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Merge remote branch 'origin/develop' into develop

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This commit is contained in:
Tom Merrick 2017-05-24 13:57:08 -05:00
commit a80ed1af4b
12 changed files with 238 additions and 16 deletions
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2
lib/spack/spack/compilers/pgi.py
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@ -77,4 +77,4 @@ def default_version(cls, comp):
on PowerPC.
"""
return get_compiler_version(
comp, '-V', r'pg[^ ]* ([0-9.-]+) [^ ]+ target on ')
comp, '-V', r'pg[^ ]* ([0-9.]+)-[0-9]+ [^ ]+ target on ')

6
var/spack/repos/builtin/packages/bcl2fastq2/package.py
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@ -39,7 +39,11 @@ class Bcl2fastq2(Package):
homepage = "https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-18.html"
url = "https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/bcl2fastq/bcl2fastq2-v2-18-0-12-tar.zip"
version('2-18-0-12', 'fbe06492117f65609c41be0c27e3215c')
version('2.18.0.12', 'fbe06492117f65609c41be0c27e3215c')
# 2.17.1.14 is no longer distributed. If you have a copy of the
# source tarball, you can drop it into a local mirror w/ the name
# mirror/bcl2fastq2/bcl2fastq2-2.17.1.14.zip and go from there.
version('2.17.1.14', '7426226c6db095862e636b95c38608d3')
depends_on('boost@1.54.0')
depends_on('cmake@2.8.9:')

3
var/spack/repos/builtin/packages/caffe/package.py
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@ -73,7 +73,8 @@ class Caffe(CMakePackage):
def cmake_args(self):
spec = self.spec
args = ['-DBLAS={0}'.format(spec['blas'].name),
args = ['-DBLAS={0}'.format('open' if spec['blas'].name == 'openblas'
else spec['blas'].name),
'-DCPU_ONLY=%s' % ('~gpu' in spec),
'-DUSE_CUDNN=%s' % ('+gpu' in spec),
'-DBUILD_python=%s' % ('+python' in spec),

4
var/spack/repos/builtin/packages/cairo/package.py
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@ -51,4 +51,8 @@ class Cairo(AutotoolsPackage):
def configure_args(self):
args = ["--disable-trace", # can cause problems with libiberty
"--enable-tee"]
if '+X' in self.spec:
args.extend(["--enable-xlib", "--enable-xcb"])
else:
args.extend(["--disable-xlib", "--disable-xcb"])
return args

3
var/spack/repos/builtin/packages/libpciaccess/package.py
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@ -29,8 +29,9 @@ class Libpciaccess(AutotoolsPackage):
"""Generic PCI access library."""
homepage = "http://cgit.freedesktop.org/xorg/lib/libpciaccess/"
url = "http://xorg.freedesktop.org/archive/individual/lib/libpciaccess-0.13.4.tar.gz"
url = "http://xorg.freedesktop.org/archive/individual/lib/libpciaccess-0.13.5.tar.gz"
version('0.13.5', '81468664fde96d1df2c3216fdf3c4a20')
version('0.13.4', 'cc1fad87da60682af1d5fa43a5da45a4')
depends_on('libtool', type='build')

4
var/spack/repos/builtin/packages/mesa-glu/package.py
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@ -34,4 +34,6 @@ class MesaGlu(AutotoolsPackage):
version('9.0.0', 'bbc57d4fe3bd3fb095bdbef6fcb977c4')
depends_on('mesa')
variant('mesa', default=True,
description='Usually depends on mesa, disable for accelerated OpenGL')
depends_on('mesa', when='+mesa')

24
var/spack/repos/builtin/packages/mummer/Makefile.patch Normal file
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@ -0,0 +1,24 @@
--- a/Makefile 2017-05-15 17:33:05.132803923 -0700
+++ b/Makefile 2017-05-16 16:01:29.264842369 -0700
@@ -35,6 +35,13 @@
TIGR_SRC_DIR := $(TOP_DIR)/src/tigr
KURTZ_SRC_DIR := $(TOP_DIR)/src/kurtz
+ifndef INSTALL_TOP_DIR
+INSTALL_TOP_DIR := $(TOP_DIR)
+endif
+INSTALL_BIN_DIR := $(INSTALL_TOP_DIR)/bin
+INSTALL_AUX_BIN_DIR := $(INSTALL_TOP_DIR)/aux_bin
+INSTALL_SCRIPT_DIR := $(INSTALL_TOP_DIR)/scripts
+
CC := $(filter /%,$(shell /bin/sh -c 'type gcc'))
CXX := $(filter /%,$(shell /bin/sh -c 'type g++'))
SED := $(filter /%,$(shell /bin/sh -c 'type sed'))
@@ -52,6 +59,7 @@
#-- EXPORT THESE VARIABLES TO OTHER MAKEFILES
export BIN_DIR AUX_BIN_DIR CXX CC CFLAGS CXXFLAGS LDFLAGS
+export INSTALL_BIN_DIR INSTALL_AUX_BIN_DIR INSTALL_SCRIPT_DIR

24
var/spack/repos/builtin/packages/mummer/package.py
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@ -34,12 +34,21 @@ class Mummer(Package):
version('3.23', 'f2422b3d2638dba4baedb71b1acdffa2')
depends_on('gnuplot')
depends_on('perl', type=('build', 'run'))
patch('Makefile.patch')
patch('scripts-Makefile.patch')
def install(self, spec, prefix):
if self.run_tests:
make('check')
make('install')
mkdirp(prefix.bin)
make('INSTALL_TOP_DIR={0}'.format(prefix))
bd = prefix.bin
abd = join_path(prefix, 'aux_bin')
sd = join_path(prefix, 'scripts')
mkdirp(bd)
mkdirp(abd)
mkdirp(sd)
bins = ["show-tiling", "show-snps", "show-coords", "show-aligns",
"show-diff", "delta-filter", "combineMUMs", "mummer",
@ -48,8 +57,11 @@ def install(self, spec, prefix):
"run-mummer1", "nucmer", "mapview", "exact-tandems"]
aux_bins = ["aux_bin/postnuc", "aux_bin/postpro",
"aux_bin/prenuc", "aux_bin/prepro"]
scripts = ["scripts/Foundation.pm"]
for b in bins:
install(b, join_path(prefix.bin, b))
for b in aux_bins:
install(b, join_path(prefix.bin, b[8:]))
for f in bins:
install(f, join_path(bd, f))
for f in aux_bins:
install(f, join_path(abd, f[8:]))
for f in scripts:
install(f, join_path(sd, f[8:]))

74
var/spack/repos/builtin/packages/mummer/scripts-Makefile.patch Normal file
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@ -0,0 +1,74 @@
--- a/scripts/Makefile 2011-12-16 18:49:26.000000000 -0800
+++ b/scripts/Makefile 2017-05-16 16:05:48.697853000 -0700
@@ -37,56 +37,56 @@
#-- not so PHONY rules --#
exact-tandems: exact-tandems.csh
$(SED) -e 's?__CSH_PATH?$(CSH)?g' \
- -e 's?__BIN_DIR?$(BIN_DIR)?g' \
- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+ -e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
+ -e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \
exact-tandems.csh > $(BIN_DIR)/exact-tandems
chmod 755 $(BIN_DIR)/exact-tandems
mapview: mapview.pl
$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
+ -e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \
mapview.pl > $(BIN_DIR)/mapview
chmod 755 $(BIN_DIR)/mapview
mummerplot: mummerplot.pl Foundation.pm
$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
- -e 's?__BIN_DIR?$(BIN_DIR)?g' \
+ -e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \
+ -e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
mummerplot.pl > $(BIN_DIR)/mummerplot
chmod 755 $(BIN_DIR)/mummerplot
dnadiff: dnadiff.pl Foundation.pm
$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
- -e 's?__BIN_DIR?$(BIN_DIR)?g' \
+ -e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \
+ -e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
dnadiff.pl > $(BIN_DIR)/dnadiff
chmod 755 $(BIN_DIR)/dnadiff
nucmer: nucmer.pl Foundation.pm
$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
- -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \
- -e 's?__BIN_DIR?$(BIN_DIR)?g' \
+ -e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \
+ -e 's?__AUX_BIN_DIR?$(INSTALL_AUX_BIN_DIR)?g' \
+ -e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
nucmer.pl > $(BIN_DIR)/nucmer
chmod 755 $(BIN_DIR)/nucmer
promer: promer.pl Foundation.pm
$(SED) -e 's?__PERL_PATH?$(PERL)?g' \
- -e 's?__SCRIPT_DIR?$(SCRIPT_DIR)?g' \
- -e 's?__AUX_BIN_DIR?$(AUX_BIN_DIR)?g' \
- -e 's?__BIN_DIR?$(BIN_DIR)?g' \
+ -e 's?__SCRIPT_DIR?$(INSTALL_SCRIPT_DIR)?g' \
+ -e 's?__AUX_BIN_DIR?$(INSTALL_AUX_BIN_DIR)?g' \
+ -e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
promer.pl > $(BIN_DIR)/promer
chmod 755 $(BIN_DIR)/promer
run-mummer1: run-mummer1.csh
$(SED) -e 's?__CSH_PATH?$(CSH)?g' \
- -e 's?__BIN_DIR?$(BIN_DIR)?g' \
+ -e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
run-mummer1.csh > $(BIN_DIR)/run-mummer1
chmod 755 $(BIN_DIR)/run-mummer1
run-mummer3: run-mummer3.csh
$(SED) -e 's?__CSH_PATH?$(CSH)?g' \
- -e 's?__BIN_DIR?$(BIN_DIR)?g' \
+ -e 's?__BIN_DIR?$(INSTALL_BIN_DIR)?g' \
run-mummer3.csh > $(BIN_DIR)/run-mummer3
chmod 755 $(BIN_DIR)/run-mummer3

1
var/spack/repos/builtin/packages/opencoarrays/package.py
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@ -36,6 +36,7 @@ class Opencoarrays(CMakePackage):
homepage = "http://www.opencoarrays.org/"
url = "https://github.com/sourceryinstitute/OpenCoarrays/releases/download/1.8.4/OpenCoarrays-1.8.4.tar.gz"
version('1.8.10', '9ba1670647db4d986634abf743abfd6a')
version('1.8.4', '7c9eaffc3a0b5748d0d840e52ec9d4ad')
version('1.8.0', 'ca78d1507b2a118c75128c6c2e093e27')
version('1.7.4', '85ba87def461e3ff5a164de2e6482930')

54
var/spack/repos/builtin/packages/r-rgl/package.py Normal file
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@ -0,0 +1,54 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class RRgl(RPackage):
"""Provides medium to high level functions for 3D interactive graphics,
including functions modelled on base graphics (plot3d(), etc.) as well as
functions for constructing representations of geometric objects (cube3d(),
etc.). Output may be on screen using OpenGL, or to various standard
3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats,
including PNG, Postscript, SVG, PGF."""
homepage = "https://r-forge.r-project.org/projects/rgl"
url = "https://cloud.r-project.org/src/contrib/rgl_0.98.1.tar.gz"
list_url = 'https://cloud.r-project.org/src/contrib/Archive/rgl'
version('0.98.1', 'bd69e1d33f1590feb4b6dc080b133e5b')
depends_on('r@3.2:3.9')
depends_on('zlib', type=('link'))
depends_on('libpng', type=('link'))
depends_on('freetype', type=('link'))
depends_on('mesa', type=('link'))
depends_on('mesa-glu', type=('link'))
depends_on('r-htmlwidgets', type=('build', 'run'))
depends_on('r-htmltools', type=('build', 'run'))
depends_on('r-knitr', type=('build', 'run'))
depends_on('r-jsonlite', type=('build', 'run'))
depends_on('r-shiny', type=('build', 'run'))
depends_on('r-magrittr', type=('build', 'run'))

45
var/spack/repos/builtin/packages/virtualgl/package.py Normal file
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@ -0,0 +1,45 @@
##############################################################################
# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/spack
# Please also see the LICENSE file for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
#
from spack import *
class Virtualgl(CMakePackage):
"""VirtualGL redirects 3D commands from a Unix/Linux OpenGL application
onto a server-side GPU and converts the rendered 3D images into a video
stream with which remote clients can interact to view and control the
3D application in real time."""
homepage = "http://www.virtualgl.org/Main/HomePage"
url = "http://downloads.sourceforge.net/project/virtualgl/2.5.2/VirtualGL-2.5.2.tar.gz"
version('2.5.2', '1a9f404f4a35afa9f56381cb33ed210c')
depends_on("libjpeg-turbo")
# virtualgl require OpenGL but also wants to link libglu
# on systems without development packages, provide with spack and depends
# on mesa-glu, but we do not want Mesa OpenGL sw emulation, so added
# variant on mesa-glu to disable dependencies on sw emulated OpenGL
depends_on("mesa-glu~mesa")