diff options
10 files changed, 0 insertions, 425 deletions
diff --git a/var/spack/repos/builtin/packages/allinea-reports/package.py b/var/spack/repos/builtin/packages/allinea-reports/package.py deleted file mode 100644 index 49496d43c9..0000000000 --- a/var/spack/repos/builtin/packages/allinea-reports/package.py +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class AllineaReports(Package): - """Allinea Performance Reports are the most effective way to characterize - and understand the performance of HPC application runs. One single-page - HTML report elegantly answers a range of vital questions for any HPC site - """ - - homepage = "http://www.allinea.com/products/allinea-performance-reports" - - version('6.0.4', '3f13b08a32682737bc05246fbb2fcc77') - - # Licensing - license_required = True - license_comment = '#' - license_files = ['licences/Licence'] - license_vars = ['ALLINEA_LICENCE_FILE', 'ALLINEA_LICENSE_FILE'] - license_url = 'http://www.allinea.com/user-guide/reports/Installation.html' - - def url_for_version(self, version): - # TODO: add support for other architectures/distributions - url = "http://content.allinea.com/downloads/" - return url + "allinea-reports-%s-Redhat-6.0-x86_64.tar" % version - - def install(self, spec, prefix): - textinstall = Executable('./textinstall.sh') - textinstall('--accept-licence', prefix) diff --git a/var/spack/repos/builtin/packages/arlecore/package.py b/var/spack/repos/builtin/packages/arlecore/package.py deleted file mode 100644 index 5c63056bd2..0000000000 --- a/var/spack/repos/builtin/packages/arlecore/package.py +++ /dev/null @@ -1,20 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Arlecore(Package): - """An Integrated Software for Population Genetics Data Analysis""" - - homepage = "http://cmpg.unibe.ch/software/arlequin35/" - url = "http://cmpg.unibe.ch/software/arlequin35/linux/arlecore_linux.zip" - - version('3.5.2.2', '347a589fc609f359eb61557a2e8ceb2f') - - depends_on('r', type=('build', 'run')) - - def install(self, spec, prefix): - install_tree('.', prefix) diff --git a/var/spack/repos/builtin/packages/globus-toolkit/package.py b/var/spack/repos/builtin/packages/globus-toolkit/package.py deleted file mode 100644 index 7a43412608..0000000000 --- a/var/spack/repos/builtin/packages/globus-toolkit/package.py +++ /dev/null @@ -1,20 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class GlobusToolkit(AutotoolsPackage): - """The Globus Toolkit is an open source software toolkit used for building - grids""" - - homepage = "http://toolkit.globus.org" - url = "http://toolkit.globus.org/ftppub/gt6/installers/src/globus_toolkit-6.0.1506371041.tar.gz" - - version('6.0.1506371041', 'e17146f68e03b3482aaea3874d4087a5') - version('6.0.1493989444', '9e9298b61d045e65732e12c9727ceaa8') - - depends_on('pkgconfig', type='build') - depends_on('openssl') diff --git a/var/spack/repos/builtin/packages/mpiblast/mpiBLAST-1.6.0-patch-110806 b/var/spack/repos/builtin/packages/mpiblast/mpiBLAST-1.6.0-patch-110806 deleted file mode 100644 index 05de8ed074..0000000000 --- a/var/spack/repos/builtin/packages/mpiblast/mpiBLAST-1.6.0-patch-110806 +++ /dev/null @@ -1,182 +0,0 @@ -diff -rwu mpiblast-1.6.0/ncbi/corelib/ncbienv.c mpiblast-1.6.0-patched/ncbi/corelib/ncbienv.c ---- mpiblast-1.6.0/ncbi/corelib/ncbienv.c 2009-11-22 01:17:48.000000000 -0500 -+++ mpiblast-1.6.0-patched/ncbi/corelib/ncbienv.c 2011-08-06 17:10:08.000000000 -0400 -@@ -1932,7 +1932,7 @@ - static char **targv = NULL; - - --#if defined(WIN_MAC) -+#if defined(WIN_MAC) || defined(OS_UNIX_DARWIN) - static FSSpec apFileSpec; - static Str255 apName; - static Handle apParam; -@@ -2047,7 +2047,7 @@ - } - } - #endif /* defined(OS_UNIX_DARWIN) */ --#endif /* defined(WIN_MAC) */ -+#endif /* defined(WIN_MAC) || defined(OS_UNIX_DARWIN) */ - - - #if defined(OS_MSWIN) || defined(OS_VMS) -diff -rwu mpiblast-1.6.0/ncbi/make/makedis.csh mpiblast-1.6.0-patched/ncbi/make/makedis.csh ---- mpiblast-1.6.0/ncbi/make/makedis.csh 2010-06-28 21:04:36.000000000 -0400 -+++ mpiblast-1.6.0-patched/ncbi/make/makedis.csh 2011-08-06 17:06:42.000000000 -0400 -@@ -1,6 +1,6 @@ - #!/bin/csh -f - # --# $Id: makedis.csh 148594 2008-12-30 15:11:36Z ucko $ -+# $Id: makedis.csh 179886 2010-01-04 17:28:02Z ucko $ - # - ## PUBLIC DOMAIN NOTICE - # National Center for Biotechnology Information -@@ -54,7 +54,7 @@ - endif - - ls -l $tar_file -- tar xvf $tar_file -+ tar xf $tar_file - else - # make sure that ncbi/build directory exists - if ( ! -d "ncbi/build" ) then -@@ -74,6 +74,7 @@ - set HAVE_MAC=0 - #we will try to build OpenGL version of vibrant - set HAVE_OGL=1 -+set MPBL_HAVE_MAC=0 - - switch ($os) - case SunOS: -@@ -164,7 +165,7 @@ - gcc -v - switch (`uname -m`) - case "ia64": -- if (-e `which ecc`) then -+ if (-e `which icc`) then - set platform=linux_ecc - else - set platform=linux -@@ -253,7 +254,11 @@ - endif - endif - set HAVE_MOTIF=0 -- set HAVE_MAC=1 -+#MPIBLAST <<< -+# set HAVE_MAC=1 -+ set MPBL_HAVE_MAC=1 -+ set HAVE_MAC=0 -+#MPIBLAST - breaksw - case NetBSD: - set platform=netbsd -@@ -319,6 +324,7 @@ - goto BADPLATFORM - endif - -+ - set noglob - # take the file $NCBI_DOT_MK and convert it to be suitable for csh eval: - # (1) remove comments at the beginning of the lines -@@ -328,6 +334,7 @@ - eval `sed -e 's/^ *#.*//g' -e 's/\$(\([a-zA-Z_]*\))/\${\1}/g' -e 's/ *= */=/g' -e 's/^\([^=]*\)=\(.*\)$/setenv \1 "\2";/' < $NCBI_DOT_MK` - unset noglob - -+ - # disable assert() unless ENABLE_ASSERT is set - if ("$?ENABLE_ASSERT" == 0) then - set NCBI_OPTFLAG="-DNDEBUG $NCBI_OPTFLAG" -@@ -441,13 +448,23 @@ - set NET_VIB=(VIB=\"blastcl3 taxblast idfetch bl2seq asn2gb tbl2asn gene2xml $NONVIBWWWBLAST \") - endif - -+# MPIBLAST <<<<< -+if ("$MPBL_HAVE_MAC" == 1) then -+set CMD='make $MFLG \ -+ CFLAGS1=\"-I/Developer/Headers/FlatCarbon $NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE $PNG_INCLUDE\" \ -+ LDFLAGS1=\"$NCBI_LDFLAGS1\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \ -+ SHELL=\"$NCBI_MAKE_SHELL\" LCL=\"$NCBI_DEFAULT_LCL\" \ -+ RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" $ALL_VIB all' -+else - set CMD='make $MFLG \ - CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1 $OGL_INCLUDE $PNG_INCLUDE\" \ - LDFLAGS1=\"$NCBI_LDFLAGS1\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \ - SHELL=\"$NCBI_MAKE_SHELL\" LCL=\"$NCBI_DEFAULT_LCL\" \ - RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" $ALL_VIB all' -+endif - eval echo $CMD - eval echo $CMD | sh -+# MPIBLAST >>>>> - - set make_stat = $status - -@@ -463,12 +480,18 @@ - endif - - # MPIBLAST <<<<< -- -+if ("$MPBL_HAVE_MAC" == 1) then - set CMD='make $MFLG -f makempiblast.unx CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1\" \ - LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \ - LCL=\"$NCBI_DEFAULT_LCL\" RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\"' -+else -+set CMD='make $MFLG -f makempiblast.unx CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1\" \ -+ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \ -+ LCL=\"$NCBI_DEFAULT_LCL\" RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\"' -+endif - eval echo $CMD - eval echo $CMD | sh -+if ($status != 0) exit $status - - if( "$platform" == "bluegenel" || "$platform" == "bluegenep" ) then - exit 0 -@@ -476,7 +499,7 @@ - # MPIBLAST >>>>> - - set CMD='make $MFLG -f makedemo.unx CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1\" \ -- LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \ -+ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \ - LCL=\"$NCBI_DEFAULT_LCL\" RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" $DEMO_VIB' - eval echo $CMD - eval echo $CMD | sh -@@ -495,7 +518,7 @@ - - - set CMD='make $MFLG -f makedemo.unx CFLAGS1=\"$NCBI_OPTFLAG $NCBI_CFLAGS1\" \ -- LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" \ -+ LDFLAGS1=\"$NCBI_LDFLAGS1\" SHELL=\"$NCBI_MAKE_SHELL\" OTHERLIBS=\"$NCBI_OTHERLIBS\" \ - LCL=\"$NCBI_DEFAULT_LCL\" RAN=\"$NCBI_RANLIB\" AR=\"$NCBI_AR\" CC=\"$NCBI_CC\" \ - THREAD_OBJ=$NCBI_THREAD_OBJ THREAD_OTHERLIBS=\"$NCBI_MT_OTHERLIBS\" \ - $DEMO_VIB $mtapps' -diff -rwu mpiblast-1.6.0/src/Makefile.am mpiblast-1.6.0-patched/src/Makefile.am ---- mpiblast-1.6.0/src/Makefile.am 2009-11-22 01:17:48.000000000 -0500 -+++ mpiblast-1.6.0-patched/src/Makefile.am 2011-08-06 17:06:42.000000000 -0400 -@@ -2,7 +2,7 @@ - -D_LARGEFILE64_SOURCE -DMPIBLAST_PIO \ - -I$(top_srcdir)/include/ -I@CONFIG_NCBIDIR@/include/ $(MPE_INCS) \ - -I@CONFIG_NCBIDIR@/corelib/ --AM_CXXFLAGS = -DMPICH_IGNORE_CXX_SEEK -DINSTALL_PREFIX="\"@prefix@\"" \ -+AM_CXXFLAGS = -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX -DINSTALL_PREFIX="\"@prefix@\"" \ - @COMPILE_FLAGS@ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE \ - -I$(top_srcdir)/include/ -I@CONFIG_NCBIDIR@/include/ $(MPE_INCS) \ - -I@CONFIG_NCBIDIR@/corelib/ -@@ -31,7 +31,7 @@ - @CONFIG_NCBIDIR@/build/blast_hooks.o -lmyncbitool -lblastcompadj -lmyncbiobj \ - -lmyncbi -L. -L@CONFIG_NCBIDIR@/lib/ $(MPE_LIBS) -lm @LINK_FLAGS@ - mpiblast_DEPENDENCIES = @GETOPT_LONG_SYSTEM@ --mpiblast_CPPFLAGS = -DUSING_MPI -DMPICH_IGNORE_CXX_SEEK -+mpiblast_CPPFLAGS = -DUSING_MPI -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX - - mpiformatdb_SOURCES = mpiformatdb.cpp mpiblast_config.cpp mpiblast_config.hpp \ - file_util.cpp file_util.hpp mpiblast_util.cpp mpiblast_util.hpp \ -diff -rwu mpiblast-1.6.0/src/pio_intercept.h mpiblast-1.6.0-patched/src/pio_intercept.h ---- mpiblast-1.6.0/src/pio_intercept.h 2009-11-22 01:17:48.000000000 -0500 -+++ mpiblast-1.6.0-patched/src/pio_intercept.h 2011-08-06 17:06:42.000000000 -0400 -@@ -60,7 +60,7 @@ - #include <txalign.h> - - /* marcros are duplicated in ncbi files to avoid header file conflict */ --#define CHECK_NULPTR(x) if(x==NULL) fprintf(stderr, "%s, line%d: cannot allocate enough memory\n", __FILE__, __LINE__); -+#define CHECK_NULPTR(x) if(x==NULL) { perror("Cannot allocate enough memory:"); exit(-1); } - - #ifndef NO_MPI - typedef struct _output_record { diff --git a/var/spack/repos/builtin/packages/mpiblast/package.py b/var/spack/repos/builtin/packages/mpiblast/package.py deleted file mode 100644 index d35bdecec7..0000000000 --- a/var/spack/repos/builtin/packages/mpiblast/package.py +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Mpiblast(AutotoolsPackage): - """mpiBLAST is a freely available, open-source, parallel implementation of - NCBI BLAST""" - - homepage = "http://www.mpiblast.org/" - url = "http://www.mpiblast.org/downloads/files/mpiBLAST-1.6.0.tgz" - - version('1.6.0', '707105ccd56825db776b50bfd81cecd5') - - patch('mpiBLAST-1.6.0-patch-110806') - - depends_on('mpi') - - def configure_args(self): - args = ['--with-mpi=%s' % self.spec['mpi'].prefix] - return args - - def build(self, spec, prefix): - make('ncbi') - make() - - def setup_environment(self, spack_env, run_env): - spack_env.set('ac_cv_path_CC', self.spec['mpi'].mpicc) - spack_env.set('ac_cv_path_CXX', self.spec['mpi'].mpicxx) diff --git a/var/spack/repos/builtin/packages/py-mxnet/package.py b/var/spack/repos/builtin/packages/py-mxnet/package.py deleted file mode 100644 index 8d78922472..0000000000 --- a/var/spack/repos/builtin/packages/py-mxnet/package.py +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class PyMxnet(PythonPackage): - """Python binding for DMLC/MXNet.""" - - homepage = "http://mxnet.io" - url = "https://github.com/sjtuhpcc/python-mxnet/archive/0.10.0.post2.tar.gz" - - version('0.10.0.post2', '64a646fbf5d1b53ce1008da1bf94d77c', - url='https://github.com/sjtuhpcc/python-mxnet/archive/0.10.0.post2.tar.gz') - - # TODO - # install_time_test_callbacks = ['install_test', 'import_module_test'] - - # import_modules = ['mxnet', 'mxnet.module', 'mxnet._ctypes', 'mxnet.rnn', - # 'mxnet._cy2', 'mxnet._cy3', 'mxnet.notebook', 'mxnet.contrib'] - - variant('cuda', default=False, description='Enable CUDA support') - - depends_on('python@2.6:2.8,3.3:') - - depends_on('py-setuptools', type=('build', 'run')) - depends_on('py-numpy@1.7.1:', type=('build', 'run')) - # depends_on('py-pip', type='build') - - depends_on('mxnet', type=('build', 'run')) - depends_on('mxnet+cuda', when='+cuda', type=('build', 'run')) - - def patch(self): - spec = self.spec - filter_file('../../../', - spec['mxnet'].prefix.lib, - 'mxnet/libinfo.py', string=True) diff --git a/var/spack/repos/builtin/packages/soap2/package.py b/var/spack/repos/builtin/packages/soap2/package.py deleted file mode 100644 index 4c1368a49e..0000000000 --- a/var/spack/repos/builtin/packages/soap2/package.py +++ /dev/null @@ -1,23 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Soap2(Package): - """Software for short oligonucleotide alignment.""" - - homepage = "http://soap.genomics.org.cn/soapaligner.html" - url = "http://soap.genomics.org.cn/down/soap2.21release.tar.gz" - - version('2.21', '563b8b7235463b68413f9e841aa40779') - - def install(self, spec, prefix): - mkdirp(prefix.bin) - mkdirp(prefix.share.man) - install('soap', prefix.bin) - install('2bwt-builder', prefix.bin) - install('soap.1', prefix.share.man) - install('soap.man', prefix.share.man) diff --git a/var/spack/repos/builtin/packages/soapindel/package.py b/var/spack/repos/builtin/packages/soapindel/package.py deleted file mode 100644 index 7c4e8065fd..0000000000 --- a/var/spack/repos/builtin/packages/soapindel/package.py +++ /dev/null @@ -1,34 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Soapindel(MakefilePackage): - """SOAPindel is focusing on calling indels from the next-generation - paired-end sequencing data.""" - - homepage = "http://soap.genomics.org.cn/soapindel.html" - - version('2.1.7.17', '317ef494173969cdc6a8244dd87d06bd', - url='http://soap.genomics.org.cn/down/SOAPindel_20130918_2.1.7.17.zip') - - depends_on('perl', type=('build', 'run')) - - build_directory = 'indel_detection.release' - - def install(self, spec, prefix): - with working_dir('indel_detection.release'): - install_tree('tools', prefix.tools) - mkdirp(prefix.lib) - install('affine_align.pm', prefix.lib) - install('indel_lib.pm', prefix.lib) - mkdirp(prefix.bin) - install('assemble_align', prefix.bin) - install('cluster_reads', prefix.bin) - - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PERL5LIB', self.prefix.lib) - run_env.prepend_path('PATH', self.prefix.tools) diff --git a/var/spack/repos/builtin/packages/soapsnp/package.py b/var/spack/repos/builtin/packages/soapsnp/package.py deleted file mode 100644 index 53d6a2b777..0000000000 --- a/var/spack/repos/builtin/packages/soapsnp/package.py +++ /dev/null @@ -1,23 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Soapsnp(MakefilePackage): - """SOAPsnp uses a method based on Bayes' theorem (the reverse probability - model) to call consensus genotype by carefully considering the data - quality, alignment, and recurring experimental errors.""" - - homepage = "http://soap.genomics.org.cn/soapsnp.html" - url = "http://soap.genomics.org.cn/down/SOAPsnp-v1.03.tar.gz" - - version('1.03', '8d69e196013657357ff840b611762ebc') - - depends_on('boost') - - def install(self, spec, prefix): - mkdirp(prefix.bin) - install('soapsnp', prefix.bin) diff --git a/var/spack/repos/builtin/packages/uberftp/package.py b/var/spack/repos/builtin/packages/uberftp/package.py deleted file mode 100644 index c3b5729f1c..0000000000 --- a/var/spack/repos/builtin/packages/uberftp/package.py +++ /dev/null @@ -1,19 +0,0 @@ -# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other -# Spack Project Developers. See the top-level COPYRIGHT file for details. -# -# SPDX-License-Identifier: (Apache-2.0 OR MIT) - -from spack import * - - -class Uberftp(AutotoolsPackage): - """UberFTP is an interactive (text-based) client for GridFTP""" - - homepage = "http://toolkit.globus.org/grid_software/data/uberftp.php" - url = "https://github.com/JasonAlt/UberFTP/archive/Version_2_8.tar.gz" - - version('2_8', sha256='8a397d6ef02bb714bb0cbdb259819fc2311f5d36231783cd520d606c97759c2a') - version('2_7', sha256='29a111a86fa70dbbc529a5d3e5a6befc1681e64e32dc019a1a6a98cd43ffb204') - version('2_6', sha256='2823a564801fb71d06fe6fbc3a37f11962af75b33c53bf698f26776ec972fe68') - - depends_on('globus-toolkit') |