From 7ba4c6200c125a651eeb10b3cde964da8f81ae22 Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Tue, 16 Oct 2018 22:53:18 -0700 Subject: relicense: remove significant contributions from peetsv - This is bundled into one commit to make it easy to revert if we do get consent from peetsv's company to relicense these contributions. - Revert "dialign-tx adding patch for gcc@5.4.0 (#6413)" - This reverts commit 09eeb991a2ac0d749ffdbfe2f1cc415dd5d5dc85. - Remove the following LGPL-2.1 packages because we have not gotten consent to relicense them: - fast-gbs - igv - metasv - perl-xml-libxml - py-cnvkit - py-crossmap - py-pybedtools - py-pyfaidx - py-pyvcf - py-vmd-python - r-cghflasso - r-dismo - r-proc - r-spatial - r-utf8 --- .../dialign-tx/dialign-1-0-2-gcc-5-4-0.patch | 80 ---------------------- .../repos/builtin/packages/dialign-tx/package.py | 2 - .../repos/builtin/packages/fast-gbs/package.py | 54 --------------- var/spack/repos/builtin/packages/igv/package.py | 54 --------------- var/spack/repos/builtin/packages/metasv/package.py | 41 ----------- .../builtin/packages/perl-xml-libxml/package.py | 35 ---------- .../repos/builtin/packages/py-cnvkit/package.py | 48 ------------- .../repos/builtin/packages/py-crossmap/package.py | 41 ----------- .../builtin/packages/py-pybedtools/package.py | 44 ------------ .../repos/builtin/packages/py-pyfaidx/package.py | 37 ---------- .../repos/builtin/packages/py-pyvcf/package.py | 39 ----------- .../builtin/packages/py-vmd-python/package.py | 41 ----------- .../repos/builtin/packages/r-cghflasso/package.py | 36 ---------- .../repos/builtin/packages/r-dismo/package.py | 40 ----------- var/spack/repos/builtin/packages/r-proc/package.py | 44 ------------ .../repos/builtin/packages/r-spatial/package.py | 37 ---------- var/spack/repos/builtin/packages/r-utf8/package.py | 38 ---------- 17 files changed, 711 deletions(-) delete mode 100644 var/spack/repos/builtin/packages/dialign-tx/dialign-1-0-2-gcc-5-4-0.patch delete mode 100644 var/spack/repos/builtin/packages/fast-gbs/package.py delete mode 100644 var/spack/repos/builtin/packages/igv/package.py delete mode 100644 var/spack/repos/builtin/packages/metasv/package.py delete mode 100644 var/spack/repos/builtin/packages/perl-xml-libxml/package.py delete mode 100644 var/spack/repos/builtin/packages/py-cnvkit/package.py delete mode 100644 var/spack/repos/builtin/packages/py-crossmap/package.py delete mode 100644 var/spack/repos/builtin/packages/py-pybedtools/package.py delete mode 100644 var/spack/repos/builtin/packages/py-pyfaidx/package.py delete mode 100644 var/spack/repos/builtin/packages/py-pyvcf/package.py delete mode 100644 var/spack/repos/builtin/packages/py-vmd-python/package.py delete mode 100644 var/spack/repos/builtin/packages/r-cghflasso/package.py delete mode 100644 var/spack/repos/builtin/packages/r-dismo/package.py delete mode 100644 var/spack/repos/builtin/packages/r-proc/package.py delete mode 100644 var/spack/repos/builtin/packages/r-spatial/package.py delete mode 100644 var/spack/repos/builtin/packages/r-utf8/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/dialign-tx/dialign-1-0-2-gcc-5-4-0.patch b/var/spack/repos/builtin/packages/dialign-tx/dialign-1-0-2-gcc-5-4-0.patch deleted file mode 100644 index 5a82f97e7b..0000000000 --- a/var/spack/repos/builtin/packages/dialign-tx/dialign-1-0-2-gcc-5-4-0.patch +++ /dev/null @@ -1,80 +0,0 @@ ---- a/source/alig.c 2008-12-06 04:10:05.000000000 -0800 -+++ b/source/alig.c 2017-11-21 10:58:31.000000000 -0800 -@@ -520,7 +520,7 @@ - * datastructure (i.e. frontiers). The given diag must be consistent - * to the given alignment ! - */ --inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg) { -+char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg) { - - char alignedSomething = 0; - int i,j,k; -diff -Naur a/source/assemble.c b/source/assemble.c ---- a/source/assemble.c 2008-12-06 04:10:05.000000000 -0800 -+++ b/source/assemble.c 2017-11-21 10:57:55.000000000 -0800 -@@ -10,7 +10,7 @@ - - extern void error(char *message); - extern void merror(char *msg1, char *msg2); --extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, -+extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix, - struct prob_dist *pdist); - extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, - struct prob_dist *pdist); -@@ -37,7 +37,7 @@ - extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos); - extern struct alignment* copy_alignment( struct alignment *o_algn, struct alignment *algn, char doDgc); - //extern char adapt_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); --extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); -+extern char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg); - //extern inline struct diag_cont* enter_sorted(struct diag_cont* backlog_diags, struct diag_cont *cand); - //extern inline char fit_fpos_diag(struct alignment *algn, struct diag* dg); - -@@ -574,7 +574,7 @@ - * returns a value <0 if there is an non-conflicting overlap - * returns 0 in all other non-conflicting cases - */ --inline char confl_diag(struct alignment *algn, char *layer, struct diag *dg1, struct diag *dg2) { -+static inline char confl_diag(struct alignment *algn, char *layer, struct diag *dg1, struct diag *dg2) { - // if(dg1->multi_dg || dg2->multi_dg) error(" confl_diag(): cannot accept multi dgs!"); - int s1_1 = dg1->seq_p1.num; - int s1_2 = dg1->seq_p2.num; -diff -Naur a/source/diag.c b/source/diag.c ---- a/source/diag.c 2008-12-06 04:10:05.000000000 -0800 -+++ b/source/diag.c 2017-11-21 10:55:43.000000000 -0800 -@@ -183,7 +183,7 @@ - * omitScore = 0: normal - * omitScore = 1: no score calculation - */ --inline void real_calc_weight(struct diag* dg, struct scr_matrix* smatrix, -+static inline void real_calc_weight(struct diag* dg, struct scr_matrix* smatrix, - struct prob_dist *pdist, char omitScore, long double **tmp_dist, struct alignment *algn ) { - - if(dg->multi_dg) { -@@ -302,7 +302,7 @@ - } - } - --inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, -+void calc_weight(struct diag* dg, struct scr_matrix* smatrix, - struct prob_dist *pdist) { - real_calc_weight(dg, smatrix, pdist, 0,NULL,NULL); - } -@@ -312,7 +312,7 @@ - /** - * calculates the overlap weight for the given diag - */ --inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, -+static inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, - struct prob_dist *pdist) { - int sn1 = dg->seq_p1.num; - int sn2 = dg->seq_p2.num; -@@ -958,7 +958,7 @@ - * The pointer returned (and the ones included in the struct) - * has to be deallocted explicitely from memory. - */ --inline struct simple_diag_col* find_diags_dialign(struct scr_matrix *smatrix, -+static inline struct simple_diag_col* find_diags_dialign(struct scr_matrix *smatrix, - struct prob_dist *pdist, struct seq* seq1, - struct seq* seq2, struct alignment *algn, - long double **tmp_dist, int round) { diff --git a/var/spack/repos/builtin/packages/dialign-tx/package.py b/var/spack/repos/builtin/packages/dialign-tx/package.py index ea7eddaf42..a5ba5ceedc 100644 --- a/var/spack/repos/builtin/packages/dialign-tx/package.py +++ b/var/spack/repos/builtin/packages/dialign-tx/package.py @@ -50,5 +50,3 @@ class DialignTx(MakefilePackage): install('dialign-tx', prefix.bin) # t-coffee recognizes as dialign-t install('dialign-tx', join_path(prefix.bin, 'dialign-t')) - - patch('dialign-1-0-2-gcc-5-4-0.patch', when='%gcc@5.4.0') diff --git a/var/spack/repos/builtin/packages/fast-gbs/package.py b/var/spack/repos/builtin/packages/fast-gbs/package.py deleted file mode 100644 index feddf105d9..0000000000 --- a/var/spack/repos/builtin/packages/fast-gbs/package.py +++ /dev/null @@ -1,54 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2018, 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/spack/spack -# Please also see the NOTICE and LICENSE files 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 FastGbs(Package): - """A bioinformatic pipeline designed to extract a high-quality SNP catalog - starting from FASTQ files obtained from sequencing - genotyping-by-sequencing (GBS) libraries.""" - - homepage = "https://bitbucket.org/jerlar73/fast-gbs" - git = "https://bitbucket.org/jerlar73/fast-gbs.git" - - version('2017-01-25', commit='3b3cbffa84d269419692067c6a3de08b3b88849c') - - depends_on('parallel', type='run') - depends_on('python@2.7:', type='run') - depends_on('sabre', type='run') - depends_on('py-cutadapt', type='run') - depends_on('bwa', type='run') - depends_on('samtools', type='run') - depends_on('platypus', type='run') - depends_on('py-pyvcf', type='run') - - def install(self, spec, prefix): - mkdirp(prefix.bin) - install('fastgbs.sh', prefix.bin) - install('parameters.txt', prefix.bin) - install('makeDir.sh', prefix.bin) - install('makeBarcodeSabre.py', prefix.bin) - install('vcf2txt.py', prefix.bin) - install('txt2unix.sh', prefix.bin) diff --git a/var/spack/repos/builtin/packages/igv/package.py b/var/spack/repos/builtin/packages/igv/package.py deleted file mode 100644 index b905520629..0000000000 --- a/var/spack/repos/builtin/packages/igv/package.py +++ /dev/null @@ -1,54 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2018, 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/spack/spack -# Please also see the NOTICE and LICENSE files 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 * -import glob - - -class Igv(Package): - """The Integrative Genomics Viewer (IGV) is a high-performance - visualization tool for interactive exploration of large, - integrated genomic datasets.""" - - homepage = "http://software.broadinstitute.org/software/igv/" - - version('2.4.5', '4c45e1b281d8e3d8630aa485c5df6949', - url='http://data.broadinstitute.org/igv/projects/downloads/2.4/IGVSource_2.4.5.zip') - version('2.3.50', '7fdb903a59d556fad25e668b38e860f8', - url='http://data.broadinstitute.org/igv/projects/downloads/2.3/IGVSource_2.3.50.zip') - - depends_on('jdk@8:', type=('build', 'run'), when='@2.4:') - depends_on('jdk@7u0:7u999', type=('build', 'run'), when='@2.3:2.3.999') - depends_on('ant', type='build') - - def install(self, spec, prefix): - ant = self.spec['ant'].command - ant('all') - mkdirp(prefix.bin) - install('igv.sh', prefix.bin) - install('igv.jar', prefix.bin) - mkdirp(prefix.lib) - files = [x for x in glob.glob("lib/*jar")] - for f in files: - install(f, prefix.lib) diff --git a/var/spack/repos/builtin/packages/metasv/package.py b/var/spack/repos/builtin/packages/metasv/package.py deleted file mode 100644 index 540b2da2b9..0000000000 --- a/var/spack/repos/builtin/packages/metasv/package.py +++ /dev/null @@ -1,41 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2018, 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/spack/spack -# Please also see the NOTICE and LICENSE files 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 Metasv(PythonPackage): - """An accurate and integrative structural-variant caller - for next generation sequencing""" - - homepage = "http://bioinform.github.io/metasv/" - url = "https://github.com/bioinform/metasv/archive/0.5.4.tar.gz" - - version('0.5.4', 'de2e21ac4f86bc4d1830bdfff95d8391') - - depends_on('py-pybedtools@0.6.9', type=('build', 'run')) - depends_on('py-pysam@0.7.7', type=('build', 'run')) - depends_on('py-pyvcf@0.6.7', type=('build', 'run')) - depends_on('py-setuptools', type=('build', 'run')) - depends_on('py-cython', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-xml-libxml/package.py b/var/spack/repos/builtin/packages/perl-xml-libxml/package.py deleted file mode 100644 index 7bb689544c..0000000000 --- a/var/spack/repos/builtin/packages/perl-xml-libxml/package.py +++ /dev/null @@ -1,35 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2018, 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/spack/spack -# Please also see the NOTICE and LICENSE files 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 PerlXmlLibxml(PerlPackage): - """This module is an interface to libxml2, providing XML and HTML parsers - with DOM, SAX and XMLReader interfaces""" - - homepage = "http://search.cpan.org/~shlomif/XML-LibXML-2.0132/LibXML.pod" - url = "http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/XML-LibXML-2.0132.tar.gz" - - version('2.0132', '43546fd9a3974f19323f9fb04861ece9') diff --git a/var/spack/repos/builtin/packages/py-cnvkit/package.py b/var/spack/repos/builtin/packages/py-cnvkit/package.py deleted file mode 100644 index 045c940206..0000000000 --- a/var/spack/repos/builtin/packages/py-cnvkit/package.py +++ /dev/null @@ -1,48 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2018, 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/spack/spack -# Please also see the NOTICE and LICENSE files 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 PyCnvkit(PythonPackage): - """A command-line toolkit and Python library for detecting copy number - variants and alterations genome-wide from high-throughput sequencing.""" - - homepage = "http://cnvkit.readthedocs.io/en/stable/" - url = "https://github.com/etal/cnvkit/archive/v0.9.2.tar.gz" - - version('0.9.2', '16612c4dcc9570f6ef9fecc42caf1745') - - depends_on('py-setuptools', type='build') - depends_on('py-biopython@1.62:', type=('build', 'run')) - depends_on('py-future@0.15.2:', type=('build', 'run')) - depends_on('py-matplotlib@1.3.1:', type=('build', 'run')) - depends_on('py-numpy@1.9:', type=('build', 'run')) - depends_on('py-pandas@0.18.1:', type=('build', 'run')) - depends_on('py-pyfaidx@0.4.7:', type=('build', 'run')) - depends_on('py-pysam@0.10.0:0.13', type=('build', 'run')) - depends_on('py-reportlab@3.0:', type=('build', 'run')) - depends_on('py-scipy@0.15.0:', type=('build', 'run')) - depends_on('bcftools@1.6', type=('build', 'run')) - depends_on('samtools@1.6', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-crossmap/package.py b/var/spack/repos/builtin/packages/py-crossmap/package.py deleted file mode 100644 index ad94df9bc4..0000000000 --- a/var/spack/repos/builtin/packages/py-crossmap/package.py +++ /dev/null @@ -1,41 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2018, 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/spack/spack -# Please also see the NOTICE and LICENSE files 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 PyCrossmap(PythonPackage): - """CrossMap is a program for convenient conversion of genome - coordinates (or annotation files) between different assemblies""" - - homepage = "http://crossmap.sourceforge.net" - url = "https://downloads.sourceforge.net/project/crossmap/CrossMap-0.2.7.tar.gz" - - version('0.2.7', '91dadec9644ee3038f20ee7a6eb8dfb7') - - depends_on('python@2.7:2.7.999', type=('build', 'run')) - depends_on('py-cython@0.17:', type='build') - depends_on('py-pysam', type=('build', 'run')) - depends_on('py-setuptools', type='build') - depends_on('py-bx-python', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pybedtools/package.py b/var/spack/repos/builtin/packages/py-pybedtools/package.py deleted file mode 100644 index 55d6d34f1f..0000000000 --- a/var/spack/repos/builtin/packages/py-pybedtools/package.py +++ /dev/null @@ -1,44 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2018, 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/spack/spack -# Please also see the NOTICE and LICENSE files 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 PyPybedtools(PythonPackage): - """pybedtools wraps and extends BEDTools and offers - feature-level manipulations from within Python.""" - - homepage = "http://daler.github.io/pybedtools" - url = "https://pypi.io/packages/source/p/pybedtools/pybedtools-0.7.10.tar.gz" - - version('0.7.10', 'f003c67e22c48b77f070538368ece70c') - version('0.6.9', 'b7df049036422d8c6951412a90e83dca') - - depends_on('py-setuptools', type='build') - depends_on('bedtools2', type=('build', 'run')) - depends_on('py-numpy', type=('build', 'run')) - depends_on('py-pandas', type=('build', 'run')) - depends_on('py-pysam@0.8.1:', type=('build', 'run'), when='@0.7.0:') - depends_on('py-pysam@0.7.7', type=('build', 'run'), when='@0.6.9') - depends_on('py-six', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pyfaidx/package.py b/var/spack/repos/builtin/packages/py-pyfaidx/package.py deleted file mode 100644 index deee8cb745..0000000000 --- a/var/spack/repos/builtin/packages/py-pyfaidx/package.py +++ /dev/null @@ -1,37 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2018, 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/spack/spack -# Please also see the NOTICE and LICENSE files 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 PyPyfaidx(PythonPackage): - """pyfaidx: efficient pythonic random access to fasta subsequences""" - - homepage = "https://pypi.python.org/pypi/pyfaidx" - url = "https://pypi.io/packages/source/p/pyfaidx/pyfaidx-0.5.3.1.tar.gz" - - version('0.5.3.1', '128074c48fdef23d41e47af73b45f040') - - depends_on('py-setuptools@0.7:', type='build') - depends_on('py-six', type='build') diff --git a/var/spack/repos/builtin/packages/py-pyvcf/package.py b/var/spack/repos/builtin/packages/py-pyvcf/package.py deleted file mode 100644 index 3a7cb21263..0000000000 --- a/var/spack/repos/builtin/packages/py-pyvcf/package.py +++ /dev/null @@ -1,39 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2018, 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/spack/spack -# Please also see the NOTICE and LICENSE files 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 PyPyvcf(PythonPackage): - """PyVCF - A Variant Call Format Parser for Python""" - - homepage = "https://github.com/jamescasbon/PyVCF" - url = "https://pypi.io/packages/source/P/PyVCF/PyVCF-0.6.8.tar.gz" - - version('0.6.8', '3cc70aa59e62dab7b4a85bd5a9f2e714') - version('0.6.7', '51b57ce99e0c2f7be2a18d08d8f87734') - - depends_on('py-setuptools', type='build') - depends_on('py-cython', type='build') - depends_on('py-pysam', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-vmd-python/package.py b/var/spack/repos/builtin/packages/py-vmd-python/package.py deleted file mode 100644 index 57c15c5ffb..0000000000 --- a/var/spack/repos/builtin/packages/py-vmd-python/package.py +++ /dev/null @@ -1,41 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2018, 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/spack/spack -# Please also see the NOTICE and LICENSE files 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 PyVmdPython(PythonPackage): - """Installable VMD as a python module""" - - homepage = "https://github.com/Eigenstate" - url = "https://github.com/Eigenstate/vmd-python/archive/v2.0.10.tar.gz" - - version('2.0.10', '8c746d961497a676053b66e3dd692794') - - depends_on('python@2.7:2.8', type=('build', 'run')) - depends_on('py-numpy', type=('build', 'run')) - depends_on('py-setuptools', type='run') - depends_on('tcl') - depends_on('netcdf') - depends_on('expat') diff --git a/var/spack/repos/builtin/packages/r-cghflasso/package.py b/var/spack/repos/builtin/packages/r-cghflasso/package.py deleted file mode 100644 index 7ef6fe07d7..0000000000 --- a/var/spack/repos/builtin/packages/r-cghflasso/package.py +++ /dev/null @@ -1,36 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2018, 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/spack/spack -# Please also see the NOTICE and LICENSE files 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 RCghflasso(RPackage): - """Spatial smoothing and hot spot detection using the fused - lasso regression""" - - homepage = "https://cran.r-project.org/package=cghFLasso" - url = "https://cran.r-project.org/src/contrib/cghFLasso_0.2-1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/cghFLasso" - - version('0.2-1', '9a714a6dda3de9e905d23dadfa5d37f1') diff --git a/var/spack/repos/builtin/packages/r-dismo/package.py b/var/spack/repos/builtin/packages/r-dismo/package.py deleted file mode 100644 index 01c5a70413..0000000000 --- a/var/spack/repos/builtin/packages/r-dismo/package.py +++ /dev/null @@ -1,40 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2018, 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/spack/spack -# Please also see the NOTICE and LICENSE files 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 RDismo(RPackage): - """Functions for species distribution modeling, that is, predicting - entire geographic distributions form occurrences at a number of - sites and the environment at these sites""" - - homepage = "http://rspatial.org/sdm" - url = "https://cran.r-project.org/src/contrib/dismo_1.1-4.tar.gz" - - version('1.1-4', '0ed11729bcf4c2ffa01a3e2ac88dabfc') - - depends_on('r@3.2:', type=('build', 'run')) - depends_on('r-raster@2.5-2:', type=('build', 'run')) - depends_on('r-sp@1.2-0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-proc/package.py b/var/spack/repos/builtin/packages/r-proc/package.py deleted file mode 100644 index d06e823000..0000000000 --- a/var/spack/repos/builtin/packages/r-proc/package.py +++ /dev/null @@ -1,44 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2018, 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/spack/spack -# Please also see the NOTICE and LICENSE files 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 RProc(RPackage): - """Tools for visualizing, smoothing and comparing receiver operating - characteristic (ROC curves). (Partial) area under the curve (AUC) - can be compared with statistical tests based on U-statistics or - bootstrap. Confidence intervals can be computed for (p)AUC or - ROC curves.""" - - homepage = "https://web.expasy.org/pROC/" - url = "https://cran.r-project.org/src/contrib/pROC_1.12.1.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/pROC" - - version('1.12.1', 'ef5fb446fd75c1a3a5e7abf9b7aa4f75') - - depends_on('r@2.14:', type=('build', 'run')) - depends_on('r-plyr', type=('build', 'run')) - depends_on('r-rcpp@0.11.1:', type=('build', 'run')) - depends_on('r-ggplot2', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-spatial/package.py b/var/spack/repos/builtin/packages/r-spatial/package.py deleted file mode 100644 index 6435d70f0e..0000000000 --- a/var/spack/repos/builtin/packages/r-spatial/package.py +++ /dev/null @@ -1,37 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2018, 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/spack/spack -# Please also see the NOTICE and LICENSE files 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 RSpatial(RPackage): - """Functions for kriging and point pattern analysis.""" - - homepage = "http://www.stats.ox.ac.uk/pub/MASS4/" - url = "https://cran.r-project.org/src/contrib/spatial_7.3-10.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/spatial" - - version('7.3-10', 'e544e3e3fd92e6868f29b8da2925b214') - - depends_on('r@3.0.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/r-utf8/package.py b/var/spack/repos/builtin/packages/r-utf8/package.py deleted file mode 100644 index bd5e5fd7c6..0000000000 --- a/var/spack/repos/builtin/packages/r-utf8/package.py +++ /dev/null @@ -1,38 +0,0 @@ -############################################################################## -# Copyright (c) 2013-2018, 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/spack/spack -# Please also see the NOTICE and LICENSE files 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 RUtf8(RPackage): - """Process and print 'UTF-8' encoded international text (Unicode). - Input, validate, normalize, encode, format, and display.""" - - homepage = "https://github.com/patperry/r-utf8" - url = "https://cran.r-project.org/src/contrib/utf8_1.1.3.tar.gz" - list_url = "https://cran.r-project.org/src/contrib/Archive/utf8" - - version('1.1.3', '3a4d84328eb3314e8ebb84d3553f7015') - - depends_on('r@2.1.0:', type=('build', 'run')) -- cgit v1.2.3-60-g2f50