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 09eeb991a2.
- 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
This commit is contained in:
Todd Gamblin
parent
470a45c516
commit
7ba4c6200c
17 changed files with 0 additions and 711 deletions
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@ -1,80 +0,0 @@
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--- a/source/alig.c 2008-12-06 04:10:05.000000000 -0800
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+++ b/source/alig.c 2017-11-21 10:58:31.000000000 -0800
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@@ -520,7 +520,7 @@
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* datastructure (i.e. frontiers). The given diag must be consistent
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* to the given alignment !
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*/
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-inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg) {
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+char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg) {
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char alignedSomething = 0;
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int i,j,k;
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diff -Naur a/source/assemble.c b/source/assemble.c
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--- a/source/assemble.c 2008-12-06 04:10:05.000000000 -0800
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+++ b/source/assemble.c 2017-11-21 10:57:55.000000000 -0800
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@@ -10,7 +10,7 @@
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extern void error(char *message);
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extern void merror(char *msg1, char *msg2);
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-extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
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+extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
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struct prob_dist *pdist);
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extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
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struct prob_dist *pdist);
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@@ -37,7 +37,7 @@
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extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos);
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extern struct alignment* copy_alignment( struct alignment *o_algn, struct alignment *algn, char doDgc);
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//extern char adapt_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
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-extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
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+extern char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
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//extern inline struct diag_cont* enter_sorted(struct diag_cont* backlog_diags, struct diag_cont *cand);
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//extern inline char fit_fpos_diag(struct alignment *algn, struct diag* dg);
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@@ -574,7 +574,7 @@
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* returns a value <0 if there is an non-conflicting overlap
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* returns 0 in all other non-conflicting cases
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*/
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-inline char confl_diag(struct alignment *algn, char *layer, struct diag *dg1, struct diag *dg2) {
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+static inline char confl_diag(struct alignment *algn, char *layer, struct diag *dg1, struct diag *dg2) {
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// if(dg1->multi_dg || dg2->multi_dg) error(" confl_diag(): cannot accept multi dgs!");
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int s1_1 = dg1->seq_p1.num;
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int s1_2 = dg1->seq_p2.num;
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diff -Naur a/source/diag.c b/source/diag.c
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--- a/source/diag.c 2008-12-06 04:10:05.000000000 -0800
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+++ b/source/diag.c 2017-11-21 10:55:43.000000000 -0800
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@@ -183,7 +183,7 @@
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* omitScore = 0: normal
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* omitScore = 1: no score calculation
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*/
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-inline void real_calc_weight(struct diag* dg, struct scr_matrix* smatrix,
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+static inline void real_calc_weight(struct diag* dg, struct scr_matrix* smatrix,
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struct prob_dist *pdist, char omitScore, long double **tmp_dist, struct alignment *algn ) {
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if(dg->multi_dg) {
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@@ -302,7 +302,7 @@
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}
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}
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-inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
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+void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
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struct prob_dist *pdist) {
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real_calc_weight(dg, smatrix, pdist, 0,NULL,NULL);
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}
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@@ -312,7 +312,7 @@
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/**
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* calculates the overlap weight for the given diag
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*/
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-inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
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+static inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
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struct prob_dist *pdist) {
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int sn1 = dg->seq_p1.num;
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int sn2 = dg->seq_p2.num;
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@@ -958,7 +958,7 @@
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* The pointer returned (and the ones included in the struct)
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* has to be deallocted explicitely from memory.
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*/
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-inline struct simple_diag_col* find_diags_dialign(struct scr_matrix *smatrix,
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+static inline struct simple_diag_col* find_diags_dialign(struct scr_matrix *smatrix,
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struct prob_dist *pdist, struct seq* seq1,
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struct seq* seq2, struct alignment *algn,
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long double **tmp_dist, int round) {
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@ -50,5 +50,3 @@ def install(self, spec, prefix):
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install('dialign-tx', prefix.bin)
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install('dialign-tx', prefix.bin)
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# t-coffee recognizes as dialign-t
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# t-coffee recognizes as dialign-t
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install('dialign-tx', join_path(prefix.bin, 'dialign-t'))
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install('dialign-tx', join_path(prefix.bin, 'dialign-t'))
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patch('dialign-1-0-2-gcc-5-4-0.patch', when='%gcc@5.4.0')
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@ -1,54 +0,0 @@
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##############################################################################
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# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
|
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# Produced at the Lawrence Livermore National Laboratory.
|
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#
|
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# This file is part of Spack.
|
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
|
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||||||
# LLNL-CODE-647188
|
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||||||
#
|
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# For details, see https://github.com/spack/spack
|
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||||||
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
|
|
||||||
#
|
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||||||
# 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.
|
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||||||
#
|
|
||||||
# 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
|
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##############################################################################
|
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from spack import *
|
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|
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|
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class FastGbs(Package):
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"""A bioinformatic pipeline designed to extract a high-quality SNP catalog
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starting from FASTQ files obtained from sequencing
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genotyping-by-sequencing (GBS) libraries."""
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homepage = "https://bitbucket.org/jerlar73/fast-gbs"
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git = "https://bitbucket.org/jerlar73/fast-gbs.git"
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version('2017-01-25', commit='3b3cbffa84d269419692067c6a3de08b3b88849c')
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depends_on('parallel', type='run')
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depends_on('python@2.7:', type='run')
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depends_on('sabre', type='run')
|
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||||||
depends_on('py-cutadapt', type='run')
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depends_on('bwa', type='run')
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depends_on('samtools', type='run')
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depends_on('platypus', type='run')
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depends_on('py-pyvcf', type='run')
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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install('fastgbs.sh', prefix.bin)
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install('parameters.txt', prefix.bin)
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install('makeDir.sh', prefix.bin)
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||||||
install('makeBarcodeSabre.py', prefix.bin)
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install('vcf2txt.py', prefix.bin)
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install('txt2unix.sh', prefix.bin)
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||||||
|
|
@ -1,54 +0,0 @@
|
||||||
##############################################################################
|
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||||||
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
|
|
||||||
# Produced at the Lawrence Livermore National Laboratory.
|
|
||||||
#
|
|
||||||
# This file is part of Spack.
|
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||||||
# 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 *
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||||||
import glob
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|
||||||
|
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||||||
|
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||||||
class Igv(Package):
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|
||||||
"""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/"
|
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||||||
|
|
||||||
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')
|
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||||||
|
|
||||||
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)
|
|
||||||
|
|
@ -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'))
|
|
||||||
|
|
@ -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')
|
|
||||||
|
|
@ -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'))
|
|
||||||
|
|
@ -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'))
|
|
||||||
|
|
@ -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'))
|
|
||||||
|
|
@ -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')
|
|
||||||
|
|
@ -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'))
|
|
||||||
|
|
@ -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')
|
|
||||||
|
|
@ -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')
|
|
||||||
|
|
@ -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'))
|
|
||||||
|
|
@ -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'))
|
|
||||||
|
|
@ -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'))
|
|
||||||
|
|
@ -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'))
|
|
||||||
Loading…
Reference in a new issue