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authorTodd Gamblin <tgamblin@llnl.gov>2018-10-16 22:53:18 -0700
committerTodd Gamblin <tgamblin@llnl.gov>2018-10-17 14:42:06 -0700
commit7ba4c6200c125a651eeb10b3cde964da8f81ae22 (patch)
treed4d7323ad9dd3ded4c73d534c864f4c545478b09
parent470a45c51659156e7d154ea890e798ce32b8767d (diff)
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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
-rw-r--r--var/spack/repos/builtin/packages/dialign-tx/dialign-1-0-2-gcc-5-4-0.patch80
-rw-r--r--var/spack/repos/builtin/packages/dialign-tx/package.py2
-rw-r--r--var/spack/repos/builtin/packages/fast-gbs/package.py54
-rw-r--r--var/spack/repos/builtin/packages/igv/package.py54
-rw-r--r--var/spack/repos/builtin/packages/metasv/package.py41
-rw-r--r--var/spack/repos/builtin/packages/perl-xml-libxml/package.py35
-rw-r--r--var/spack/repos/builtin/packages/py-cnvkit/package.py48
-rw-r--r--var/spack/repos/builtin/packages/py-crossmap/package.py41
-rw-r--r--var/spack/repos/builtin/packages/py-pybedtools/package.py44
-rw-r--r--var/spack/repos/builtin/packages/py-pyfaidx/package.py37
-rw-r--r--var/spack/repos/builtin/packages/py-pyvcf/package.py39
-rw-r--r--var/spack/repos/builtin/packages/py-vmd-python/package.py41
-rw-r--r--var/spack/repos/builtin/packages/r-cghflasso/package.py36
-rw-r--r--var/spack/repos/builtin/packages/r-dismo/package.py40
-rw-r--r--var/spack/repos/builtin/packages/r-proc/package.py44
-rw-r--r--var/spack/repos/builtin/packages/r-spatial/package.py37
-rw-r--r--var/spack/repos/builtin/packages/r-utf8/package.py38
17 files changed, 0 insertions, 711 deletions
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'))