-
Notifications
You must be signed in to change notification settings - Fork 2
/
requirements-conda.yml
404 lines (403 loc) · 13 KB
/
requirements-conda.yml
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
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
name: peppro
channels:
- conda-forge
- bioconda
- r
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=1_gnu
- _r-mutex=1.0.1=anacondar_1
- alsa-lib=1.2.3=h516909a_0
- attmap=0.13.0=pyhd8ed1ab_0
- attrs=21.2.0=pyhd8ed1ab_0
- bedtools=2.30.0=h7d7f7ad_2
- binutils_impl_linux-64=2.36.1=h193b22a_2
- binutils_linux-64=2.36=hf3e587d_1
- bioconductor-annotationdbi=1.54.0=r41hdfd78af_0
- bioconductor-annotationfilter=1.16.0=r41hdfd78af_0
- bioconductor-annotationhub=3.0.0=r41hdfd78af_0
- bioconductor-biobase=2.52.0=r41hd029910_0
- bioconductor-biocfilecache=2.0.0=r41hdfd78af_0
- bioconductor-biocgenerics=0.38.0=r41hdfd78af_0
- bioconductor-biocio=1.2.0=r41hdfd78af_0
- bioconductor-biocparallel=1.26.0=r41h399db7b_0
- bioconductor-biocversion=3.13.1=r41hdfd78af_0
- bioconductor-biomart=2.48.0=r41hdfd78af_0
- bioconductor-biostrings=2.60.0=r41hd029910_0
- bioconductor-bsgenome=1.60.0=r41hdfd78af_0
- bioconductor-delayedarray=0.18.0=r41hd029910_0
- bioconductor-ensembldb=2.16.0=r41hdfd78af_0
- bioconductor-experimenthub=2.0.0=r41hdfd78af_0
- bioconductor-genomeinfodb=1.28.0=r41hdfd78af_0
- bioconductor-genomeinfodbdata=1.2.6=r41hdfd78af_0
- bioconductor-genomicalignments=1.28.0=r41hd029910_0
- bioconductor-genomicfeatures=1.44.0=r41hdfd78af_0
- bioconductor-genomicranges=1.44.0=r41hd029910_0
- bioconductor-interactivedisplaybase=1.30.0=r41hdfd78af_0
- bioconductor-iranges=2.26.0=r41hd029910_0
- bioconductor-keggrest=1.32.0=r41hdfd78af_0
- bioconductor-matrixgenerics=1.4.0=r41hdfd78af_0
- bioconductor-protgenerics=1.24.0=r41hdfd78af_0
- bioconductor-rhtslib=1.24.0=r41hd029910_0
- bioconductor-rsamtools=2.8.0=r41h399db7b_0
- bioconductor-rtracklayer=1.52.0=r41hd029910_0
- bioconductor-s4vectors=0.30.0=r41hd029910_0
- bioconductor-summarizedexperiment=1.22.0=r41hdfd78af_0
- bioconductor-xvector=0.32.0=r41hd029910_0
- bioconductor-zlibbioc=1.38.0=r41hd029910_0
- bowtie2=2.4.2=py39hc9c6fcd_2
- brotlipy=0.7.0=py39h3811e60_1001
- bwidget=1.9.14=ha770c72_1
- bzip2=1.0.8=h7f98852_4
- c-ares=1.18.1=h7f98852_0
- ca-certificates=2021.10.8=ha878542_0
- cairo=1.16.0=h6cf1ce9_1008
- cffi=1.14.6=py39h4bc2ebd_1
- chardet=4.0.0=py39hf3d152e_1
- colorama=0.4.4=pyh9f0ad1d_0
- commonmark=0.9.1=py_0
- coreutils=8.31=h516909a_0
- coverage=6.1.1=py39h3811e60_0
- cryptography=35.0.0=py39h95dcef6_1
- curl=7.79.1=h2574ce0_1
- cutadapt>=2.9
- cykhash=1.0.2=py39hf149a3a_2
- cython=0.29.24=py39he80948d_0
- fastqc=0.11.9=hdfd78af_1
- fastq-pair
- fastp
- flash
- font-ttf-dejavu-sans-mono=2.37=hab24e00_0
- font-ttf-inconsolata=3.000=h77eed37_0
- font-ttf-source-code-pro=2.038=h77eed37_0
- font-ttf-ubuntu=0.83=hab24e00_0
- fontconfig=2.13.1=hba837de_1005
- fonts-conda-ecosystem=1=0
- fonts-conda-forge=1=0
- freetype=2.10.4=h0708190_1
- fribidi=1.0.10=h36c2ea0_0
- future=0.18.2=py39hf3d152e_3
- gawk=5.1.0=h7f98852_0
- gcc_impl_linux-64=9.4.0=h03d3576_11
- gcc_linux-64=9.4.0=h391b98a_1
- genrich=0.6.1=h5bf99c6_1
- gettext=0.19.8.1=h73d1719_1008
- gfortran_impl_linux-64=9.4.0=h0003116_11
- gfortran_linux-64=9.4.0=hf0ab688_1
- giflib=5.2.1=h36c2ea0_2
- graphite2=1.3.13=h58526e2_1001
- grep=3.4=h9d02d08_1
- gsl=2.6=he838d99_2
- gxx_impl_linux-64=9.4.0=h03d3576_11
- gxx_linux-64=9.4.0=h0316aca_1
- harfbuzz=2.9.1=h83ec7ef_1
- hmmratac=1.2.10=hdfd78af_1
- homer=4.11=pl5262h7d875b9_5
- htslib=1.14=h9093b5e_0
- icu=68.2=h9c3ff4c_0
- importlib-metadata=4.8.1=py39hf3d152e_0
- iniconfig=1.1.1=pyh9f0ad1d_0
- jbig=2.1=h7f98852_2003
- jinja2=3.0.2=pyhd8ed1ab_0
- jpeg=9d=h36c2ea0_0
- jsonschema=4.1.2=pyhd8ed1ab_0
- kernel-headers_linux-64=2.6.32=he073ed8_15
- krb5=1.19.2=hcc1bbae_2
- lcms2=2.12=hddcbb42_0
- ld_impl_linux-64=2.36.1=hea4e1c9_2
- lerc=2.2.1=h9c3ff4c_0
- libblas=3.9.0=12_linux64_openblas
- libcblas=3.9.0=12_linux64_openblas
- libcurl=7.79.1=h2574ce0_1
- libdeflate=1.7=h7f98852_5
- libedit=3.1.20191231=he28a2e2_2
- libev=4.33=h516909a_1
- libffi=3.4.2=h9c3ff4c_4
- libgcc-devel_linux-64=9.4.0=hd854feb_11
- libgcc-ng=11.2.0=h1d223b6_11
- libgfortran-ng=11.2.0=h69a702a_11
- libgfortran5=11.2.0=h5c6108e_11
- libgit2=1.3.0=hee63804_1
- libglib=2.70.0=h174f98d_1
- libgomp=11.2.0=h1d223b6_11
- libiconv=1.16=h516909a_0
- libidn2=2.3.2=h7f98852_0
- liblapack=3.9.0=12_linux64_openblas
- libnghttp2=1.43.0=h812cca2_1
- libopenblas=0.3.18=pthreads_h8fe5266_0
- libpng=1.6.37=h21135ba_2
- libsanitizer=9.4.0=h79bfe98_11
- libssh2=1.10.0=ha56f1ee_2
- libstdcxx-devel_linux-64=9.4.0=hd854feb_11
- libstdcxx-ng=11.2.0=he4da1e4_11
- libtiff=4.3.0=hf544144_1
- libunistring=0.9.10=h7f98852_0
- libuuid=2.32.1=h7f98852_1000
- libwebp-base=1.2.1=h7f98852_0
- libxcb=1.13=h7f98852_1003
- libxml2=2.9.12=h72842e0_0
- libzlib=1.2.11=h36c2ea0_1013
- lz4-c=1.9.3=h9c3ff4c_1
- make=4.3=hd18ef5c_1
- markupsafe=2.0.1=py39h3811e60_0
- more-itertools=8.10.0=pyhd8ed1ab_0
- mysql-connector-c=6.1.11=h6eb9d5d_1007
- ncurses=6.2=h58526e2_4
- numpy=1.21.3=py39hdbf815f_0
- openblas=0.3.18=pthreads_h4748800_0
- openjdk=11.0.9.1=h5cc2fde_1
- openssl=1.1.1l=h7f98852_0
- oyaml=1.0=pyhd8ed1ab_0
- packaging=21.0=pyhd8ed1ab_0
- pango=1.48.10=hb8ff022_1
- pathlib2=2.3.6=py39hf3d152e_0
- pcre=8.45=h9c3ff4c_0
- pcre2=10.37=h032f7d1_0
- peppy=0.31.1=pyhd8ed1ab_0
- perl=5.26.2=h36c2ea0_1008
- picard=2.26.4=hdfd78af_0
- pigz=2.6=h27826a3_0
- pip=21.3.1=pyhd8ed1ab_0
- piper=0.12.1=py_1
- pixman=0.40.0=h36c2ea0_0
- pluggy=1.0.0=py39hf3d152e_1
- preseq=2.0.3=hc216eb9_5
- psutil=5.8.0=py39h3811e60_1
- pthread-stubs=0.4=h36c2ea0_1001
- py=1.10.0=pyhd3deb0d_0
- pycparser=2.20=pyh9f0ad1d_2
- pyfaidx=0.6.3.1=pyh5e36f6f_0
- pygments=2.10.0=pyhd8ed1ab_0
- pyopenssl=21.0.0=pyhd8ed1ab_0
- pyparsing=3.0.4=pyhd8ed1ab_0
- pysocks=1.7.1=py39hf3d152e_3
- pytest=6.2.5=py39hf3d152e_0
- python=3.9.7=hb7a2778_3_cpython
- python-dateutil=2.8.2=pyhd8ed1ab_0
- python-levenshtein=0.12.2=py39h3811e60_0
- python_abi=3.9=2_cp39
- pytz=2021.3=pyhd8ed1ab_0
- r-askpass=1.1=r41hcfec24a_2
- r-assertthat=0.2.1=r41hc72bb7e_2
- r-backports=1.3.0=r41hcfec24a_0
- r-base=4.1.1=hb67fd72_0
- r-essentials=4.1
- r-gert
- r-base64enc=0.1_3=r41hcfec24a_1004
- r-bh=1.75.0_0=r41hc72bb7e_0
- r-biocmanager=1.30.16=r41hc72bb7e_0
- r-bit=4.0.4=r41hcfec24a_0
- r-bit64=4.0.5=r41hcfec24a_0
- r-bitops=1.0_7=r41hcfec24a_0
- r-blob=1.2.2=r41hc72bb7e_0
- r-brew=1.0_6=r41hc72bb7e_1003
- r-brio=1.1.2=r41hcfec24a_0
- r-bslib=0.3.1=r41hc72bb7e_0
- r-cachem=1.0.6=r41hcfec24a_0
- r-callr=3.7.0=r41hc72bb7e_0
- r-catools=1.18.2=r41h03ef668_0
- r-cli=3.1.0=r41h03ef668_0
- r-clipr=0.7.1=r41hc72bb7e_0
- r-colorspace=2.0_2=r41hcfec24a_0
- r-commonmark=1.7=r41hcfec24a_1002
- r-covr=3.5.1=r41h03ef668_0
- r-cpp11=0.4.0=r41hc72bb7e_0
- r-crayon=1.4.2=r41hc72bb7e_0
- r-credentials=1.3.1=r41hc72bb7e_0
- r-crosstalk=1.1.1=r41hc72bb7e_0
- r-curl=4.3.2=r41hcfec24a_0
- r-data.table=1.14.2=r41hcfec24a_0
- r-dbi=1.1.1=r41hc72bb7e_0
- r-dbplyr=2.1.1=r41hc72bb7e_0
- r-desc=1.4.0=r41hc72bb7e_0
- r-devtools=2.4.2=r41hc72bb7e_0
- r-diffobj=0.3.5=r41hcfec24a_0
- r-digest=0.6.28=r41h03ef668_0
- r-dplyr=1.0.7=r41h03ef668_0
- r-dt=0.19=r41hc72bb7e_0
- r-ellipsis=0.3.2=r41hcfec24a_0
- r-evaluate=0.14=r41hc72bb7e_2
- r-fansi=0.4.2=r41hcfec24a_0
- r-farver=2.1.0=r41h03ef668_0
- r-fastmap=1.1.0=r41h03ef668_0
- r-filelock=1.0.2=r41hcfec24a_1002
- r-fontawesome=0.2.2=r41hc72bb7e_0
- r-formatr=1.11=r41hc72bb7e_0
- r-fs=1.5.0=r41h03ef668_0
- r-futile.logger=1.4.3=r41hc72bb7e_1003
- r-futile.options=1.0.1=r41hc72bb7e_1002
- r-generics=0.1.1=r41hc72bb7e_0
- r-gert=1.4.1=r41h29657ab_1
- r-ggplot2=3.3.5=r41hc72bb7e_0
- r-gh=1.3.0=r41hc72bb7e_0
- r-git2r=0.28.0=r41hf628c3e_1
- r-gitcreds=0.1.1=r41hc72bb7e_0
- r-glue=1.4.2=r41hcfec24a_0
- r-gplots=3.1.1=r41hc72bb7e_0
- r-gtable=0.3.0=r41hc72bb7e_3
- r-gtools=3.9.2=r41hcfec24a_0
- r-highr=0.9=r41hc72bb7e_0
- r-hms=1.1.1=r41hc72bb7e_0
- r-htmltools=0.5.2=r41h03ef668_0
- r-htmlwidgets=1.5.4=r41hc72bb7e_0
- r-httpuv=1.6.3=r41h03ef668_0
- r-httr=1.4.2=r41hc72bb7e_0
- r-ini=0.3.1=r41hc72bb7e_1003
- r-isoband=0.2.5=r41h03ef668_0
- r-jquerylib=0.1.4=r41hc72bb7e_0
- r-jsonlite=1.7.2=r41hcfec24a_0
- r-kernsmooth=2.23_20=r41h742201e_0
- r-knitr=1.35=r41hc72bb7e_0
- r-labeling=0.4.2=r41hc72bb7e_0
- r-lambda.r=1.2.4=r41hc72bb7e_1
- r-later=1.2.0=r41h03ef668_0
- r-lattice=0.20_45=r41hcfec24a_0
- r-lazyeval=0.2.2=r41hcfec24a_2
- r-lifecycle=1.0.1=r41hc72bb7e_0
- r-magrittr=2.0.1=r41hcfec24a_1
- r-markdown=1.1=r41hcfec24a_1
- r-mass=7.3_54=r41hcfec24a_0
- r-matrix=1.3_4=r41he454529_0
- r-matrixstats=0.61.0=r41hcfec24a_0
- r-memoise=2.0.0=r41hc72bb7e_0
- r-mgcv=1.8_38=r41he454529_0
- r-mime=0.12=r41hcfec24a_0
- r-munsell=0.5.0=r41hc72bb7e_1003
- r-nlme=3.1_153=r41h859d828_0
- r-openssl=1.4.5=r41he36bf35_1
- r-pillar=1.6.4=r41hc72bb7e_0
- r-pkgbuild=1.2.0=r41hc72bb7e_0
- r-pkgconfig=2.0.3=r41hc72bb7e_1
- r-pkgload=1.2.3=r41h03ef668_0
- r-plogr=0.2.0=r41hc72bb7e_1003
- r-png=0.1_7=r41hcfec24a_1004
- r-praise=1.0.0=r41hc72bb7e_1004
- r-prettyunits=1.1.1=r41hc72bb7e_1
- r-processx=3.5.2=r41hcfec24a_0
- r-progress=1.2.2=r41hc72bb7e_2
- r-promises=1.2.0.1=r41h03ef668_0
- r-ps=1.6.0=r41hcfec24a_0
- r-purrr=0.3.4=r41hcfec24a_1
- r-r6=2.5.1=r41hc72bb7e_0
- r-rappdirs=0.3.3=r41hcfec24a_0
- r-rcmdcheck=1.4.0=r41h785f33e_0
- r-rcolorbrewer=1.1_2=r41h785f33e_1003
- r-rcpp=1.0.7=r41h03ef668_0
- r-rcurl=1.98_1.5=r41hcfec24a_0
- r-rematch2=2.1.2=r41hc72bb7e_1
- r-remotes=2.4.1=r41hc72bb7e_0
- r-restfulr=0.0.13=r41hdf9a8c9_1
- r-rex=1.2.0=r41hc72bb7e_1
- r-rjson=0.2.20=r41h03ef668_1002
- r-rlang=0.4.12=r41hcfec24a_0
- r-roxygen2=7.1.2=r41h03ef668_0
- r-rprojroot=2.0.2=r41hc72bb7e_0
- r-rsqlite=2.2.8=r41h03ef668_0
- r-rstudioapi=0.13=r41hc72bb7e_0
- r-rversions=2.1.1=r41hc72bb7e_0
- r-sass=0.4.0=r41h03ef668_0
- r-scales=1.1.1=r41hc72bb7e_0
- r-sessioninfo=1.2.0=r41hc72bb7e_0
- r-shiny=1.7.1=r41h785f33e_0
- r-snow=0.4_4=r41hc72bb7e_0
- r-sourcetools=0.1.7=r41h9c3ff4c_1002
- r-stringi=1.7.5=r41hcabe038_0
- r-stringr=1.4.0=r41hc72bb7e_2
- r-sys=3.4=r41hcfec24a_0
- r-testthat=3.1.0=r41h03ef668_0
- r-tibble=3.1.5=r41hcfec24a_0
- r-tidyselect=1.1.1=r41hc72bb7e_0
- r-usethis=2.1.3=r41hc72bb7e_0
- r-utf8=1.2.2=r41hcfec24a_0
- r-vctrs=0.3.8=r41hcfec24a_1
- r-viridislite=0.4.0=r41hc72bb7e_0
- r-waldo=0.3.1=r41hc72bb7e_0
- r-whisker=0.4=r41hc72bb7e_1
- r-withr=2.4.2=r41hc72bb7e_0
- r-xfun=0.27=r41h03ef668_0
- r-xml=3.99_0.8=r41hcfec24a_0
- r-xml2=1.3.2=r41h03ef668_1
- r-xopen=1.0.0=r41hc72bb7e_1003
- r-xtable=1.8_4=r41hc72bb7e_3
- r-yaml=2.2.1=r41hcfec24a_1
- r-zip=2.2.0=r41hcfec24a_0
- readline=8.1=h46c0cb4_0
- refgenie=0.12.0=pyhdfd78af_0
- rich=10.12.0=py39hf3d152e_0
- rust=1.56.0=h61edd41_0
- rust-std-x86_64-unknown-linux-gnu=1.56.0=hc1431ca_0
- samblaster=0.1.26=h7d875b9_1
- samtools=1.14=hb421002_0
- sed=4.8=he412f7d_0
- seqkit
- seqtk
- six=1.16.0=pyh6c4a22f_0
- sqlite=3.36.0=h9cd32fc_2
- sysroot_linux-64=2.12=he073ed8_15
- tbb=2020.2=h4bd325d_4
- tk=8.6.11=h27826a3_1
- tktable=2.10=hb7b940f_3
- toml=0.10.2=pyhd8ed1ab_0
- tomli=1.2.2=pyhd8ed1ab_0
- typing_extensions=3.10.0.2=pyha770c72_0
- tzdata=2021e=he74cb21_0
- ubiquerg=0.6.1=pyh9f0ad1d_0
- ucsc-bedgraphtobigwig=377=h0b8a92a_2
- ucsc-bedtobigbed=377=h0b8a92a_2
- ucsc-bigwigcat=377=h0b8a92a_2
- ucsc-bigwigmerge=377=h0b8a92a_2
- ucsc-wigtobigwig=377=h0b8a92a_2
- unzip=6.0=h7f98852_2
- urllib3=1.26.7=pyhd8ed1ab_0
- veracitools=0.1.3=py_0
- wget=1.20.3=ha56f1ee_1
- wheel=0.37.0=pyhd8ed1ab_1
- xorg-fixesproto=5.0=h7f98852_1002
- xorg-inputproto=2.3.2=h7f98852_1002
- xorg-kbproto=1.0.7=h7f98852_1002
- xorg-libice=1.0.10=h7f98852_0
- xorg-libsm=1.2.3=hd9c2040_1000
- xorg-libx11=1.7.2=h7f98852_0
- xorg-libxau=1.0.9=h7f98852_0
- xorg-libxdmcp=1.1.3=h7f98852_0
- xorg-libxext=1.3.4=h7f98852_1
- xorg-libxfixes=5.0.3=h7f98852_1004
- xorg-libxi=1.7.10=h7f98852_0
- xorg-libxrender=0.9.10=h7f98852_1003
- xorg-libxt=1.2.1=h7f98852_2
- xorg-libxtst=1.2.3=h7f98852_1002
- xorg-recordproto=1.14.2=h7f98852_1002
- xorg-renderproto=0.11.1=h7f98852_1002
- xorg-xextproto=7.3.0=h7f98852_1002
- xorg-xproto=7.0.31=h7f98852_1007
- xz=5.2.5=h516909a_1
- yacman=0.8.3=pyhd8ed1ab_0
- yaml=0.2.5=h516909a_0
- zipp=3.6.0=pyhd8ed1ab_0
- zlib=1.2.11=h36c2ea0_1013
- zstd=1.5.0=ha95c52a_0
- pip:
- bio==1.3.2
- biopython==1.79
- biothings-client==0.2.6
- certifi==2021.10.8
- charset-normalizer==2.0.7
- codecov==2.1.12
- divvy==0.6.0
- eido==0.1.5
- hypothesis==4.38.0
- idna==3.3
- logmuse==0.2.7
- looper==1.3.1
- mygene==3.2.2
- pandas==1.3.4
- pararead==0.7.0
- piper>=0.12.3
- pyrsistent==0.18.0
- pysam==0.17.0
- pyyaml==6.0
- refgenconf==0.12.1
- requests==2.26.0
- setuptools==58.4.0
- tqdm==4.62.3