Gentoo Archives: gentoo-commits

From: Justin Lecher <jlec@g.o>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/wgs-assembler/, sci-physics/openmx/, sci-biology/bismark/, ...
Date: Sun, 05 Feb 2017 05:21:36
Message-Id: 1486271879.01a5062038a8bc55319bb81222c9f1bcd369cb20.jlec@gentoo
1 commit: 01a5062038a8bc55319bb81222c9f1bcd369cb20
2 Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
3 AuthorDate: Fri Feb 3 16:27:18 2017 +0000
4 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
5 CommitDate: Sun Feb 5 05:17:59 2017 +0000
6 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=01a50620
7
8 Shorten all DESCRIPTION to <80 chars
9
10 Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
11
12 sci-biology/beagle/beagle-4.0.ebuild | 2 +-
13 sci-biology/bismark/bismark-0.13.0.ebuild | 2 +-
14 sci-biology/blue/blue-1.1.2.ebuild | 2 +-
15 sci-biology/blue/blue-1.1.3.ebuild | 2 +-
16 sci-biology/cdbfasta/cdbfasta-0.1.ebuild | 2 +-
17 sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild | 2 +-
18 sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild | 2 +-
19 sci-biology/fastqc/fastqc-0.11.3.ebuild | 2 +-
20 sci-biology/generecon/generecon-1.2.1-r1.ebuild | 2 +-
21 sci-biology/genometools/genometools-1.5.7.ebuild | 2 +-
22 sci-biology/genseed/genseed-1.0.22.ebuild | 2 +-
23 sci-biology/hydra-sv/hydra-sv-0.5.3.ebuild | 2 +-
24 sci-biology/kmergenie/kmergenie-1.6971.ebuild | 2 +-
25 sci-biology/lastz/lastz-1.03.66.ebuild | 2 +-
26 sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild | 2 +-
27 sci-biology/mgblast/mgblast-0.1.ebuild | 2 +-
28 sci-biology/mira/mira-4.9.5.ebuild | 2 +-
29 sci-biology/ngsview/ngsview-0.91.ebuild | 2 +-
30 sci-biology/perlprimer/perlprimer-1.1.21.ebuild | 2 +-
31 sci-biology/pileup/pileup-0.6.ebuild | 2 +-
32 sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild | 2 +-
33 sci-biology/samstat/samstat-20130708.ebuild | 2 +-
34 sci-biology/samtools/samtools-1.0-r2.ebuild | 2 +-
35 sci-biology/samtools/samtools-1.1-r1.ebuild | 2 +-
36 sci-biology/samtools/samtools-1.2-r1.ebuild | 2 +-
37 sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild | 2 +-
38 sci-biology/sclust/sclust-0.1.ebuild | 2 +-
39 sci-biology/sequin/sequin-20121202.ebuild | 2 +-
40 sci-biology/sgp2/sgp2-1.1.ebuild | 2 +-
41 sci-biology/sickle/sickle-1.33.ebuild | 2 +-
42 sci-biology/sickle/sickle-9999.ebuild | 2 +-
43 sci-biology/skewer-bin/skewer-bin-0.1.104.ebuild | 2 +-
44 sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild | 2 +-
45 sci-biology/stacks/stacks-1.44.ebuild | 2 +-
46 sci-biology/subread/subread-1.4.6.ebuild | 2 +-
47 sci-biology/symap/symap-4.0.ebuild | 2 +-
48 sci-biology/tgicl/tgicl-2.1.ebuild | 2 +-
49 sci-biology/trowel/trowel-0.1.4.1.ebuild | 2 +-
50 sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild | 2 +-
51 sci-chemistry/chooch/chooch-5.0.2-r1.ebuild | 2 +-
52 sci-chemistry/concoord/concoord-2.1.2.ebuild | 2 +-
53 sci-chemistry/concoord/concoord-2.1.ebuild | 2 +-
54 sci-chemistry/mddnmr/mddnmr-2.4-r1.ebuild | 2 +-
55 sci-chemistry/modelfree/modelfree-4.20.ebuild | 2 +-
56 sci-chemistry/mtz2hkl/mtz2hkl-0.3.ebuild | 2 +-
57 sci-chemistry/redcat/redcat-3.ebuild | 2 +-
58 sci-chemistry/rosetta/rosetta-3.4.ebuild | 2 +-
59 sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild | 2 +-
60 sci-chemistry/talosn/talosn-4.01.2013.148.15.55-r3.ebuild | 2 +-
61 sci-chemistry/talosn/talosn-4.12.2015.147.15.40.ebuild | 2 +-
62 sci-geosciences/pydap_handlers_cdms/pydap_handlers_cdms-0.2.0.1.ebuild | 2 +-
63 sci-libs/asl/asl-0.1.7.ebuild | 2 +-
64 sci-libs/asl/asl-9999.ebuild | 2 +-
65 sci-libs/ipp/ipp-8.2.2.187-r1.ebuild | 2 +-
66 sci-mathematics/apron/apron-0.9.10-r1.ebuild | 2 +-
67 sci-misc/elmer-gui/elmer-gui-9999.ebuild | 2 +-
68 sci-misc/mitlm/mitlm-0.4.1.ebuild | 2 +-
69 sci-physics/abinit/abinit-7.10.4.ebuild | 2 +-
70 sci-physics/abinit/abinit-7.4.2-r1.ebuild | 2 +-
71 sci-physics/abinit/abinit-7.6.4-r1.ebuild | 2 +-
72 sci-physics/mc-tester/mc-tester-1.25.0.ebuild | 2 +-
73 sci-physics/openmx/openmx-3.6.ebuild | 2 +-
74 sci-physics/openmx/openmx-3.7.8.ebuild | 2 +-
75 63 files changed, 63 insertions(+), 63 deletions(-)
76
77 diff --git a/sci-biology/beagle/beagle-4.0.ebuild b/sci-biology/beagle/beagle-4.0.ebuild
78 index 70caec7..c370265 100644
79 --- a/sci-biology/beagle/beagle-4.0.ebuild
80 +++ b/sci-biology/beagle/beagle-4.0.ebuild
81 @@ -6,7 +6,7 @@ EAPI=5
82
83 inherit java-pkg-2 java-ant-2
84
85 -DESCRIPTION="Genotype calling/phasing, imputation of ungenotyped markers, identity-by-descent segment detection"
86 +DESCRIPTION="Genotype calling/phasing, imputation of ungenotyped markers"
87 HOMEPAGE="http://faculty.washington.edu/browning/beagle/beagle.html"
88 SRC_URI="http://faculty.washington.edu/browning/beagle/beagle.r1399.src.zip
89 http://faculty.washington.edu/browning/beagle/beagle.03Mar15.pdf
90
91 diff --git a/sci-biology/bismark/bismark-0.13.0.ebuild b/sci-biology/bismark/bismark-0.13.0.ebuild
92 index 1f6616e..64f06c0 100644
93 --- a/sci-biology/bismark/bismark-0.13.0.ebuild
94 +++ b/sci-biology/bismark/bismark-0.13.0.ebuild
95 @@ -6,7 +6,7 @@ EAPI=5
96
97 inherit toolchain-funcs
98
99 -DESCRIPTION="A tool to map bisulfite converted sequence reads and determine cytosine methylation states"
100 +DESCRIPTION="Map bisulfite converted sequence reads and determine cytosine methylation states"
101 HOMEPAGE="http://www.bioinformatics.babraham.ac.uk/projects/bismark/"
102 SRC_URI="http://www.bioinformatics.babraham.ac.uk/projects/${PN}/${PN}_v${PV}.tar.gz"
103
104
105 diff --git a/sci-biology/blue/blue-1.1.2.ebuild b/sci-biology/blue/blue-1.1.2.ebuild
106 index 4591d3c..efb3480 100644
107 --- a/sci-biology/blue/blue-1.1.2.ebuild
108 +++ b/sci-biology/blue/blue-1.1.2.ebuild
109 @@ -4,7 +4,7 @@
110
111 EAPI=5
112
113 -DESCRIPTION="Error corrector for Illummina and Roche/454 able to also fix insertions and deletions"
114 +DESCRIPTION="Error corrector for Illummina and Roche/454, inculding insertions and deletions"
115 HOMEPAGE="http://www.bioinformatics.csiro.au/blue"
116 SRC_URI="
117 http://www.bioinformatics.csiro.au/public/files/Linux-${PV}.tar.gz -> ${P}.tar.gz
118
119 diff --git a/sci-biology/blue/blue-1.1.3.ebuild b/sci-biology/blue/blue-1.1.3.ebuild
120 index 4591d3c..59561cc 100644
121 --- a/sci-biology/blue/blue-1.1.3.ebuild
122 +++ b/sci-biology/blue/blue-1.1.3.ebuild
123 @@ -4,7 +4,7 @@
124
125 EAPI=5
126
127 -DESCRIPTION="Error corrector for Illummina and Roche/454 able to also fix insertions and deletions"
128 +DESCRIPTION="Error corrector for Illummina and Roche/454, including insertions and deletions"
129 HOMEPAGE="http://www.bioinformatics.csiro.au/blue"
130 SRC_URI="
131 http://www.bioinformatics.csiro.au/public/files/Linux-${PV}.tar.gz -> ${P}.tar.gz
132
133 diff --git a/sci-biology/cdbfasta/cdbfasta-0.1.ebuild b/sci-biology/cdbfasta/cdbfasta-0.1.ebuild
134 index 06cc243..1dcd7f6 100644
135 --- a/sci-biology/cdbfasta/cdbfasta-0.1.ebuild
136 +++ b/sci-biology/cdbfasta/cdbfasta-0.1.ebuild
137 @@ -4,7 +4,7 @@
138
139 EAPI=5
140
141 -DESCRIPTION="FASTA record indexing/retrievieng utility, a part of TIGR Gene Indices project tools"
142 +DESCRIPTION="FASTA record indexing/retrievieng utility"
143 HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software"
144 SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/cdbfasta/cdbfasta.tar.gz"
145
146
147 diff --git a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild
148 index 10f36ce..c582526 100644
149 --- a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild
150 +++ b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild
151 @@ -7,7 +7,7 @@ EAPI=5
152 PERL_EXPORT_PHASE_FUNCTIONS=no
153 inherit perl-module eutils toolchain-funcs
154
155 -DESCRIPTION="Assemble and compare genotype variants (variant discovery without reference sequence)"
156 +DESCRIPTION="Genotype variant discovery without reference sequence"
157 HOMEPAGE="http://cortexassembler.sourceforge.net/index_cortex_var.html"
158 SRC_URI="http://sourceforge.net/projects/cortexassembler/files/cortex_var/latest/CORTEX_release_v1.0.5.21.tgz
159 http://cortexassembler.sourceforge.net/cortex_var_user_manual.pdf"
160
161 diff --git a/sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild b/sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild
162 index 1346fd2..fa60ef7 100644
163 --- a/sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild
164 +++ b/sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild
165 @@ -4,7 +4,7 @@
166
167 EAPI=5
168
169 -DESCRIPTION="Annotate VCF files and prioritize genome/exome mutations (Jannovar, UCSC KnownGenes, hg19)"
170 +DESCRIPTION="Annotate VCF files and prioritize genome/exome mutations"
171 HOMEPAGE="http://www.sanger.ac.uk/science/tools/exomiser"
172 SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/exomiser-cli-${PV}-distribution.zip
173 ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/GenomiserREADME -> ${PN}.README
174
175 diff --git a/sci-biology/fastqc/fastqc-0.11.3.ebuild b/sci-biology/fastqc/fastqc-0.11.3.ebuild
176 index 64b41ab..f558a75 100644
177 --- a/sci-biology/fastqc/fastqc-0.11.3.ebuild
178 +++ b/sci-biology/fastqc/fastqc-0.11.3.ebuild
179 @@ -6,7 +6,7 @@ EAPI=5
180
181 inherit java-pkg-2 eutils java-ant-2
182
183 -DESCRIPTION="Perl-based wrapper around java apps to quality control FASTA/FASTQ sequence files"
184 +DESCRIPTION="Quality control FASTA/FASTQ sequence files"
185 HOMEPAGE="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
186 SRC_URI="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v"${PV}"_source.zip"
187
188
189 diff --git a/sci-biology/generecon/generecon-1.2.1-r1.ebuild b/sci-biology/generecon/generecon-1.2.1-r1.ebuild
190 index d3c8acb..81c81ba 100644
191 --- a/sci-biology/generecon/generecon-1.2.1-r1.ebuild
192 +++ b/sci-biology/generecon/generecon-1.2.1-r1.ebuild
193 @@ -6,7 +6,7 @@ EAPI=5
194
195 inherit autotools eutils
196
197 -DESCRIPTION="Disequilibrium gene mapping based on coalescent theory using Bayesian Markov Chain MC methods"
198 +DESCRIPTION="Disequilibrium gene mapping based on coalescent theory using Bayesian MC methods"
199 HOMEPAGE="http://www.daimi.au.dk/~mailund/GeneRecon/"
200 SRC_URI="http://www.daimi.au.dk/~mailund/GeneRecon/download/${P}.tar.gz"
201
202
203 diff --git a/sci-biology/genometools/genometools-1.5.7.ebuild b/sci-biology/genometools/genometools-1.5.7.ebuild
204 index b62bfe1..2a78a5c 100644
205 --- a/sci-biology/genometools/genometools-1.5.7.ebuild
206 +++ b/sci-biology/genometools/genometools-1.5.7.ebuild
207 @@ -4,7 +4,7 @@
208
209 EAPI=5
210
211 -DESCRIPTION="A collection of tools for bioinformatics (notably Tallymer, Readjoiner, gff3validator)"
212 +DESCRIPTION="Tools for bioinformatics (notably Tallymer, Readjoiner, gff3validator)"
213 HOMEPAGE="http://genometools.org"
214 SRC_URI="http://genometools.org/pub/${P}.tar.gz"
215
216
217 diff --git a/sci-biology/genseed/genseed-1.0.22.ebuild b/sci-biology/genseed/genseed-1.0.22.ebuild
218 index 92b1812..70919b8 100644
219 --- a/sci-biology/genseed/genseed-1.0.22.ebuild
220 +++ b/sci-biology/genseed/genseed-1.0.22.ebuild
221 @@ -4,7 +4,7 @@
222
223 EAPI=5
224
225 -DESCRIPTION="Seed-driven progressive assembly program using legacy NCBI blast, CAP3, and optionally cross_match"
226 +DESCRIPTION="Seed-driven progressive assembly program"
227 HOMEPAGE="http://www.coccidia.icb.usp.br/genseed/"
228 SRC_URI="http://www.coccidia.icb.usp.br/genseed/download/${P}.tar.gz"
229
230
231 diff --git a/sci-biology/hydra-sv/hydra-sv-0.5.3.ebuild b/sci-biology/hydra-sv/hydra-sv-0.5.3.ebuild
232 index ba64ab2..0130578 100644
233 --- a/sci-biology/hydra-sv/hydra-sv-0.5.3.ebuild
234 +++ b/sci-biology/hydra-sv/hydra-sv-0.5.3.ebuild
235 @@ -4,7 +4,7 @@
236
237 EAPI=5
238
239 -DESCRIPTION="Detection of structural variation breakpoints in unique and duplicated genomic regions"
240 +DESCRIPTION="Detection of structural variation breakpoints"
241 HOMEPAGE="http://code.google.com/p/hydra-sv/"
242 SRC_URI="http://hydra-sv.googlecode.com/files/Hydra.v${PV}.tar.gz"
243
244
245 diff --git a/sci-biology/kmergenie/kmergenie-1.6971.ebuild b/sci-biology/kmergenie/kmergenie-1.6971.ebuild
246 index ef96c0a..6762ecd 100644
247 --- a/sci-biology/kmergenie/kmergenie-1.6971.ebuild
248 +++ b/sci-biology/kmergenie/kmergenie-1.6971.ebuild
249 @@ -8,7 +8,7 @@ inherit eutils
250
251 PYTHON_COMPAT=( python{2_6,2_7} )
252
253 -DESCRIPTION="Estimate best k-mer length to be used in novo assemblies (default set during compilation is 121)"
254 +DESCRIPTION="Estimate best k-mer length to be used in novo assemblies"
255 HOMEPAGE="http://kmergenie.bx.psu.edu/"
256 SRC_URI="http://kmergenie.bx.psu.edu/"${P}".tar.gz"
257
258
259 diff --git a/sci-biology/lastz/lastz-1.03.66.ebuild b/sci-biology/lastz/lastz-1.03.66.ebuild
260 index a3b2ae1..99d9c22 100644
261 --- a/sci-biology/lastz/lastz-1.03.66.ebuild
262 +++ b/sci-biology/lastz/lastz-1.03.66.ebuild
263 @@ -6,7 +6,7 @@ EAPI=5
264
265 inherit eutils flag-o-matic toolchain-funcs
266
267 -DESCRIPTION="A pairwise DNA sequence aligner (also chromosome to chromosome), a BLASTZ replacement"
268 +DESCRIPTION="A pairwise DNA sequence aligner, a BLASTZ replacement"
269 HOMEPAGE="http://www.bx.psu.edu/~rsharris/lastz/"
270 SRC_URI="http://www.bx.psu.edu/~rsharris/lastz/newer/${P}.tar.gz"
271
272
273 diff --git a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild b/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
274 index 5701bb8..59c098d 100644
275 --- a/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
276 +++ b/sci-biology/manatee-jcvi/manatee-jcvi-2.4.3.ebuild
277 @@ -4,7 +4,7 @@
278
279 EAPI=5
280
281 -DESCRIPTION="genome annotation tool: view, modify, and store annotation for prokaryotic and eukaryotic genomes"
282 +DESCRIPTION="Genome annotation tool"
283 HOMEPAGE="http://manatee.sourceforge.net/jcvi/downloads.shtml"
284 SRC_URI="http://downloads.sourceforge.net/project/manatee/manatee/manatee-2.4.3/manatee-2.4.3.tgz"
285
286
287 diff --git a/sci-biology/mgblast/mgblast-0.1.ebuild b/sci-biology/mgblast/mgblast-0.1.ebuild
288 index 0a95c2e..0114713 100644
289 --- a/sci-biology/mgblast/mgblast-0.1.ebuild
290 +++ b/sci-biology/mgblast/mgblast-0.1.ebuild
291 @@ -4,7 +4,7 @@
292
293 EAPI=5
294
295 -DESCRIPTION="Customized version of megablast from TIGR Gene Indices project used by tgicl and gicl utilities"
296 +DESCRIPTION="Customized version of megablast from TIGR Gene Indices project"
297 HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
298 SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/mgblast.tar.gz"
299
300
301 diff --git a/sci-biology/mira/mira-4.9.5.ebuild b/sci-biology/mira/mira-4.9.5.ebuild
302 index c77a962..268d607 100644
303 --- a/sci-biology/mira/mira-4.9.5.ebuild
304 +++ b/sci-biology/mira/mira-4.9.5.ebuild
305 @@ -9,7 +9,7 @@ MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to
306
307 inherit autotools eutils multilib
308
309 -DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina"
310 +DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler"
311 HOMEPAGE="http://www.chevreux.org/projects_mira.html"
312 SRC_URI="
313 http://sourceforge.net/projects/mira-assembler/files/MIRA/development/"${PN}"-"${MY_PV}".tar.bz2
314
315 diff --git a/sci-biology/ngsview/ngsview-0.91.ebuild b/sci-biology/ngsview/ngsview-0.91.ebuild
316 index 8d46197..863bf10 100644
317 --- a/sci-biology/ngsview/ngsview-0.91.ebuild
318 +++ b/sci-biology/ngsview/ngsview-0.91.ebuild
319 @@ -6,7 +6,7 @@ EAPI=5
320
321 inherit qt4-r2
322
323 -DESCRIPTION="Display, edit next-gen sequence alignment (BED, BLAST, Eland, mapview processed MAQ, Corona formats)"
324 +DESCRIPTION="Display, edit NGS alignments"
325 HOMEPAGE="http://sourceforge.net/projects/ngsview"
326 SRC_URI="mirror://sourceforge/projects/${PN}/files/${PN}/${P}.tar.gz"
327
328
329 diff --git a/sci-biology/perlprimer/perlprimer-1.1.21.ebuild b/sci-biology/perlprimer/perlprimer-1.1.21.ebuild
330 index e6f00dc..235a0ab 100644
331 --- a/sci-biology/perlprimer/perlprimer-1.1.21.ebuild
332 +++ b/sci-biology/perlprimer/perlprimer-1.1.21.ebuild
333 @@ -4,7 +4,7 @@
334
335 EAPI=5
336
337 -DESCRIPTION="GUI application written in Perl to design primers for standard PCR, bisulphite PCR and Real-time PCR"
338 +DESCRIPTION="Primers design for standard PCR, bisulphite PCR and Real-time PCR"
339 HOMEPAGE="http://perlprimer.sourceforge.net/"
340 SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
341
342
343 diff --git a/sci-biology/pileup/pileup-0.6.ebuild b/sci-biology/pileup/pileup-0.6.ebuild
344 index 77322f4..260ad8a 100644
345 --- a/sci-biology/pileup/pileup-0.6.ebuild
346 +++ b/sci-biology/pileup/pileup-0.6.ebuild
347 @@ -4,7 +4,7 @@
348
349 EAPI=5
350
351 -DESCRIPTION="SSAHA2-based pipeline to align reads into format also understood by samtools, maq"
352 +DESCRIPTION="SSAHA2-based pipeline to align reads"
353 HOMEPAGE="http://www.sanger.ac.uk/resources/software/ssaha2/"
354 SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/pileup.tgz"
355
356
357 diff --git a/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild b/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild
358 index 4b6f645..df1a092 100644
359 --- a/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild
360 +++ b/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild
361 @@ -4,7 +4,7 @@
362
363 EAPI=6
364
365 -DESCRIPTION="Convert from ace to gap4 (of staden v1.x), not needed to convert ace for gap5 of staden v2"
366 +DESCRIPTION="ace to gap4 converter"
367 HOMEPAGE="http://genome.imb-jena.de/software/roche454ace2caf"
368 SRC_URI="http://genome.imb-jena.de/software/roche454ace2caf/download/src/roche454ace2gap-2010-12-08.tgz"
369
370
371 diff --git a/sci-biology/samstat/samstat-20130708.ebuild b/sci-biology/samstat/samstat-20130708.ebuild
372 index 61c4135..bfd17cd 100644
373 --- a/sci-biology/samstat/samstat-20130708.ebuild
374 +++ b/sci-biology/samstat/samstat-20130708.ebuild
375 @@ -6,7 +6,7 @@ EAPI=5
376
377 inherit eutils
378
379 -DESCRIPTION="Show statistics of BAM/SAM (error profiles, nucleotide composition, base quals, len. distribution)"
380 +DESCRIPTION="Statistics of BAM/SAM files"
381 HOMEPAGE="http://samstat.sourceforge.net"
382 SRC_URI="http://sourceforge.net/projects/samstat/files/samstat.tgz"
383
384
385 diff --git a/sci-biology/samtools/samtools-1.0-r2.ebuild b/sci-biology/samtools/samtools-1.0-r2.ebuild
386 index b10e681..4c85410 100644
387 --- a/sci-biology/samtools/samtools-1.0-r2.ebuild
388 +++ b/sci-biology/samtools/samtools-1.0-r2.ebuild
389 @@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
390
391 inherit eutils multilib python-r1 toolchain-funcs
392
393 -DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
394 +DESCRIPTION="Utilities for SAM (Sequence Alignment/Map)"
395 HOMEPAGE="http://www.htslib.org/"
396 SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
397
398
399 diff --git a/sci-biology/samtools/samtools-1.1-r1.ebuild b/sci-biology/samtools/samtools-1.1-r1.ebuild
400 index 9941156..5932f8d 100644
401 --- a/sci-biology/samtools/samtools-1.1-r1.ebuild
402 +++ b/sci-biology/samtools/samtools-1.1-r1.ebuild
403 @@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
404
405 inherit eutils multilib python-r1 toolchain-funcs
406
407 -DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
408 +DESCRIPTION="Utilities for SAM (Sequence Alignment/Map)"
409 HOMEPAGE="http://www.htslib.org/"
410 SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
411
412
413 diff --git a/sci-biology/samtools/samtools-1.2-r1.ebuild b/sci-biology/samtools/samtools-1.2-r1.ebuild
414 index dcbd07b..87d702b 100644
415 --- a/sci-biology/samtools/samtools-1.2-r1.ebuild
416 +++ b/sci-biology/samtools/samtools-1.2-r1.ebuild
417 @@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
418
419 inherit eutils multilib python-r1 toolchain-funcs
420
421 -DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
422 +DESCRIPTION="Utilities for SAM (Sequence Alignment/Map)"
423 HOMEPAGE="http://www.htslib.org/"
424 SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
425
426
427 diff --git a/sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild b/sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild
428 index 0a7ae54..b57b6a0 100644
429 --- a/sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild
430 +++ b/sci-biology/scaffold_builder/scaffold_builder-20131122-r1.ebuild
431 @@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
432
433 inherit python-r1
434
435 -DESCRIPTION="Combine FASTA contigs from a de novo assembly into scaffolds using a reference genome"
436 +DESCRIPTION="Combine FASTA contigs from a de novo assembly into scaffolds"
437 HOMEPAGE="
438 http://sourceforge.net/projects/scaffold-b
439 http://edwards.sdsu.edu/scaffold_builder"
440
441 diff --git a/sci-biology/sclust/sclust-0.1.ebuild b/sci-biology/sclust/sclust-0.1.ebuild
442 index cb5fe1f..1ee71b6 100644
443 --- a/sci-biology/sclust/sclust-0.1.ebuild
444 +++ b/sci-biology/sclust/sclust-0.1.ebuild
445 @@ -4,7 +4,7 @@
446
447 EAPI=5
448
449 -DESCRIPTION="seeded clustering tool by processing pairwise alignments from TIGR Gene Indices project tools"
450 +DESCRIPTION="Seeded clustering tool by processing pairwise alignments"
451 HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/"
452 SRC_URI="
453 ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/${PN}.tar.gz
454
455 diff --git a/sci-biology/sequin/sequin-20121202.ebuild b/sci-biology/sequin/sequin-20121202.ebuild
456 index f0fc001..da9832e 100644
457 --- a/sci-biology/sequin/sequin-20121202.ebuild
458 +++ b/sci-biology/sequin/sequin-20121202.ebuild
459 @@ -6,7 +6,7 @@ EAPI=5
460
461 inherit eutils
462
463 -DESCRIPTION="A tool to facilitate submission of data to the GenBank, EMBL, and DDBJ sequence databases"
464 +DESCRIPTION="Facilitate submission of data to the GenBank, EMBL, and DDBJ sequence databases"
465 HOMEPAGE="http://www.ncbi.nlm.nih.gov/Sequin/"
466 SRC_URI="
467 amd64? ( ftp://ftp.ncbi.nih.gov/sequin/sequin.linux-x86_64.tar.gz -> ${P}-x86_64.tar.gz )
468
469 diff --git a/sci-biology/sgp2/sgp2-1.1.ebuild b/sci-biology/sgp2/sgp2-1.1.ebuild
470 index 0c8f94f..b8ab027 100644
471 --- a/sci-biology/sgp2/sgp2-1.1.ebuild
472 +++ b/sci-biology/sgp2/sgp2-1.1.ebuild
473 @@ -6,7 +6,7 @@ EAPI=5
474
475 inherit eutils
476
477 -DESCRIPTION="Find ORFs by comparing two genomic/EST sequences using tblastx and geneid ab initio predictions"
478 +DESCRIPTION="Find ORFs by comparing two genomic/EST sequences"
479 HOMEPAGE="http://genome.crg.es/software/sgp2/"
480 SRC_URI="ftp://genome.crg.es/pub/software/sgp2/sgp2_v1.1.May_8_2012.tar.gz"
481
482
483 diff --git a/sci-biology/sickle/sickle-1.33.ebuild b/sci-biology/sickle/sickle-1.33.ebuild
484 index c790d5b..1d79478 100644
485 --- a/sci-biology/sickle/sickle-1.33.ebuild
486 +++ b/sci-biology/sickle/sickle-1.33.ebuild
487 @@ -8,7 +8,7 @@ inherit eutils eutils toolchain-funcs
488
489 [ "$PV" == "9999" ] && inherit git-r3
490
491 -DESCRIPTION="Windowed adaptive quality-based trimming tool for FASTQ data from Illumina/Solexa"
492 +DESCRIPTION="Windowed adaptive quality-based trimming tool for FASTQ data"
493 HOMEPAGE="https://github.com/najoshi/sickle"
494 if [ "$PV" == "9999" ]; then
495 EGIT_REPO_URI="https://github.com/najoshi/sickle"
496
497 diff --git a/sci-biology/sickle/sickle-9999.ebuild b/sci-biology/sickle/sickle-9999.ebuild
498 index c790d5b..1d79478 100644
499 --- a/sci-biology/sickle/sickle-9999.ebuild
500 +++ b/sci-biology/sickle/sickle-9999.ebuild
501 @@ -8,7 +8,7 @@ inherit eutils eutils toolchain-funcs
502
503 [ "$PV" == "9999" ] && inherit git-r3
504
505 -DESCRIPTION="Windowed adaptive quality-based trimming tool for FASTQ data from Illumina/Solexa"
506 +DESCRIPTION="Windowed adaptive quality-based trimming tool for FASTQ data"
507 HOMEPAGE="https://github.com/najoshi/sickle"
508 if [ "$PV" == "9999" ]; then
509 EGIT_REPO_URI="https://github.com/najoshi/sickle"
510
511 diff --git a/sci-biology/skewer-bin/skewer-bin-0.1.104.ebuild b/sci-biology/skewer-bin/skewer-bin-0.1.104.ebuild
512 index c873326..772cd67 100644
513 --- a/sci-biology/skewer-bin/skewer-bin-0.1.104.ebuild
514 +++ b/sci-biology/skewer-bin/skewer-bin-0.1.104.ebuild
515 @@ -4,7 +4,7 @@
516
517 EAPI=5
518
519 -DESCRIPTION="Adaptor and MID removal / trimming tool, also for Illumina-oriented paired-end reads"
520 +DESCRIPTION="Adaptor and MID removal / trimming tool"
521 HOMEPAGE="http://sourceforge.net/projects/skewer"
522 SRC_URI="
523 http://sourceforge.net/projects/skewer/files/Binaries/skewer-0.1.104-linux-x86_64
524
525 diff --git a/sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild b/sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild
526 index 694fc7d..fda5368 100644
527 --- a/sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild
528 +++ b/sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild
529 @@ -7,7 +7,7 @@ EAPI=5
530 MY_PN="${PN%-bin}"
531 MY_P="${MY_PN}-${PV}"
532
533 -DESCRIPTION="Pairwise sequence alignment mapping DNA reads onto genomic reference, better over SSAHA2"
534 +DESCRIPTION="Pairwise sequence alignment mapping DNA reads onto genomic reference"
535 HOMEPAGE="http://www.sanger.ac.uk/resources/software/smalt/"
536 SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/${MY_PN}/${MY_P}.tgz"
537
538
539 diff --git a/sci-biology/stacks/stacks-1.44.ebuild b/sci-biology/stacks/stacks-1.44.ebuild
540 index 0b4ca80..4861732 100644
541 --- a/sci-biology/stacks/stacks-1.44.ebuild
542 +++ b/sci-biology/stacks/stacks-1.44.ebuild
543 @@ -8,7 +8,7 @@ AUTOTOOLS_AUTORECONF=yes
544
545 inherit flag-o-matic eutils perl-module webapp autotools
546
547 -DESCRIPTION="Analyze restriction enzyme data, draw gen. maps, population genomics (RAD-seq sequencing)"
548 +DESCRIPTION="Analyze restriction enzyme data, draw gen. maps, population genomics"
549 HOMEPAGE="http://creskolab.uoregon.edu/stacks"
550 SRC_URI="http://creskolab.uoregon.edu/stacks/source/${P}.tar.gz"
551
552
553 diff --git a/sci-biology/subread/subread-1.4.6.ebuild b/sci-biology/subread/subread-1.4.6.ebuild
554 index 3f42edf..ac164fd 100644
555 --- a/sci-biology/subread/subread-1.4.6.ebuild
556 +++ b/sci-biology/subread/subread-1.4.6.ebuild
557 @@ -6,7 +6,7 @@ EAPI=5
558
559 [ "$PV" == "9999" ] && inherit subversion
560
561 -DESCRIPTION="NGS suite for read mapping, analysis of mapped reads, summary of exon/intron/gene counts"
562 +DESCRIPTION="NGS suite for analysis of mapped reads, summary of exon/intron/gene counts"
563 HOMEPAGE="http://bioinf.wehi.edu.au/featureCounts/"
564 if [ "$PV" == "9999" ]; then
565 ESVN_REPO_URI="https://subread.svn.sourceforge.net/svnroot/subread/trunk"
566
567 diff --git a/sci-biology/symap/symap-4.0.ebuild b/sci-biology/symap/symap-4.0.ebuild
568 index 42ce623..9fe8c96 100644
569 --- a/sci-biology/symap/symap-4.0.ebuild
570 +++ b/sci-biology/symap/symap-4.0.ebuild
571 @@ -4,7 +4,7 @@
572
573 EAPI=5
574
575 -DESCRIPTION="Synteny Mapping and Analysis Program between chromosomes, contigs and physical maps"
576 +DESCRIPTION="Synteny Mapping and Analysis Program"
577 HOMEPAGE="http://www.agcol.arizona.edu/software/symap/"
578 SRC_URI="symap_40.tar.gz"
579
580
581 diff --git a/sci-biology/tgicl/tgicl-2.1.ebuild b/sci-biology/tgicl/tgicl-2.1.ebuild
582 index ae10de3..190b419 100644
583 --- a/sci-biology/tgicl/tgicl-2.1.ebuild
584 +++ b/sci-biology/tgicl/tgicl-2.1.ebuild
585 @@ -6,7 +6,7 @@ EAPI=5
586
587 inherit perl-module
588
589 -DESCRIPTION="TIGR perl scripts for clustering large EST/mRNAs datasets and aceconv, mgblast and pvmsx binaries"
590 +DESCRIPTION="TIGR perl scripts for clustering"
591 HOMEPAGE="http://sourceforge.net/projects/tgicl"
592 SRC_URI="http://sourceforge.net/projects/tgicl/files/tgicl%20v2.1/TGICL-2.1.tar.gz"
593
594
595 diff --git a/sci-biology/trowel/trowel-0.1.4.1.ebuild b/sci-biology/trowel/trowel-0.1.4.1.ebuild
596 index ae4282f..bfdd7b0 100644
597 --- a/sci-biology/trowel/trowel-0.1.4.1.ebuild
598 +++ b/sci-biology/trowel/trowel-0.1.4.1.ebuild
599 @@ -4,7 +4,7 @@
600
601 EAPI=5
602
603 -DESCRIPTION="Error corrector for genomic Illumina FASTQ reads using QUALs and not coverage info"
604 +DESCRIPTION="Error corrector for genomic Illumina FASTQ reads"
605 HOMEPAGE="http://sourceforge.net/projects/trowel-ec"
606 SRC_URI="http://downloads.sourceforge.net/project/trowel-ec/src/trowel.0.1.4.1.src.tar.gz"
607
608
609 diff --git a/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild
610 index 35f7f58..a1aaaca 100644
611 --- a/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild
612 +++ b/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild
613 @@ -10,7 +10,7 @@ inherit eutils python-single-r1 toolchain-funcs
614
615 MY_PV="${PV/_}" # convert from _rc2 to rc2
616
617 -DESCRIPTION="De novo whole-genome shotgun DNA sequence OLC assembler (Celera Assembler, CABOG)"
618 +DESCRIPTION="De novo whole-genome shotgun DNA sequence OLC assembler"
619 HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/"
620 SRC_URI="http://sourceforge.net/projects/${PN}/files/${PN}/wgs-8.3/wgs-${MY_PV}.tar.bz2"
621
622
623 diff --git a/sci-chemistry/chooch/chooch-5.0.2-r1.ebuild b/sci-chemistry/chooch/chooch-5.0.2-r1.ebuild
624 index 7341392..87f91cf 100644
625 --- a/sci-chemistry/chooch/chooch-5.0.2-r1.ebuild
626 +++ b/sci-chemistry/chooch/chooch-5.0.2-r1.ebuild
627 @@ -8,7 +8,7 @@ AUTOTOOLS_AUTORECONF=true
628
629 inherit autotools-utils multilib toolchain-funcs
630
631 -DESCRIPTION="a program that will automatically determine values of the anomalous scattering factors"
632 +DESCRIPTION="Automatically determine values of the anomalous scattering factors"
633 HOMEPAGE="http://www.gwyndafevans.co.uk/id2.html"
634 SRC_URI="ftp://ftp.ccp4.ac.uk/${PN}/${PV}/packed/${P}.tar.gz"
635
636
637 diff --git a/sci-chemistry/concoord/concoord-2.1.2.ebuild b/sci-chemistry/concoord/concoord-2.1.2.ebuild
638 index e6308ea..e1e2bd9 100644
639 --- a/sci-chemistry/concoord/concoord-2.1.2.ebuild
640 +++ b/sci-chemistry/concoord/concoord-2.1.2.ebuild
641 @@ -4,7 +4,7 @@
642
643 EAPI=5
644
645 -DESCRIPTION="Method to generate protein conformations around a known structure based on geometric restrictions"
646 +DESCRIPTION="Protein conformations around a known structure based on geometric restrictions"
647 HOMEPAGE="http://www.mpibpc.mpg.de/groups/de_groot/concoord/concoord.html"
648 SRC_URI="
649 amd64? ( http://www3.mpibpc.mpg.de/groups/de_groot/${PN}/${PN}_${PV}_linux64.tgz )
650
651 diff --git a/sci-chemistry/concoord/concoord-2.1.ebuild b/sci-chemistry/concoord/concoord-2.1.ebuild
652 index 8ec96b9..6f5ec47 100644
653 --- a/sci-chemistry/concoord/concoord-2.1.ebuild
654 +++ b/sci-chemistry/concoord/concoord-2.1.ebuild
655 @@ -4,7 +4,7 @@
656
657 EAPI=5
658
659 -DESCRIPTION="Method to generate protein conformations around a known structure based on geometric restrictions"
660 +DESCRIPTION="Protein conformations around a known structure based on geometric restrictions"
661 HOMEPAGE="http://www.mpibpc.mpg.de/groups/de_groot/concoord/concoord.html"
662 SRC_URI="
663 amd64? ( http://www.mpibpc.mpg.de/groups/de_groot/concoord/concoord2.1_linux_x86_64.tgz )
664
665 diff --git a/sci-chemistry/mddnmr/mddnmr-2.4-r1.ebuild b/sci-chemistry/mddnmr/mddnmr-2.4-r1.ebuild
666 index 8123048..4909fbe 100644
667 --- a/sci-chemistry/mddnmr/mddnmr-2.4-r1.ebuild
668 +++ b/sci-chemistry/mddnmr/mddnmr-2.4-r1.ebuild
669 @@ -10,7 +10,7 @@ inherit python-single-r1
670
671 MY_P="${PN}${PV}"
672
673 -DESCRIPTION="Program for processing of non-uniformly sampled (NUS) multidimensional NMR spectra"
674 +DESCRIPTION="Program for processing of NUS multidimensional NMR spectra"
675 HOMEPAGE="http://www.nmr.gu.se/~mdd/"
676 SRC_URI="http://pc8.nmr.gu.se/~mdd/Downloads/${MY_P}.tgz"
677
678
679 diff --git a/sci-chemistry/modelfree/modelfree-4.20.ebuild b/sci-chemistry/modelfree/modelfree-4.20.ebuild
680 index a40d489..66f5721 100644
681 --- a/sci-chemistry/modelfree/modelfree-4.20.ebuild
682 +++ b/sci-chemistry/modelfree/modelfree-4.20.ebuild
683 @@ -6,7 +6,7 @@ EAPI=5
684
685 inherit fortran-2 multilib
686
687 -DESCRIPTION="A program for optimizing Lipari-Szabo model free parameters to heteronuclear relaxation data"
688 +DESCRIPTION="Optimizing Lipari-Szabo model free parameters to heteronuclear relaxation data"
689 HOMEPAGE="http://www.palmer.hs.columbia.edu/software/modelfree.html"
690 SRC_URI="http://www.palmer.hs.columbia.edu/software/modelfree4_linux.tar.gz"
691
692
693 diff --git a/sci-chemistry/mtz2hkl/mtz2hkl-0.3.ebuild b/sci-chemistry/mtz2hkl/mtz2hkl-0.3.ebuild
694 index 08696a4..bc7cf14 100644
695 --- a/sci-chemistry/mtz2hkl/mtz2hkl-0.3.ebuild
696 +++ b/sci-chemistry/mtz2hkl/mtz2hkl-0.3.ebuild
697 @@ -6,7 +6,7 @@ EAPI=5
698
699 inherit eutils toolchain-funcs
700
701 -DESCRIPTION="Intended to facilitate the transition from refmac5 refinement to shelxh or shelxl refinement"
702 +DESCRIPTION="Facilitate the transition from refmac5 refinement to shelxh or shelxl refinement"
703 HOMEPAGE="http://shelx.uni-ac.gwdg.de/~tg/research/programs/conv/mtz2x/mtz2hkl/"
704 SRC_URI="http://shelx.uni-ac.gwdg.de/~tg/research/programs/conv/mtz2x/${PN}/downloads/${PV}/${PN}_v${PV}.tar.gz"
705
706
707 diff --git a/sci-chemistry/redcat/redcat-3.ebuild b/sci-chemistry/redcat/redcat-3.ebuild
708 index bf8d739..3105334 100644
709 --- a/sci-chemistry/redcat/redcat-3.ebuild
710 +++ b/sci-chemistry/redcat/redcat-3.ebuild
711 @@ -6,7 +6,7 @@ EAPI=5
712
713 inherit cmake-utils java-pkg-2
714
715 -DESCRIPTION="Analysis of residual dipolar couplings (RDCs) for structure validation and elucidation"
716 +DESCRIPTION="Analysis of RDCs for structure validation and elucidation"
717 HOMEPAGE="http://ifestos.cse.sc.edu/software.php"
718 SRC_URI="http://ifestos.cse.sc.edu/downloads.php?get=Redcat.${PV}.tar.gz -> Redcat.${PV}.tar.gz"
719
720
721 diff --git a/sci-chemistry/rosetta/rosetta-3.4.ebuild b/sci-chemistry/rosetta/rosetta-3.4.ebuild
722 index 139641e..241cdba 100644
723 --- a/sci-chemistry/rosetta/rosetta-3.4.ebuild
724 +++ b/sci-chemistry/rosetta/rosetta-3.4.ebuild
725 @@ -11,7 +11,7 @@ inherit eutils multilib prefix scons-utils toolchain-funcs versionator
726 #MY_P="${PN}$(get_major_version)_source"
727 MY_P="${PN}${PV}_source"
728
729 -DESCRIPTION="Prediction and design of protein structures, folding mechanisms, and protein-protein interactions"
730 +DESCRIPTION="Prediction of protein structures and protein-protein interactions"
731 HOMEPAGE="http://www.rosettacommons.org/"
732 SRC_URI="${MY_P}.tgz patch_rosetta3.4_to_CSROSETTA3_ver1.3.txt"
733
734
735 diff --git a/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild b/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild
736 index b56d269..18e43cb 100644
737 --- a/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild
738 +++ b/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild
739 @@ -12,7 +12,7 @@ MY_PV="$(delete_all_version_separators $(get_version_component_range 1-2))"
740 MY_PATCH="20120106"
741 MY_P="${PN}-v${MY_PV}-linux"
742
743 -DESCRIPTION="Predicts both the backbone and side chain 1H, 13C and 15N chemical shifts for proteins"
744 +DESCRIPTION="Predicts of backbone and side chain 1H, 13C and 15N CS for proteins"
745 HOMEPAGE="http://shiftx2.wishartlab.com/"
746 SRC_URI="http://shiftx2.wishartlab.com/download/${MY_P}-${MY_PATCH}.tgz"
747
748
749 diff --git a/sci-chemistry/talosn/talosn-4.01.2013.148.15.55-r3.ebuild b/sci-chemistry/talosn/talosn-4.01.2013.148.15.55-r3.ebuild
750 index f28e0fb..081c944 100644
751 --- a/sci-chemistry/talosn/talosn-4.01.2013.148.15.55-r3.ebuild
752 +++ b/sci-chemistry/talosn/talosn-4.01.2013.148.15.55-r3.ebuild
753 @@ -6,7 +6,7 @@ EAPI=5
754
755 inherit java-pkg-opt-2
756
757 -DESCRIPTION="Prediction of Protein Backbone and Sidechain Torsion Angles from NMR Chemical Shifts"
758 +DESCRIPTION="Prediction of Protein bb and sc Torsion Angles from NMR Chemical Shifts"
759 HOMEPAGE="http://spin.niddk.nih.gov/bax/software/TALOS-N/"
760 SRC_URI="http://spin.niddk.nih.gov/bax/software/TALOS-N/talosn.tZ -> ${P}.tgz"
761
762
763 diff --git a/sci-chemistry/talosn/talosn-4.12.2015.147.15.40.ebuild b/sci-chemistry/talosn/talosn-4.12.2015.147.15.40.ebuild
764 index f28e0fb..081c944 100644
765 --- a/sci-chemistry/talosn/talosn-4.12.2015.147.15.40.ebuild
766 +++ b/sci-chemistry/talosn/talosn-4.12.2015.147.15.40.ebuild
767 @@ -6,7 +6,7 @@ EAPI=5
768
769 inherit java-pkg-opt-2
770
771 -DESCRIPTION="Prediction of Protein Backbone and Sidechain Torsion Angles from NMR Chemical Shifts"
772 +DESCRIPTION="Prediction of Protein bb and sc Torsion Angles from NMR Chemical Shifts"
773 HOMEPAGE="http://spin.niddk.nih.gov/bax/software/TALOS-N/"
774 SRC_URI="http://spin.niddk.nih.gov/bax/software/TALOS-N/talosn.tZ -> ${P}.tgz"
775
776
777 diff --git a/sci-geosciences/pydap_handlers_cdms/pydap_handlers_cdms-0.2.0.1.ebuild b/sci-geosciences/pydap_handlers_cdms/pydap_handlers_cdms-0.2.0.1.ebuild
778 index c0cc917..94fabb2 100644
779 --- a/sci-geosciences/pydap_handlers_cdms/pydap_handlers_cdms-0.2.0.1.ebuild
780 +++ b/sci-geosciences/pydap_handlers_cdms/pydap_handlers_cdms-0.2.0.1.ebuild
781 @@ -11,7 +11,7 @@ inherit distutils-r1
782 MY_PN=${PN//_/.}
783 MY_P=${P//_/.}
784
785 -DESCRIPTION="CDMS handler for Pydap server that supports netCDF, HDF, GrADS/GRIB, or PCMDI DRS"
786 +DESCRIPTION="CDMS handler for Pydap server"
787 HOMEPAGE="http://pydap.org/handlers.html#cdms"
788 SRC_URI="mirror://pypi/${MY_PN:0:1}/${MY_PN}/${MY_P}.tar.gz"
789
790
791 diff --git a/sci-libs/asl/asl-0.1.7.ebuild b/sci-libs/asl/asl-0.1.7.ebuild
792 index cdec05f..f698a05 100644
793 --- a/sci-libs/asl/asl-0.1.7.ebuild
794 +++ b/sci-libs/asl/asl-0.1.7.ebuild
795 @@ -10,7 +10,7 @@ CMAKE_MAKEFILE_GENERATOR="${CMAKE_MAKEFILE_GENERATOR:-ninja}"
796
797 inherit cmake-utils
798
799 -DESCRIPTION="Advanced Simulation Library - hardware accelerated multiphysics simulation platform"
800 +DESCRIPTION="Hardware accelerated multiphysics simulation platform"
801 HOMEPAGE="http://asl.org.il/"
802 SRC_URI="https://github.com/AvtechScientific/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
803
804
805 diff --git a/sci-libs/asl/asl-9999.ebuild b/sci-libs/asl/asl-9999.ebuild
806 index 81ecd1d..3f4b64e 100644
807 --- a/sci-libs/asl/asl-9999.ebuild
808 +++ b/sci-libs/asl/asl-9999.ebuild
809 @@ -10,7 +10,7 @@ CMAKE_MAKEFILE_GENERATOR="${CMAKE_MAKEFILE_GENERATOR:-ninja}"
810
811 inherit cmake-utils git-r3
812
813 -DESCRIPTION="Advanced Simulation Library - hardware accelerated multiphysics simulation platform"
814 +DESCRIPTION="Hardware accelerated multiphysics simulation platform"
815 HOMEPAGE="http://asl.org.il/"
816 SRC_URI=""
817 EGIT_REPO_URI="git://github.com/AvtechScientific/${MY_PN}.git"
818
819 diff --git a/sci-libs/ipp/ipp-8.2.2.187-r1.ebuild b/sci-libs/ipp/ipp-8.2.2.187-r1.ebuild
820 index 076a4a9..f44e0f4 100644
821 --- a/sci-libs/ipp/ipp-8.2.2.187-r1.ebuild
822 +++ b/sci-libs/ipp/ipp-8.2.2.187-r1.ebuild
823 @@ -12,7 +12,7 @@ INTEL_SINGLE_ARCH=false
824
825 inherit intel-sdp
826
827 -DESCRIPTION="Intel Integrated Performance Primitive library for multimedia and data processing"
828 +DESCRIPTION="Intel Integrated Performance Primitive library"
829 HOMEPAGE="http://software.intel.com/en-us/articles/intel-ipp/"
830
831 IUSE=""
832
833 diff --git a/sci-mathematics/apron/apron-0.9.10-r1.ebuild b/sci-mathematics/apron/apron-0.9.10-r1.ebuild
834 index 622c06b..21d7f01 100644
835 --- a/sci-mathematics/apron/apron-0.9.10-r1.ebuild
836 +++ b/sci-mathematics/apron/apron-0.9.10-r1.ebuild
837 @@ -6,7 +6,7 @@ EAPI="5"
838
839 inherit eutils toolchain-funcs
840
841 -DESCRIPTION="Static analysis of the numerical variables of a program by Abstract Interpretation"
842 +DESCRIPTION="Static analysis of the numerical variables by Abstract Interpretation"
843 HOMEPAGE="http://apron.cri.ensmp.fr/library/"
844 SRC_URI="http://apron.cri.ensmp.fr/library/${P}.tgz"
845
846
847 diff --git a/sci-misc/elmer-gui/elmer-gui-9999.ebuild b/sci-misc/elmer-gui/elmer-gui-9999.ebuild
848 index b33a150..6db93d0 100644
849 --- a/sci-misc/elmer-gui/elmer-gui-9999.ebuild
850 +++ b/sci-misc/elmer-gui/elmer-gui-9999.ebuild
851 @@ -11,7 +11,7 @@ inherit autotools eutils qt4-r2 subversion python-single-r1 versionator
852 ELMER_ROOT="elmerfem"
853 MY_PN=ElmerGUI
854
855 -DESCRIPTION="a collection of finite element programs, libraries, and visualization tools, New Elmer pre-processor"
856 +DESCRIPTION="Finite element programs, libraries, visualization tools"
857 HOMEPAGE="http://www.csc.fi/english/pages/elmer"
858 SRC_URI=""
859 ESVN_REPO_URI="https://elmerfem.svn.sourceforge.net/svnroot/elmerfem/trunk/${MY_PN}"
860
861 diff --git a/sci-misc/mitlm/mitlm-0.4.1.ebuild b/sci-misc/mitlm/mitlm-0.4.1.ebuild
862 index a1d3e74..c343d16 100644
863 --- a/sci-misc/mitlm/mitlm-0.4.1.ebuild
864 +++ b/sci-misc/mitlm/mitlm-0.4.1.ebuild
865 @@ -6,7 +6,7 @@ EAPI="5"
866
867 inherit autotools
868
869 -DESCRIPTION="A set of tools designed for the efficient estimation of statistical n-gram language models"
870 +DESCRIPTION="Tools designed for efficient estimation of statistical n-gram language models"
871 HOMEPAGE="https://github.com/mitlm/mitlm"
872 SRC_URI="https://github.com/${PN}/${PN}/releases/download/v${PV}/${PN}_${PV}.tar.gz -> ${P}.tar.gz"
873
874
875 diff --git a/sci-physics/abinit/abinit-7.10.4.ebuild b/sci-physics/abinit/abinit-7.10.4.ebuild
876 index ed16815..48c31f3 100644
877 --- a/sci-physics/abinit/abinit-7.10.4.ebuild
878 +++ b/sci-physics/abinit/abinit-7.10.4.ebuild
879 @@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
880
881 inherit autotools-utils eutils flag-o-matic fortran-2 multilib python-single-r1 toolchain-funcs
882
883 -DESCRIPTION="Find total energy, charge density and electronic structure using density functional theory"
884 +DESCRIPTION="Total energy, charge density and electronic structure using DFT"
885 HOMEPAGE="http://www.abinit.org/"
886 SRC_URI="http://ftp.abinit.org/${P}.tar.gz"
887
888
889 diff --git a/sci-physics/abinit/abinit-7.4.2-r1.ebuild b/sci-physics/abinit/abinit-7.4.2-r1.ebuild
890 index 51f7ee7..45b7caa 100644
891 --- a/sci-physics/abinit/abinit-7.4.2-r1.ebuild
892 +++ b/sci-physics/abinit/abinit-7.4.2-r1.ebuild
893 @@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
894
895 inherit autotools-utils eutils flag-o-matic fortran-2 multilib python-single-r1 toolchain-funcs
896
897 -DESCRIPTION="Find total energy, charge density and electronic structure using density functional theory"
898 +DESCRIPTION="Total energy, charge density and electronic structure using DFT"
899 HOMEPAGE="http://www.abinit.org/"
900 SRC_URI="http://ftp.abinit.org/${P}.tar.gz"
901
902
903 diff --git a/sci-physics/abinit/abinit-7.6.4-r1.ebuild b/sci-physics/abinit/abinit-7.6.4-r1.ebuild
904 index 61ba323..6dd7323 100644
905 --- a/sci-physics/abinit/abinit-7.6.4-r1.ebuild
906 +++ b/sci-physics/abinit/abinit-7.6.4-r1.ebuild
907 @@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
908
909 inherit autotools-utils eutils flag-o-matic fortran-2 multilib python-single-r1 toolchain-funcs
910
911 -DESCRIPTION="Find total energy, charge density and electronic structure using density functional theory"
912 +DESCRIPTION="Total energy, charge density and electronic structure using DFT"
913 HOMEPAGE="http://www.abinit.org/"
914 SRC_URI="http://ftp.abinit.org/${P}.tar.gz"
915
916
917 diff --git a/sci-physics/mc-tester/mc-tester-1.25.0.ebuild b/sci-physics/mc-tester/mc-tester-1.25.0.ebuild
918 index 78eff0e..84b7cd9 100644
919 --- a/sci-physics/mc-tester/mc-tester-1.25.0.ebuild
920 +++ b/sci-physics/mc-tester/mc-tester-1.25.0.ebuild
921 @@ -8,7 +8,7 @@ inherit eutils
922
923 MYPN=MC-TESTER
924
925 -DESCRIPTION="A universal tool for comparisons of Monte Carlo predictions in High Energy Physics"
926 +DESCRIPTION="Comparisons of Monte Carlo predictions in High Energy Physics"
927 HOMEPAGE="http://mc-tester.web.cern.ch/MC-TESTER/"
928 SRC_URI="http://mc-tester.web.cern.ch/MC-TESTER/${MYPN}-${PV}.tar.gz"
929 LICENSE="CPC GPL-2+"
930
931 diff --git a/sci-physics/openmx/openmx-3.6.ebuild b/sci-physics/openmx/openmx-3.6.ebuild
932 index 978d5f3..02176eb 100644
933 --- a/sci-physics/openmx/openmx-3.6.ebuild
934 +++ b/sci-physics/openmx/openmx-3.6.ebuild
935 @@ -6,7 +6,7 @@ EAPI=5
936
937 inherit eutils multilib toolchain-funcs
938
939 -DESCRIPTION="Material eXplorer using DFT, NC pseudopotentials, and pseudo-atomic localized basis functions"
940 +DESCRIPTION="Material eXplorer"
941 HOMEPAGE="http://www.openmx-square.org/"
942 SRC_URI="
943 http://www.openmx-square.org/${PN}${PV}.tar.gz
944
945 diff --git a/sci-physics/openmx/openmx-3.7.8.ebuild b/sci-physics/openmx/openmx-3.7.8.ebuild
946 index 3468aa1..a227c0b 100644
947 --- a/sci-physics/openmx/openmx-3.7.8.ebuild
948 +++ b/sci-physics/openmx/openmx-3.7.8.ebuild
949 @@ -8,7 +8,7 @@ inherit eutils multilib toolchain-funcs fortran-2
950
951 PATCHDATE="14Feb17"
952
953 -DESCRIPTION="Material eXplorer using DFT, NC pseudopotentials, and pseudo-atomic localized basis functions"
954 +DESCRIPTION="Material eXplorer"
955 HOMEPAGE="http://www.openmx-square.org/"
956 SRC_URI="
957 http://www.openmx-square.org/${PN}${PV%.[0-9]}.tar.gz