebuild:
+ sys-cluster/openmpi: bump 1.8.8 and sync with gx86 (java support)
+
16 Jul 2015; Justin Bronder <jsbronder@gentoo.org> -openmpi-1.8.1.ebuild,
-openmpi-1.8.3.ebuild, -openmpi-1.8.4-r4.ebuild, -openmpi-1.8.5.ebuild,
-openmpi-1.8.6.ebuild:
diff --git a/sys-cluster/openmpi/Manifest b/sys-cluster/openmpi/Manifest
index e075e8c4c..77ba3dbf3 100644
--- a/sys-cluster/openmpi/Manifest
+++ b/sys-cluster/openmpi/Manifest
@@ -1,4 +1,4 @@
DIST openmpi-1.6.5.tar.bz2 10943881 SHA256 fe37bab89b5ef234e0ac82dc798282c2ab08900bf564a1ec27239d3f1ad1fc85 SHA512 b0ede0264cd9263b8ba59ec51d17ad47b5f20d49d219ca05f7c396d608398d517b2023a46a2535fd6191160d709e4805c4de436dcfee56eda287383bd69f9652 WHIRLPOOL d0288677827c1deba17295ee1b69cd21da294ac314cc49404389b4c286384f9f2f229cae4c4fd62511e7f20abc510998642d6a2edfac3f16f83078f474f8e735
DIST openmpi-1.7.3.tar.bz2 12479769 SHA256 438d96c178dbf5a1bc92fa1d238a8225d87b64af26ce2a07789faaf312117e45 SHA512 a66d3b1df2a7dc76df4ffa0083919cefb0e7d4133f80bfd5c1c4bf6c5254f2a4773e3c4c9069c39b1467057c406eba3ea892d4a86030b0bd8097d12073af8ef8 WHIRLPOOL 5509f48370f5a00fee68048df5d84824fa63e528df617fc9209840f3077c2c868dbf2c3da964334e7a80c428056a5e2f9a39ddcda9967350e68222444ca918f0
DIST openmpi-1.8.4.tar.bz2 13488749 SHA256 23158d916e92c80e2924016b746a93913ba7fae9fff51bf68d5c2a0ae39a2f8a SHA512 d4c8ce2bd3359cf2e85958b58ba18b52c9cef6676718eb3d948309b164b2f54544f8f8419ef6881c7a51ba268a876cd56e9b2d340a106a16fa25fb9fc3e4eff9 WHIRLPOOL 793f64ad44c2e3451a269bcb53d747d15a01649978d80f13599596e1bdd6a6011b50fdd60222bbe3a4ebe567a4785b2660e3c1eb09bdba77420581a0062480a2
-DIST openmpi-1.8.7.tar.bz2 13228742 SHA256 da629e9bd820a379cfafe15f842ee9b628d7451856085ccc23ee75ab3e1b48c7 SHA512 953e007b00c9753bafc05d13e6f686c9aa47f76f55fcc4eda565174d410de059e07862b7e667d15df13afb80418661d9a8d5ee17fdcc211d3e044992cd9ceede WHIRLPOOL 374edbca97262217dfe405414deff2f6a3cacc06daec56e3356ea76f27804ef3caa3f37050dc8a81f257b83c1ced49fd5f66647c2cba4892fbe4ec9746a6f84e
+DIST openmpi-1.8.8.tar.bz2 13231433 SHA256 a28382d1e6a36f4073412dc00836ff2524e42b674da9caf6ca7377baad790b94 SHA512 8ca2e3ebb9d9ba0f33faba9bef76fe95293721b73619cbc18176611074a56c277e9ab6cae7fa6c87ace11f16151c1bc495b2a8dbc8ad064d5a8f89f5d431a660 WHIRLPOOL e36186452978ba7a368c83b84b8b089f6995450fa866b7b8300d32eec7e64a816abf5f301dc716bf25b3b45b987489952ffc4b7057f4407677f2a2df5ee67cdd
diff --git a/sys-cluster/openmpi/openmpi-1.8.7.ebuild b/sys-cluster/openmpi/openmpi-1.8.8.ebuild
index 4d23574d4..56716fcb9 100644
--- a/sys-cluster/openmpi/openmpi-1.8.7.ebuild
+++ b/sys-cluster/openmpi/openmpi-1.8.8.ebuild
@@ -6,7 +6,7 @@ EAPI=5
FORTRAN_NEEDED=fortran
-inherit cuda eutils flag-o-matic fortran-2 multilib mpi toolchain-funcs versionator
+inherit cuda eutils flag-o-matic fortran-2 java-pkg-opt-2 multilib mpi toolchain-funcs versionator
MY_P=${P/-mpi}
S=${WORKDIR}/${MY_P}
@@ -35,7 +35,7 @@ SRC_URI="http://www.open-mpi.org/software/ompi/v$(get_version_component_range 1-
LICENSE="BSD"
SLOT="0"
KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux"
-IUSE="cma cuda +cxx elibc_FreeBSD fortran heterogeneous ipv6 mpi-threads numa romio threads vt
+IUSE="cma cuda +cxx elibc_FreeBSD fortran heterogeneous ipv6 java mpi-threads numa romio threads vt
${IUSE_OPENMPI_FABRICS} ${IUSE_OPENMPI_RM} ${IUSE_OPENMPI_OFED_FEATURES}"
REQUIRED_USE="openmpi_rm_slurm? ( !openmpi_rm_pbs )
@@ -61,6 +61,7 @@ RDEPEND="
sys-libs/zlib
cuda? ( dev-util/nvidia-cuda-toolkit )
elibc_FreeBSD? ( dev-libs/libexecinfo )
+ java? ( >=virtual/jre-1.6 )
openmpi_fabrics_ofed? ( sys-infiniband/ofed:* )
openmpi_fabrics_knem? ( sys-cluster/knem )
openmpi_fabrics_open-mx? ( sys-cluster/open-mx )
@@ -69,10 +70,12 @@ RDEPEND="
openmpi_rm_slurm? ( sys-cluster/slurm )
openmpi_ofed_features_rdmacm? ( sys-infiniband/librdmacm:* )
$(mpi_imp_deplist)"
-DEPEND="${RDEPEND}"
+DEPEND="${RDEPEND}
+ java? ( >=virtual/jdk-1.6 )"
pkg_setup() {
fortran-2_pkg_setup
+ java-pkg-opt-2_pkg_setup
MPI_ESELECT_FILE="eselect.mpi.openmpi"
if use mpi-threads; then
@@ -114,6 +117,13 @@ src_configure() {
myconf+=(--enable-mpi-fortran=no)
fi
+ if use java; then
+ # We must always build with the right -source and -target
+ # flags. Passing flags to javac isn't explicitly supported here
+ # but we can cheat by overriding the configure test for javac.
+ export ac_cv_path_JAVAC="$(java-pkg_get-javac) $(java-pkg_javac-args)"
+ fi
+
! use vt && myconf+=(--enable-contrib-no-build=vt)
econf $(mpi_econf_args) "${myconf[@]}" \
@@ -123,6 +133,8 @@ src_configure() {
$(use_enable romio io-romio) \
$(use_enable heterogeneous) \
$(use_enable ipv6) \
+ $(use_enable java) \
+ $(use_enable java mpi-java) \
$(use_enable mpi-threads mpi-thread-multiple) \
$(use_with openmpi_fabrics_ofed verbs "${EPREFIX}"/usr) \
$(use_with openmpi_fabrics_knem knem "${EPREFIX}"/usr) \
@@ -150,6 +162,14 @@ src_install () {
# Remove la files, no static libs are installed and we have pkg-config
find "${ED}"/$(mpi_root)/usr/$(get_libdir)/ -type f -name '*.la' -delete
+ if use java; then
+ local mpi_jar="${ED}"/$(mpi_root)/usr/$(get_libdir)/mpi.jar
+ java-pkg_dojar "${mpi_jar}"
+ # We don't want to install the jar file twice
+ # so let's clean after ourselves.
+ rm "${mpi_jar}" || die
+ fi
+
mpi_dodoc README AUTHORS NEWS VERSION || die
mpi_imp_add_eselect
}