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Create env.yml (#6)

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- Create env.yml (ddafadf5c8ea19fa70bf50f2f4122d1633d60956)


Co-authored-by: Ryan Keivanfar <[email protected]>

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  1. env.yml +345 -0
env.yml ADDED
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1
+ name: tahoeformer_env
2
+ channels:
3
+ - pytorch
4
+ - nvidia
5
+ - bioconda
6
+ - conda-forge
7
+ dependencies:
8
+ - _openmp_mutex=4.5=3_kmp_llvm
9
+ - alsa-lib=1.2.8=h166bdaf_0
10
+ - argcomplete=3.6.2=pyhd8ed1ab_0
11
+ - argh=0.31.3=pyhd8ed1ab_1
12
+ - asttokens=3.0.0=pyhd8ed1ab_1
13
+ - attr=2.5.1=h166bdaf_1
14
+ - bcftools=1.17=h3cc50cf_1
15
+ - biopython=1.85=py310ha75aee5_1
16
+ - blas=1.0=mkl
17
+ - brotli=1.1.0=hb9d3cd8_2
18
+ - brotli-bin=1.1.0=hb9d3cd8_2
19
+ - bzip2=1.0.8=h4bc722e_7
20
+ - c-ares=1.34.5=hb9d3cd8_0
21
+ - ca-certificates=2025.4.26=hbd8a1cb_0
22
+ - cached-property=1.5.2=hd8ed1ab_1
23
+ - cached_property=1.5.2=pyha770c72_1
24
+ - cairo=1.16.0=ha61ee94_1014
25
+ - certifi=2025.4.26=pyhd8ed1ab_0
26
+ - comm=0.2.2=pyhd8ed1ab_1
27
+ - contourpy=1.3.2=py310h3788b33_0
28
+ - cpython=3.10.17=py310hd8ed1ab_0
29
+ - cramjam=2.10.0=py310hed47299_0
30
+ - cuda-cudart=12.1.105=0
31
+ - cuda-cupti=12.1.105=0
32
+ - cuda-libraries=12.1.0=0
33
+ - cuda-nvrtc=12.1.105=0
34
+ - cuda-nvtx=12.1.105=0
35
+ - cuda-opencl=12.9.19=0
36
+ - cuda-runtime=12.1.0=0
37
+ - cuda-version=12.9=3
38
+ - cudnn=9.9.0.52=h3828807_0
39
+ - cycler=0.12.1=pyhd8ed1ab_1
40
+ - dbus=1.13.6=h5008d03_3
41
+ - debugpy=1.8.14=py310hf71b8c6_0
42
+ - decorator=5.2.1=pyhd8ed1ab_0
43
+ - exceptiongroup=1.2.2=pyhd8ed1ab_1
44
+ - executing=2.2.0=pyhd8ed1ab_0
45
+ - expat=2.7.0=h5888daf_0
46
+ - fastparquet=2024.11.0=py310hf462985_0
47
+ - fftw=3.3.10=nompi_hf1063bd_110
48
+ - filelock=3.18.0=pyhd8ed1ab_0
49
+ - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
50
+ - font-ttf-inconsolata=3.000=h77eed37_0
51
+ - font-ttf-source-code-pro=2.038=h77eed37_0
52
+ - font-ttf-ubuntu=0.83=h77eed37_3
53
+ - fontconfig=2.14.2=h14ed4e7_0
54
+ - fonts-conda-ecosystem=1=0
55
+ - fonts-conda-forge=1=0
56
+ - fonttools=4.57.0=py310h89163eb_0
57
+ - freetype=2.12.1=h267a509_2
58
+ - fsspec=2025.3.2=pyhd8ed1ab_0
59
+ - gettext=0.24.1=h5888daf_0
60
+ - gettext-tools=0.24.1=h5888daf_0
61
+ - gffutils=0.13=pyh7cba7a3_0
62
+ - glib=2.80.2=hf974151_0
63
+ - glib-tools=2.80.2=hb6ce0ca_0
64
+ - gmp=6.3.0=hac33072_2
65
+ - gmpy2=2.2.1=py310he8512ff_0
66
+ - graphite2=1.3.13=h59595ed_1003
67
+ - gsl=2.7=he838d99_0
68
+ - gst-plugins-base=1.21.3=h4243ec0_1
69
+ - gstreamer=1.21.3=h25f0c4b_1
70
+ - gstreamer-orc=0.4.41=h17648ed_0
71
+ - h5py=3.9.0=nompi_py310h367e799_100
72
+ - harfbuzz=6.0.0=h8e241bc_0
73
+ - hdf5=1.14.0=nompi_h5231ba7_103
74
+ - htslib=1.17=h6bc39ce_1
75
+ - icu=70.1=h27087fc_0
76
+ - importlib-metadata=8.6.1=pyha770c72_0
77
+ - ipykernel=6.29.5=pyh3099207_0
78
+ - ipython=8.36.0=pyh907856f_0
79
+ - jack=1.9.22=h11f4161_0
80
+ - jedi=0.19.2=pyhd8ed1ab_1
81
+ - jinja2=3.1.6=pyhd8ed1ab_0
82
+ - joblib=1.5.0=pyhd8ed1ab_0
83
+ - jpeg=9e=h0b41bf4_3
84
+ - jupyter_client=8.6.3=pyhd8ed1ab_1
85
+ - jupyter_core=5.7.2=pyh31011fe_1
86
+ - keyutils=1.6.1=h166bdaf_0
87
+ - kiwisolver=1.4.7=py310h3788b33_0
88
+ - krb5=1.20.1=hf9c8cef_0
89
+ - lame=3.100=h166bdaf_1003
90
+ - lcms2=2.15=hfd0df8a_0
91
+ - ld_impl_linux-64=2.43=h712a8e2_4
92
+ - lerc=4.0.0=h0aef613_1
93
+ - libaec=1.1.3=h59595ed_0
94
+ - libasprintf=0.24.1=h8e693c7_0
95
+ - libasprintf-devel=0.24.1=h8e693c7_0
96
+ - libblas=3.9.0=16_linux64_mkl
97
+ - libbrotlicommon=1.1.0=hb9d3cd8_2
98
+ - libbrotlidec=1.1.0=hb9d3cd8_2
99
+ - libbrotlienc=1.1.0=hb9d3cd8_2
100
+ - libcap=2.66=ha37c62d_0
101
+ - libcblas=3.9.0=16_linux64_mkl
102
+ - libclang=15.0.7=default_h127d8a8_5
103
+ - libclang13=15.0.7=default_h5d6823c_5
104
+ - libcublas=12.1.0.26=0
105
+ - libcufft=11.0.2.4=0
106
+ - libcufile=1.14.0.30=4
107
+ - libcups=2.3.3=h36d4200_3
108
+ - libcurand=10.3.10.19=0
109
+ - libcurl=7.87.0=h6312ad2_0
110
+ - libcusolver=11.4.4.55=0
111
+ - libcusparse=12.0.2.55=0
112
+ - libdb=6.2.32=h9c3ff4c_0
113
+ - libdeflate=1.17=h0b41bf4_0
114
+ - libedit=3.1.20250104=pl5321h7949ede_0
115
+ - libev=4.33=hd590300_2
116
+ - libevent=2.1.10=h9b69904_4
117
+ - libexpat=2.7.0=h5888daf_0
118
+ - libffi=3.4.6=h2dba641_1
119
+ - libflac=1.4.3=h59595ed_0
120
+ - libgcc=14.2.0=h767d61c_2
121
+ - libgcc-ng=14.2.0=h69a702a_2
122
+ - libgcrypt=1.11.0=ha770c72_2
123
+ - libgcrypt-devel=1.11.0=hb9d3cd8_2
124
+ - libgcrypt-lib=1.11.0=hb9d3cd8_2
125
+ - libgcrypt-tools=1.11.0=hb9d3cd8_2
126
+ - libgettextpo=0.24.1=h5888daf_0
127
+ - libgettextpo-devel=0.24.1=h5888daf_0
128
+ - libgfortran=14.2.0=h69a702a_2
129
+ - libgfortran-ng=14.2.0=h69a702a_2
130
+ - libgfortran5=14.2.0=hf1ad2bd_2
131
+ - libglib=2.80.2=hf974151_0
132
+ - libgpg-error=1.55=h3f2d84a_0
133
+ - libhwloc=2.9.1=hd6dc26d_0
134
+ - libiconv=1.18=h4ce23a2_1
135
+ - liblapack=3.9.0=16_linux64_mkl
136
+ - libllvm15=15.0.7=hadd5161_1
137
+ - libltdl=2.4.3a=h5888daf_0
138
+ - libnghttp2=1.51.0=hdcd2b5c_0
139
+ - libnpp=12.0.2.50=0
140
+ - libnsl=2.0.1=hd590300_0
141
+ - libnvjitlink=12.1.105=0
142
+ - libnvjpeg=12.1.1.14=0
143
+ - libogg=1.3.5=hd0c01bc_1
144
+ - libopus=1.5.2=hd0c01bc_0
145
+ - libpng=1.6.43=h2797004_0
146
+ - libpq=15.1=h2baec63_3
147
+ - libsndfile=1.2.2=hc60ed4a_1
148
+ - libsodium=1.0.18=h36c2ea0_1
149
+ - libsqlite=3.46.0=hde9e2c9_0
150
+ - libssh2=1.10.0=haa6b8db_3
151
+ - libstdcxx=14.2.0=h8f9b012_2
152
+ - libstdcxx-ng=14.2.0=h4852527_2
153
+ - libsystemd0=252=h2a991cd_0
154
+ - libtiff=4.5.0=h6adf6a1_2
155
+ - libtool=2.5.4=h5888daf_0
156
+ - libudev1=253=h0b41bf4_0
157
+ - libuuid=2.38.1=h0b41bf4_0
158
+ - libvorbis=1.3.7=h9c3ff4c_0
159
+ - libwebp-base=1.5.0=h851e524_0
160
+ - libxcb=1.13=h7f98852_1004
161
+ - libxcrypt=4.4.36=hd590300_1
162
+ - libxkbcommon=1.5.0=h79f4944_1
163
+ - libxml2=2.10.3=hca2bb57_4
164
+ - libzlib=1.2.13=h4ab18f5_6
165
+ - llvm-openmp=15.0.7=h0cdce71_0
166
+ - lz4-c=1.9.4=hcb278e6_0
167
+ - markupsafe=3.0.2=py310h89163eb_1
168
+ - matplotlib=3.9.1=py310hff52083_1
169
+ - matplotlib-base=3.9.1=py310hf02ac8c_2
170
+ - matplotlib-inline=0.1.7=pyhd8ed1ab_1
171
+ - mkl=2022.2.1=h84fe81f_16997
172
+ - mpc=1.3.1=h24ddda3_1
173
+ - mpfr=4.2.1=h90cbb55_3
174
+ - mpg123=1.32.9=hc50e24c_0
175
+ - mpmath=1.3.0=pyhd8ed1ab_1
176
+ - munkres=1.1.4=pyh9f0ad1d_0
177
+ - mysql-common=8.0.32=h14678bc_0
178
+ - mysql-libs=8.0.32=h54cf53e_0
179
+ - ncurses=6.5=h2d0b736_3
180
+ - nest-asyncio=1.6.0=pyhd8ed1ab_1
181
+ - networkx=3.4.2=pyh267e887_2
182
+ - nspr=4.36=h5888daf_0
183
+ - nss=3.100=hca3bf56_0
184
+ - numpy=1.26.4=py310hb13e2d6_0
185
+ - ocl-icd=2.3.3=hb9d3cd8_0
186
+ - opencl-headers=2024.10.24=h5888daf_0
187
+ - openjpeg=2.5.0=hfec8fc6_2
188
+ - openssl=1.1.1w=hd590300_0
189
+ - pandas=2.2.3=py310h5eaa309_3
190
+ - parso=0.8.4=pyhd8ed1ab_1
191
+ - patsy=1.0.1=pyhd8ed1ab_1
192
+ - pcre2=10.43=hcad00b1_0
193
+ - perl=5.32.1=7_hd590300_perl5
194
+ - pexpect=4.9.0=pyhd8ed1ab_1
195
+ - pickleshare=0.7.5=pyhd8ed1ab_1004
196
+ - pillow=9.4.0=py310h023d228_1
197
+ - pip=25.1.1=pyh8b19718_0
198
+ - pixman=0.46.0=h29eaf8c_0
199
+ - platformdirs=4.3.7=pyh29332c3_0
200
+ - ply=3.11=pyhd8ed1ab_3
201
+ - prompt-toolkit=3.0.51=pyha770c72_0
202
+ - psutil=7.0.0=py310ha75aee5_0
203
+ - pthread-stubs=0.4=hb9d3cd8_1002
204
+ - ptyprocess=0.7.0=pyhd8ed1ab_1
205
+ - pulseaudio=16.1=h4ab2085_1
206
+ - pure_eval=0.2.3=pyhd8ed1ab_1
207
+ - pygments=2.19.1=pyhd8ed1ab_0
208
+ - pyparsing=3.2.3=pyhd8ed1ab_1
209
+ - pyqt=5.15.7=py310hab646b1_3
210
+ - pyqt5-sip=12.11.0=py310heca2aa9_3
211
+ - pysam=0.21.0=py310hff46b53_0
212
+ - python=3.10.8=h257c98d_0_cpython
213
+ - python-dateutil=2.9.0.post0=pyhff2d567_1
214
+ - python-tzdata=2025.2=pyhd8ed1ab_0
215
+ - python_abi=3.10=7_cp310
216
+ - pytorch=2.5.1=py3.10_cuda12.1_cudnn9.1.0_0
217
+ - pytorch-cuda=12.1=ha16c6d3_6
218
+ - pytorch-mutex=1.0=cuda
219
+ - pytz=2025.2=pyhd8ed1ab_0
220
+ - pyvcf3=1.0.3=pyhdfd78af_0
221
+ - pyyaml=6.0.2=py310h89163eb_2
222
+ - pyzmq=26.2.0=py310h71f11fc_1
223
+ - qhull=2020.2=h434a139_5
224
+ - qt-main=5.15.6=h18908ee_6
225
+ - readline=8.2=h8c095d6_2
226
+ - samtools=1.18=hd87286a_0
227
+ - scikit-learn=1.6.1=py310h27f47ee_0
228
+ - scipy=1.15.2=py310h1d65ade_0
229
+ - seaborn=0.13.2=hd8ed1ab_3
230
+ - seaborn-base=0.13.2=pyhd8ed1ab_3
231
+ - setuptools=80.1.0=pyhff2d567_0
232
+ - simplejson=3.20.1=py310ha75aee5_0
233
+ - sip=6.7.12=py310hc6cd4ac_0
234
+ - six=1.17.0=pyhd8ed1ab_0
235
+ - stack_data=0.6.3=pyhd8ed1ab_1
236
+ - statsmodels=0.14.4=py310hf462985_0
237
+ - tbb=2021.9.0=hf52228f_0
238
+ - threadpoolctl=3.6.0=pyhecae5ae_0
239
+ - tk=8.6.13=noxft_h4845f30_101
240
+ - toml=0.10.2=pyhd8ed1ab_1
241
+ - tomli=2.2.1=pyhd8ed1ab_1
242
+ - torchtriton=3.1.0=py310
243
+ - tornado=6.4.2=py310ha75aee5_0
244
+ - traitlets=5.14.3=pyhd8ed1ab_1
245
+ - typing_extensions=4.13.2=pyh29332c3_0
246
+ - tzdata=2025b=h78e105d_0
247
+ - unicodedata2=16.0.0=py310ha75aee5_0
248
+ - wcwidth=0.2.13=pyhd8ed1ab_1
249
+ - wheel=0.45.1=pyhd8ed1ab_1
250
+ - xcb-util=0.4.0=h516909a_0
251
+ - xcb-util-image=0.4.0=h166bdaf_0
252
+ - xcb-util-keysyms=0.4.0=h516909a_0
253
+ - xcb-util-renderutil=0.3.9=h166bdaf_0
254
+ - xcb-util-wm=0.4.1=h516909a_0
255
+ - xkeyboard-config=2.38=h0b41bf4_0
256
+ - xorg-kbproto=1.0.7=hb9d3cd8_1003
257
+ - xorg-libice=1.1.2=hb9d3cd8_0
258
+ - xorg-libsm=1.2.6=he73a12e_0
259
+ - xorg-libx11=1.8.4=h0b41bf4_0
260
+ - xorg-libxau=1.0.12=hb9d3cd8_0
261
+ - xorg-libxdmcp=1.1.5=hb9d3cd8_0
262
+ - xorg-libxext=1.3.4=h0b41bf4_2
263
+ - xorg-libxrender=0.9.10=h7f98852_1003
264
+ - xorg-renderproto=0.11.1=hb9d3cd8_1003
265
+ - xorg-xextproto=7.3.0=hb9d3cd8_1004
266
+ - xorg-xproto=7.0.31=hb9d3cd8_1008
267
+ - xz=5.2.6=h166bdaf_0
268
+ - yaml=0.2.5=h7f98852_2
269
+ - zeromq=4.3.5=h59595ed_1
270
+ - zipp=3.21.0=pyhd8ed1ab_1
271
+ - zlib=1.2.13=h4ab18f5_6
272
+ - zstd=1.5.6=ha6fb4c9_0
273
+ - pip:
274
+ - accelerate==1.6.0
275
+ - aiohappyeyeballs==2.6.1
276
+ - aiohttp==3.11.18
277
+ - aiosignal==1.3.2
278
+ - annotated-types==0.7.0
279
+ - arrow==1.3.0
280
+ - async-timeout==5.0.1
281
+ - attrs==21.4.0
282
+ - binaryornot==0.4.4
283
+ - chardet==5.2.0
284
+ - charset-normalizer==3.4.2
285
+ - click==8.1.8
286
+ - colorlog==6.9.0
287
+ - cookiecutter==2.6.0
288
+ - deprecation==2.1.0
289
+ - discrete-key-value-bottleneck-pytorch==0.1.1
290
+ - docker-pycreds==0.4.0
291
+ - einops==0.8.1
292
+ - einx==0.3.0
293
+ - enformer-pytorch==0.8.10
294
+ - frozendict==2.4.6
295
+ - frozenlist==1.6.0
296
+ - future==1.0.0
297
+ - gitdb==4.0.12
298
+ - gitpython==3.1.44
299
+ - huggingface-hub==0.30.2
300
+ - idna==3.10
301
+ - kipoi==0.8.6
302
+ - kipoi-conda==0.3.1
303
+ - kipoi-utils==0.7.7
304
+ - kipoiseq==0.7.1
305
+ - lightning==2.5.1.post0
306
+ - lightning-utilities==0.14.3
307
+ - markdown-it-py==3.0.0
308
+ - mdurl==0.1.2
309
+ - multidict==6.4.3
310
+ - natsort==8.4.0
311
+ - ncls==0.0.68
312
+ - packaging==24.2
313
+ - polars==1.29.0
314
+ - propcache==0.3.1
315
+ - protobuf==6.30.2
316
+ - pydantic==2.11.4
317
+ - pydantic-core==2.33.2
318
+ - pyfaidx==0.8.1.4
319
+ - pyranges==0.1.4
320
+ - python-slugify==8.0.4
321
+ - pytorch-lightning==2.5.1.post0
322
+ - rdkit-pypi==2022.9.5
323
+ - regex==2024.11.6
324
+ - related==0.7.3
325
+ - requests==2.32.3
326
+ - rich==14.0.0
327
+ - safetensors==0.5.3
328
+ - sentry-sdk==2.27.0
329
+ - setproctitle==1.3.6
330
+ - smmap==5.0.2
331
+ - sorted-nearest==0.0.39
332
+ - sympy==1.13.1
333
+ - tabulate==0.9.0
334
+ - text-unidecode==1.3
335
+ - tinydb==4.8.2
336
+ - tokenizers==0.21.1
337
+ - torchmetrics==1.7.1
338
+ - tqdm==4.67.1
339
+ - transformers==4.51.3
340
+ - types-python-dateutil==2.9.0.20241206
341
+ - typing-inspection==0.4.0
342
+ - urllib3==2.4.0
343
+ - vector-quantize-pytorch==1.22.16
344
+ - wandb==0.19.10
345
+ - yarl==1.20.0