/
container.yaml
306 lines (306 loc) · 14.2 KB
/
container.yaml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
url: https://biocontainers.pro/tools/sprai
maintainer: '@vsoch'
description: shpc-registry automated BioContainers addition for sprai
latest:
0.9.9.23--py27pl5.22.0_0: sha256:88a77ad8f9d7d7b2873ea7a811a02cbbd00a10c4827bdf86da5b21c38401cd08
tags:
0.9.9.23--py27pl5.22.0_0: sha256:88a77ad8f9d7d7b2873ea7a811a02cbbd00a10c4827bdf86da5b21c38401cd08
docker: quay.io/biocontainers/sprai
aliases:
AtacDriver.py: /usr/local/bin/AtacDriver.py
Catrack: /usr/local/bin/Catrack
DAM2fasta: /usr/local/bin/DAM2fasta
DB2fasta: /usr/local/bin/DB2fasta
DB2quiva: /usr/local/bin/DB2quiva
DBdust: /usr/local/bin/DBdust
DBrm: /usr/local/bin/DBrm
DBshow: /usr/local/bin/DBshow
DBsplit: /usr/local/bin/DBsplit
DBstats: /usr/local/bin/DBstats
ESTmapper.pl: /usr/local/bin/ESTmapper.pl
HPCdaligner: /usr/local/bin/HPCdaligner
HPCmapper: /usr/local/bin/HPCmapper
LAcat: /usr/local/bin/LAcat
LAcheck: /usr/local/bin/LAcheck
LAmerge: /usr/local/bin/LAmerge
LAshow: /usr/local/bin/LAshow
LAsort: /usr/local/bin/LAsort
LAsplit: /usr/local/bin/LAsplit
PBcR: /usr/local/bin/PBcR
aalookup_unit_test: /usr/local/bin/aalookup_unit_test
aascan_unit_test: /usr/local/bin/aascan_unit_test
addCNSToStore: /usr/local/bin/addCNSToStore
addReadsToUnitigs: /usr/local/bin/addReadsToUnitigs
align_format_unit_test: /usr/local/bin/align_format_unit_test
analyzeBest: /usr/local/bin/analyzeBest
analyzePosMap: /usr/local/bin/analyzePosMap
analyzeScaffolds: /usr/local/bin/analyzeScaffolds
asmOutputFasta: /usr/local/bin/asmOutputFasta
asmOutputStatistics: /usr/local/bin/asmOutputStatistics
asmToAGP.pl: /usr/local/bin/asmToAGP.pl
atac.pl: /usr/local/bin/atac.pl
bam2sam: /usr/local/bin/bam2sam
bdbloader_unit_test: /usr/local/bin/bdbloader_unit_test
bfmtx2m4.pl: /usr/local/bin/bfmtx2m4.pl
bl2seq_unit_test: /usr/local/bin/bl2seq_unit_test
blasr: /usr/local/bin/blasr
blast_format_unit_test: /usr/local/bin/blast_format_unit_test
blast_services_unit_test: /usr/local/bin/blast_services_unit_test
blast_unit_test: /usr/local/bin/blast_unit_test
blastdb_format_unit_test: /usr/local/bin/blastdb_format_unit_test
blastdiag_unit_test: /usr/local/bin/blastdiag_unit_test
blastengine_unit_test: /usr/local/bin/blastengine_unit_test
blastextend_unit_test: /usr/local/bin/blastextend_unit_test
blastfilter_unit_test: /usr/local/bin/blastfilter_unit_test
blasthits_unit_test: /usr/local/bin/blasthits_unit_test
blastinput_unit_test: /usr/local/bin/blastinput_unit_test
blastoptions_unit_test: /usr/local/bin/blastoptions_unit_test
blastsetup_unit_test: /usr/local/bin/blastsetup_unit_test
bogart: /usr/local/bin/bogart
bogus: /usr/local/bin/bogus
bogusness: /usr/local/bin/bogusness
buildPosMap: /usr/local/bin/buildPosMap
buildRefContigs: /usr/local/bin/buildRefContigs
buildUnitigs: /usr/local/bin/buildUnitigs
ca2ace.pl: /usr/local/bin/ca2ace.pl
ca_ikki_v5.pl: /usr/local/bin/ca_ikki_v5.pl
caqc.pl: /usr/local/bin/caqc.pl
caqc_help.ini: /usr/local/bin/caqc_help.ini
cat-corrects: /usr/local/bin/cat-corrects
cat-erates: /usr/local/bin/cat-erates
cgw: /usr/local/bin/cgw
cgwDump: /usr/local/bin/cgwDump
check_circularity.pl: /usr/local/bin/check_circularity.pl
check_redundancy.pl: /usr/local/bin/check_redundancy.pl
chimChe: /usr/local/bin/chimChe
chimera: /usr/local/bin/chimera
classifyMates: /usr/local/bin/classifyMates
classifyMatesApply: /usr/local/bin/classifyMatesApply
classifyMatesPairwise: /usr/local/bin/classifyMatesPairwise
cleanAtac: /usr/local/bin/cleanAtac
cleanPolishes: /usr/local/bin/cleanPolishes
clumpMaker: /usr/local/bin/clumpMaker
coalesceMatches: /usr/local/bin/coalesceMatches
comparePolishes: /usr/local/bin/comparePolishes
computeCoverageStat: /usr/local/bin/computeCoverageStat
configureESTmapper.pl: /usr/local/bin/configureESTmapper.pl
convert-fasta-to-v2.pl: /usr/local/bin/convert-fasta-to-v2.pl
convertOverlap: /usr/local/bin/convertOverlap
convertPolishes: /usr/local/bin/convertPolishes
convertSamToCA: /usr/local/bin/convertSamToCA
convertToAtac: /usr/local/bin/convertToAtac
convertToExtent: /usr/local/bin/convertToExtent
convertToPBCNS: /usr/local/bin/convertToPBCNS
correct-frags: /usr/local/bin/correct-frags
correct-olaps: /usr/local/bin/correct-olaps
correctGaps: /usr/local/bin/correctGaps
correctPacBio: /usr/local/bin/correctPacBio
ctgcns: /usr/local/bin/ctgcns
daligner: /usr/local/bin/daligner
dazcon: /usr/local/bin/dazcon
deduplicate: /usr/local/bin/deduplicate
delta_unit_test: /usr/local/bin/delta_unit_test
demotePosMap: /usr/local/bin/demotePosMap
depthOfPolishes: /usr/local/bin/depthOfPolishes
detectChimera: /usr/local/bin/detectChimera
dfq2fq_v2.pl: /usr/local/bin/dfq2fq_v2.pl
dumbbell_filter.pl: /usr/local/bin/dumbbell_filter.pl
dumpCloneMiddles: /usr/local/bin/dumpCloneMiddles
dumpPBRLayoutStore: /usr/local/bin/dumpPBRLayoutStore
dumpSingletons: /usr/local/bin/dumpSingletons
erate-estimate: /usr/local/bin/erate-estimate
estimate-mer-threshold: /usr/local/bin/estimate-mer-threshold
existDB: /usr/local/bin/existDB
extendClearRanges: /usr/local/bin/extendClearRanges
extendClearRangesPartition: /usr/local/bin/extendClearRangesPartition
extractSequence: /usr/local/bin/extractSequence
extractUnmapped: /usr/local/bin/extractUnmapped
extract_fq.pl: /usr/local/bin/extract_fq.pl
extractmessages: /usr/local/bin/extractmessages
ezez4makefile_v4.pl: /usr/local/bin/ezez4makefile_v4.pl
ezez4qsub_vx1.pl: /usr/local/bin/ezez4qsub_vx1.pl
ezez_vx1.pl: /usr/local/bin/ezez_vx1.pl
fa2fq.pl: /usr/local/bin/fa2fq.pl
falcon-bench: /usr/local/bin/falcon-bench
falcon-print-routes: /usr/local/bin/falcon-print-routes
falcon_sense: /usr/local/bin/falcon_sense
fasta2DAM: /usr/local/bin/fasta2DAM
fasta2DB: /usr/local/bin/fasta2DB
fastaToCA: /usr/local/bin/fastaToCA
fastqAnalyze: /usr/local/bin/fastqAnalyze
fastqSample: /usr/local/bin/fastqSample
fastqSimulate: /usr/local/bin/fastqSimulate
fastqSimulate-sort: /usr/local/bin/fastqSimulate-sort
fastqToCA: /usr/local/bin/fastqToCA
filterEST: /usr/local/bin/filterEST
filterESTsimple: /usr/local/bin/filterESTsimple
filterMRNA: /usr/local/bin/filterMRNA
filterNULL: /usr/local/bin/filterNULL
filterOverlap: /usr/local/bin/filterOverlap
filterPolishes: /usr/local/bin/filterPolishes
filtertest: /usr/local/bin/filtertest
finalTrim: /usr/local/bin/finalTrim
fixPolishesIID: /usr/local/bin/fixPolishesIID
fixUnitigs: /usr/local/bin/fixUnitigs
fq2fa.pl: /usr/local/bin/fq2fa.pl
fq2idfq.pl: /usr/local/bin/fq2idfq.pl
fqfilt.pl: /usr/local/bin/fqfilt.pl
fragmentDepth: /usr/local/bin/fragmentDepth
fragsInVars: /usr/local/bin/fragsInVars
frgs2clones: /usr/local/bin/frgs2clones
gapShifter: /usr/local/bin/gapShifter
gapinfo_unit_test: /usr/local/bin/gapinfo_unit_test
gatekeeper: /usr/local/bin/gatekeeper
gatekeeperbench: /usr/local/bin/gatekeeperbench
gencode_singleton_unit_test: /usr/local/bin/gencode_singleton_unit_test
gene_info_unit_test: /usr/local/bin/gene_info_unit_test
get_target_fasta_records.pl: /usr/local/bin/get_target_fasta_records.pl
get_top_20x_fa.pl: /usr/local/bin/get_top_20x_fa.pl
gkpStoreCreate: /usr/local/bin/gkpStoreCreate
gkpStoreDumpFASTQ: /usr/local/bin/gkpStoreDumpFASTQ
greedyFragmentTiling: /usr/local/bin/greedyFragmentTiling
greedy_layout_to_IUM: /usr/local/bin/greedy_layout_to_IUM
happy-clones-span-clumps: /usr/local/bin/happy-clones-span-clumps
headPolishes: /usr/local/bin/headPolishes
heavychains: /usr/local/bin/heavychains
hitConverter: /usr/local/bin/hitConverter
hspfilter_besthit_unit_test: /usr/local/bin/hspfilter_besthit_unit_test
hspfilter_culling_unit_test: /usr/local/bin/hspfilter_culling_unit_test
hspstream_unit_test: /usr/local/bin/hspstream_unit_test
initialTrim: /usr/local/bin/initialTrim
kmer-mask: /usr/local/bin/kmer-mask
leaff: /usr/local/bin/leaff
lengthFilter: /usr/local/bin/lengthFilter
linkhsp_unit_test: /usr/local/bin/linkhsp_unit_test
magicblast_unit_test: /usr/local/bin/magicblast_unit_test
makeplot.pl: /usr/local/bin/makeplot.pl
mapMers: /usr/local/bin/mapMers
mapMers-depth: /usr/local/bin/mapMers-depth
mappedCoverage: /usr/local/bin/mappedCoverage
markRepeatUnique: /usr/local/bin/markRepeatUnique
markUniqueUnique: /usr/local/bin/markUniqueUnique
matchExtender: /usr/local/bin/matchExtender
merTrim: /usr/local/bin/merTrim
merTrimApply: /usr/local/bin/merTrimApply
mercy: /usr/local/bin/mercy
mergeCounts: /usr/local/bin/mergeCounts
mergePolishes: /usr/local/bin/mergePolishes
mergeqc.pl: /usr/local/bin/mergeqc.pl
metagenomics_ovl_analyses: /usr/local/bin/metagenomics_ovl_analyses
mismatchCounter: /usr/local/bin/mismatchCounter
msa2pssm_unit_test: /usr/local/bin/msa2pssm_unit_test
mt19937ar-test: /usr/local/bin/mt19937ar-test
ntlookup_unit_test: /usr/local/bin/ntlookup_unit_test
ntscan_unit_test: /usr/local/bin/ntscan_unit_test
olap-from-seeds: /usr/local/bin/olap-from-seeds
optionshandle_unit_test: /usr/local/bin/optionshandle_unit_test
outputLayout: /usr/local/bin/outputLayout
overlap: /usr/local/bin/overlap
overlapInCore: /usr/local/bin/overlapInCore
overlapStats: /usr/local/bin/overlapStats
overlapStore: /usr/local/bin/overlapStore
overlapStoreBucketizer: /usr/local/bin/overlapStoreBucketizer
overlapStoreBuild: /usr/local/bin/overlapStoreBuild
overlapStoreIndexer: /usr/local/bin/overlapStoreIndexer
overlapStoreSorter: /usr/local/bin/overlapStoreSorter
overlap_partition: /usr/local/bin/overlap_partition
overmerry: /usr/local/bin/overmerry
pacBioToCA: /usr/local/bin/pacBioToCA
parseSNP: /usr/local/bin/parseSNP
partition_fa.pl: /usr/local/bin/partition_fa.pl
pbdagcon: /usr/local/bin/pbdagcon
pbindex: /usr/local/bin/pbindex
pbindexdump: /usr/local/bin/pbindexdump
pbmerge: /usr/local/bin/pbmerge
pbutgcns: /usr/local/bin/pbutgcns
phiblast_unit_test: /usr/local/bin/phiblast_unit_test
pickBestPair: /usr/local/bin/pickBestPair
pickBestPolish: /usr/local/bin/pickBestPolish
pickUniquePolish: /usr/local/bin/pickUniquePolish
plotCoverageVsIdentity: /usr/local/bin/plotCoverageVsIdentity
positionDB: /usr/local/bin/positionDB
prelimsearch_unit_test: /usr/local/bin/prelimsearch_unit_test
projectFeatures: /usr/local/bin/projectFeatures
psibl2seq_unit_test: /usr/local/bin/psibl2seq_unit_test
psiblast_iteration_unit_test: /usr/local/bin/psiblast_iteration_unit_test
psiblast_unit_test: /usr/local/bin/psiblast_unit_test
pssmcreate_unit_test: /usr/local/bin/pssmcreate_unit_test
pssmenginefreqratios_unit_test: /usr/local/bin/pssmenginefreqratios_unit_test
querydata_unit_test: /usr/local/bin/querydata_unit_test
queryinfo_unit_test: /usr/local/bin/queryinfo_unit_test
quiva2DB: /usr/local/bin/quiva2DB
realignPolishes: /usr/local/bin/realignPolishes
redoalignment_unit_test: /usr/local/bin/redoalignment_unit_test
remote_blast_unit_test: /usr/local/bin/remote_blast_unit_test
removeDuplicate: /usr/local/bin/removeDuplicate
removeMateOverlap: /usr/local/bin/removeMateOverlap
removeRedundant: /usr/local/bin/removeRedundant
remove_fragment: /usr/local/bin/remove_fragment
replaceUIDwithName-fastq: /usr/local/bin/replaceUIDwithName-fastq
replaceUIDwithName-posmap: /usr/local/bin/replaceUIDwithName-posmap
reportAlignmentDifferences: /usr/local/bin/reportAlignmentDifferences
resolveSurrogates: /usr/local/bin/resolveSurrogates
rewriteCache: /usr/local/bin/rewriteCache
rps_unit_test: /usr/local/bin/rps_unit_test
runCA: /usr/local/bin/runCA
runCA-dedupe: /usr/local/bin/runCA-dedupe
runCA-overlapStoreBuild: /usr/local/bin/runCA-overlapStoreBuild
runCA.bak: /usr/local/bin/runCA.bak
runConcurrently.pl: /usr/local/bin/runConcurrently.pl
run_greedy.csh: /usr/local/bin/run_greedy.csh
scoreblk_unit_test: /usr/local/bin/scoreblk_unit_test
seagen: /usr/local/bin/seagen
search_strategy_unit_test: /usr/local/bin/search_strategy_unit_test
seatac: /usr/local/bin/seatac
seqdb_unit_test: /usr/local/bin/seqdb_unit_test
seqinfosrc_unit_test: /usr/local/bin/seqinfosrc_unit_test
seqsrc_unit_test: /usr/local/bin/seqsrc_unit_test
setupfactory_unit_test: /usr/local/bin/setupfactory_unit_test
sffToCA: /usr/local/bin/sffToCA
show-corrects: /usr/local/bin/show-corrects
sim4db: /usr/local/bin/sim4db
simple: /usr/local/bin/simple
simulator: /usr/local/bin/simulator
sortHits: /usr/local/bin/sortHits
sortPolishes: /usr/local/bin/sortPolishes
splitUnitigs: /usr/local/bin/splitUnitigs
split_query_unit_test: /usr/local/bin/split_query_unit_test
stat_unit_test: /usr/local/bin/stat_unit_test
statsGenerator: /usr/local/bin/statsGenerator
subj_ranges_unit_test: /usr/local/bin/subj_ranges_unit_test
summarizePolishes: /usr/local/bin/summarizePolishes
terminate: /usr/local/bin/terminate
terminator: /usr/local/bin/terminator
test-merStream: /usr/local/bin/test-merStream
test-seqCache: /usr/local/bin/test-seqCache
test-seqStream: /usr/local/bin/test-seqStream
testAtac: /usr/local/bin/testAtac
tigStore: /usr/local/bin/tigStore
tracearchiveToCA: /usr/local/bin/tracearchiveToCA
traceback_unit_test: /usr/local/bin/traceback_unit_test
tracebacksearch_unit_test: /usr/local/bin/tracebacksearch_unit_test
tracedb-to-frg.pl: /usr/local/bin/tracedb-to-frg.pl
trimFastqByQVWindow: /usr/local/bin/trimFastqByQVWindow
uidclient: /usr/local/bin/uidclient
uniform_search_unit_test: /usr/local/bin/uniform_search_unit_test
uniqPolishes: /usr/local/bin/uniqPolishes
uniqueFilter: /usr/local/bin/uniqueFilter
unitigger: /usr/local/bin/unitigger
upgrade-v8-to-v9: /usr/local/bin/upgrade-v8-to-v9
upgrade-v9-to-v10: /usr/local/bin/upgrade-v9-to-v10
utg2fasta: /usr/local/bin/utg2fasta
utgcns: /usr/local/bin/utgcns
utgcnsfix: /usr/local/bin/utgcnsfix
vennPolishes: /usr/local/bin/vennPolishes
version_reference_unit_test: /usr/local/bin/version_reference_unit_test
writedb_unit_test: /usr/local/bin/writedb_unit_test
meryl: /usr/local/bin/meryl
test_pcre: /usr/local/bin/test_pcre
config_data: /usr/local/bin/config_data
jellyfish: /usr/local/bin/jellyfish
blastdbcp: /usr/local/bin/blastdbcp
gene_info_reader: /usr/local/bin/gene_info_reader
seqdb_demo: /usr/local/bin/seqdb_demo
seqdb_perf: /usr/local/bin/seqdb_perf
perl5.22.0: /usr/local/bin/perl5.22.0
c2ph: /usr/local/bin/c2ph