diff options
Diffstat (limited to 'var')
10 files changed, 236 insertions, 50 deletions
diff --git a/var/spack/repos/builtin/packages/bcftools/package.py b/var/spack/repos/builtin/packages/bcftools/package.py new file mode 100644 index 0000000000..a1b4a06dbb --- /dev/null +++ b/var/spack/repos/builtin/packages/bcftools/package.py @@ -0,0 +1,43 @@ +############################################################################## +# 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 Bcftools(Package): + """BCFtools is a set of utilities that manipulate variant calls in the + Variant Call Format (VCF) and its binary counterpart BCF. All + commands work transparently with both VCFs and BCFs, both + uncompressed and BGZF-compressed.""" + + homepage = "http://samtools.github.io/bcftools/" + url = "https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2" + + version('1.3.1', '575001e9fca37cab0c7a7287ad4b1cdb') + + depends_on('zlib') + + def install(self, spec, prefix): + make("prefix=%s" % prefix, "all") + make("prefix=%s" % prefix, "install") diff --git a/var/spack/repos/builtin/packages/bwa/package.py b/var/spack/repos/builtin/packages/bwa/package.py new file mode 100644 index 0000000000..bb6763629b --- /dev/null +++ b/var/spack/repos/builtin/packages/bwa/package.py @@ -0,0 +1,52 @@ +############################################################################## +# 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 Bwa(Package): + """Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.""" + + homepage = "http://github.com/lh3/bwa" + url = "https://github.com/lh3/bwa/releases/download/v0.7.15/bwa-0.7.15.tar.bz2" + + version('0.7.15', 'fcf470a46a1dbe2f96a1c5b87c530554') + + depends_on('zlib') + + def install(self, spec, prefix): + filter_file(r'^INCLUDES=', + "INCLUDES=-I%s" % spec['zlib'].prefix.include, 'Makefile') + filter_file(r'^LIBS=', "LIBS=-L%s " % spec['zlib'].prefix.lib, + 'Makefile') + make() + + mkdirp(prefix.bin) + install('bwa', join_path(prefix.bin, 'bwa')) + set_executable(join_path(prefix.bin, 'bwa')) + mkdirp(prefix.doc) + install('README.md', prefix.doc) + install('NEWS.md', prefix.doc) + mkdirp(prefix.man1) + install('bwa.1', prefix.man1) diff --git a/var/spack/repos/builtin/packages/cube/package.py b/var/spack/repos/builtin/packages/cube/package.py index 40c2cc6893..09237f87c3 100644 --- a/var/spack/repos/builtin/packages/cube/package.py +++ b/var/spack/repos/builtin/packages/cube/package.py @@ -28,8 +28,8 @@ from spack import * class Cube(Package): """ - Cube the profile viewer for Score-P and Scalasca profiles. It displays a multi-dimensional performance space - consisting of the dimensions: + Cube the profile viewer for Score-P and Scalasca profiles. It displays a + multi-dimensional performance space consisting of the dimensions: - performance metric - call path - system resource @@ -38,14 +38,17 @@ class Cube(Package): homepage = "http://www.scalasca.org/software/cube-4.x/download.html" url = "http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist/cube-4.2.3.tar.gz" + version('4.3.4', '50f73060f55311cb12c5b3cb354d59fa', + url='http://apps.fz-juelich.de/scalasca/releases/cube/4.3/dist/cube-4.3.4.tar.gz') version('4.3.3', '07e109248ed8ffc7bdcce614264a2909', url='http://apps.fz-juelich.de/scalasca/releases/cube/4.3/dist/cube-4.3.3.tar.gz') - version('4.2.3', '8f95b9531f5a8f8134f279c2767c9b20', url="http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist/cube-4.2.3.tar.gz") # TODO : add variant that builds GUI on top of Qt + depends_on('zlib') + def install(self, spec, prefix): configure_args = ["--prefix=%s" % prefix, "--without-paraver", diff --git a/var/spack/repos/builtin/packages/htslib/package.py b/var/spack/repos/builtin/packages/htslib/package.py new file mode 100644 index 0000000000..1a8b8fd2f5 --- /dev/null +++ b/var/spack/repos/builtin/packages/htslib/package.py @@ -0,0 +1,41 @@ +############################################################################## +# 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 Htslib(Package): + """C library for high-throughput sequencing data formats.""" + + homepage = "https://github.com/samtools/htslib" + url = "https://github.com/samtools/htslib/releases/download/1.3.1/htslib-1.3.1.tar.bz2" + + version('1.3.1', '16d78f90b72f29971b042e8da8be6843') + + depends_on('zlib') + + def install(self, spec, prefix): + configure('--prefix={0}'.format(prefix)) + make() + make('install') diff --git a/var/spack/repos/builtin/packages/opari2/package.py b/var/spack/repos/builtin/packages/opari2/package.py index 510fff9fc2..e901f8ed39 100644 --- a/var/spack/repos/builtin/packages/opari2/package.py +++ b/var/spack/repos/builtin/packages/opari2/package.py @@ -25,18 +25,24 @@ from spack import * + class Opari2(Package): """ - OPARI2 is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and - runtime library calls with calls to the POMP2 measurement interface. OPARI2 will provide you with a new - initialization method that allows for multi-directory and parallel builds as well as the usage of pre-instrumented - libraries. Furthermore, an efficient way of tracking parent-child relationships was added. Additionally, we extended - OPARI2 to support instrumentation of OpenMP 3.0 tied tasks. + OPARI2 is a source-to-source instrumentation tool for OpenMP and hybrid + codes. It surrounds OpenMP directives and runtime library calls with calls + to the POMP2 measurement interface. OPARI2 will provide you with a new + initialization method that allows for multi-directory and parallel builds + as well as the usage of pre-instrumented libraries. Furthermore, an + efficient way of tracking parent-child relationships was added. + Additionally, we extended OPARI2 to support instrumentation of OpenMP 3.0 + tied tasks. """ homepage = "http://www.vi-hps.org/projects/score-p" url = "http://www.vi-hps.org/upload/packages/opari2/opari2-1.1.2.tar.gz" + version('2.0', '72350dbdb6139f2e68a5055a4f0ba16c', + url='http://www.vi-hps.org/upload/packages/opari2/opari2-2.0.tar.gz') version('1.1.4', '245d3d11147a06de77909b0805f530c0', url='http://www.vi-hps.org/upload/packages/opari2/opari2-1.1.4.tar.gz') version('1.1.2', '9a262c7ca05ff0ab5f7775ae96f3539e') diff --git a/var/spack/repos/builtin/packages/samtools/package.py b/var/spack/repos/builtin/packages/samtools/package.py index f5c7f4431f..6b0b224785 100644 --- a/var/spack/repos/builtin/packages/samtools/package.py +++ b/var/spack/repos/builtin/packages/samtools/package.py @@ -24,19 +24,27 @@ ############################################################################## from spack import * + class Samtools(Package): - """SAM Tools provide various utilities for manipulating alignments in the SAM format, - including sorting, merging, indexing and generating + """SAM Tools provide various utilities for manipulating alignments in + the SAM format, including sorting, merging, indexing and generating alignments in a per-position format""" homepage = "www.htslib.org" - version('1.2','988ec4c3058a6ceda36503eebecd4122',url = "https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2") + url = "https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2" - depends_on("zlib") - depends_on("mpc") - parallel=False - patch("samtools1.2.patch",level=0) + version('1.3.1', 'a7471aa5a1eb7fc9cc4c6491d73c2d88') + version('1.2', '988ec4c3058a6ceda36503eebecd4122') - def install(self, spec, prefix): - make("prefix=%s" % prefix, "install") + depends_on("ncurses") + depends_on("htslib", when='@1.3.1:') # htslib became standalone + depends_on('zlib', when='@1.2') # needed for builtin htslib + def install(self, spec, prefix): + if self.spec.version >= Version('1.3.1'): + configure('--prefix={0}'.format(prefix), '--with-ncurses') + make() + make('install') + else: + make("prefix=%s" % prefix) + make("prefix=%s" % prefix, "install") diff --git a/var/spack/repos/builtin/packages/samtools/samtools1.2.patch b/var/spack/repos/builtin/packages/samtools/samtools1.2.patch deleted file mode 100644 index ead3ab4e2c..0000000000 --- a/var/spack/repos/builtin/packages/samtools/samtools1.2.patch +++ /dev/null @@ -1,20 +0,0 @@ ---- Makefile 2015-02-03 08:27:34.000000000 -0800 -+++ Makefile.new 2015-07-21 10:38:27.881406892 -0700 -@@ -26,7 +26,7 @@ - CFLAGS = -g -Wall -O2 - LDFLAGS = - LDLIBS = --DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -+DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 - LOBJS= bam_aux.o bam.o bam_import.o sam.o \ - sam_header.o bam_plbuf.o - AOBJS= bam_index.o bam_plcmd.o sam_view.o \ -@@ -37,7 +37,7 @@ - faidx.o stats.o stats_isize.o bam_flags.o bam_split.o \ - bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o - INCLUDES= -I. -I$(HTSDIR) --LIBCURSES= -lcurses # -lXCurses -+#LIBCURSES= -lcurses # -lXCurses - - prefix = /usr/local - exec_prefix = $(prefix) diff --git a/var/spack/repos/builtin/packages/scorep/package.py b/var/spack/repos/builtin/packages/scorep/package.py index 633511a15a..d40e08740f 100644 --- a/var/spack/repos/builtin/packages/scorep/package.py +++ b/var/spack/repos/builtin/packages/scorep/package.py @@ -28,20 +28,28 @@ from spack import * class Scorep(Package): """ - The Score-P measurement infrastructure is a highly scalable and easy-to-use tool suite for profiling, event - tracing, and online analysis of HPC applications. + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. """ homepage = "http://www.vi-hps.org/projects/score-p" url = "http://www.vi-hps.org/upload/packages/scorep/scorep-1.2.3.tar.gz" + version('2.0.2', '8f00e79e1b5b96e511c5ebecd10b2888', + url='http://www.vi-hps.org/upload/packages/scorep/scorep-2.0.2.tar.gz') version('1.4.2', '3b9a042b13bdd5836452354e6567f71e', url='http://www.vi-hps.org/upload/packages/scorep/scorep-1.4.2.tar.gz') version('1.3', '9db6f957b7f51fa01377a9537867a55c', url='http://www.vi-hps.org/upload/packages/scorep/scorep-1.3.tar.gz') ########## - # Dependencies for SCORE-P are quite tight. See the homepage for more information. + # Dependencies for SCORE-P are quite tight. See the homepage for more + # information. + # SCOREP 2.0.2 + depends_on('otf2@2.0', when='@2.0.2') + depends_on('opari2@2.0', when='@2.0.2') + depends_on('cube@4.3:4.4', when='@2.0.2') # SCOREP 1.4.2 depends_on('otf2@1.5:1.6', when='@1.4.2') depends_on('opari2@1.1.4', when='@1.4.2') @@ -56,17 +64,18 @@ class Scorep(Package): depends_on("papi") def install(self, spec, prefix): - configure = Executable( join_path(self.stage.source_path, 'configure') ) + configure = Executable(join_path(self.stage.source_path, 'configure')) with working_dir('spack-build', create=True): - configure_args = ["--prefix=%s" % prefix, - "--with-otf2=%s" % spec['otf2'].prefix.bin, - "--with-opari2=%s" % spec['opari2'].prefix.bin, - "--with-cube=%s" % spec['cube'].prefix.bin, - "--with-papi-header=%s" % spec['papi'].prefix.include, - "--with-papi-lib=%s" % spec['papi'].prefix.lib, - "--enable-shared", - "CFLAGS=-fPIC", - "CXXFLAGS=-fPIC"] + configure_args = [ + "--prefix=%s" % prefix, + "--with-otf2=%s" % spec['otf2'].prefix.bin, + "--with-opari2=%s" % spec['opari2'].prefix.bin, + "--with-cube=%s" % spec['cube'].prefix.bin, + "--with-papi-header=%s" % spec['papi'].prefix.include, + "--with-papi-lib=%s" % spec['papi'].prefix.lib, + "--enable-shared", + "CFLAGS=-fPIC", + "CXXFLAGS=-fPIC"] configure(*configure_args) make() make("install") diff --git a/var/spack/repos/builtin/packages/seqtk/package.py b/var/spack/repos/builtin/packages/seqtk/package.py new file mode 100644 index 0000000000..ca168c176c --- /dev/null +++ b/var/spack/repos/builtin/packages/seqtk/package.py @@ -0,0 +1,43 @@ +############################################################################## +# 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 Seqtk(Package): + """Toolkit for processing sequences in FASTA/Q formats.""" + + homepage = "https://github.com/lh3/seqtk" + url = "https://github.com/lh3/seqtk/archive/v1.1.tar.gz" + + version('1.2', '255ffe05bf2f073dc57abcff97f11a37') + version('1.1', 'ebf5cc57698a217150c2250494e039a2') + + depends_on('zlib') + + def install(self, spec, prefix): + make() + mkdirp(prefix.bin) + install('seqtk', prefix.bin) + set_executable(join_path(prefix.bin, 'seqtk')) diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 4d1d27e74a..1d83e055c9 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -45,6 +45,7 @@ class Trilinos(Package): homepage = "https://trilinos.org/" url = "http://trilinos.csbsju.edu/download/files/trilinos-12.2.1-Source.tar.gz" + version('12.6.4', 'db25056617c688f6f25092376a03200f') version('12.6.3', '960f5f4d3f7c3da818e5a5fb4684559eff7e0c25f959ef576561b8a52f0e4d1e') version('12.6.2', '0c076090508170ddee5efeed317745027f9418319720dc40a072e478775279f9') version('12.6.1', 'adcf2d3aab74cdda98f88fee19cd1442604199b0515ee3da4d80cbe8f37d00e4') |