Comments (1)
cmlakhan
commented on September 4, 2024
If it helps here are the packages installed in the conda environment
# packages in environment at /sc/arion/projects/ad-omics/clakhani/conda/envs/enformer_lightning:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_llvm conda-forge
absl-py 1.0.0 pyhd8ed1ab_0 conda-forge
accelerate 0.5.1 py_0 fastai
aiohttp 3.7.0 py39h07f9747_0 conda-forge
alembic 1.7.7 pypi_0 pypi
argcomplete 2.0.0 pypi_0 pypi
argh 0.26.2 pypi_0 pypi
arrow 1.2.2 pypi_0 pypi
asciitree 0.3.3 pypi_0 pypi
async-timeout 3.0.1 py_1000 conda-forge
attrs 21.4.0 pyhd8ed1ab_0 conda-forge
autopage 0.5.0 pypi_0 pypi
axial-positional-embedding 0.2.1 pypi_0 pypi
binaryornot 0.4.4 pypi_0 pypi
blas 1.0 mkl defaults
blinker 1.4 py_1 conda-forge
bottleneck 1.3.2 py39hdd57654_1 defaults
brotli 1.0.9 he6710b0_2 defaults
brotlipy 0.7.0 py39h3811e60_1003 conda-forge
bzip2 1.0.8 h7b6447c_0 defaults
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2021.10.8 ha878542_0 conda-forge
cachetools 4.2.4 pyhd8ed1ab_0 conda-forge
certifi 2021.10.8 py39hf3d152e_1 conda-forge
cffi 1.14.6 py39he32792d_0 conda-forge
chardet 3.0.4 py39h079e4ff_1008 conda-forge
charset-normalizer 2.0.9 pyhd8ed1ab_0 conda-forge
click 8.0.3 py39hf3d152e_1 conda-forge
cliff 3.10.1 pypi_0 pypi
cmaes 0.8.2 pypi_0 pypi
cmd2 2.4.1 pypi_0 pypi
colorama 0.4.4 pyh9f0ad1d_0 conda-forge
coloredlogs 15.0.1 pypi_0 pypi
colorlog 6.6.0 pypi_0 pypi
cookiecutter 1.7.3 pypi_0 pypi
cryptography 36.0.1 py39h95dcef6_0 conda-forge
cudatoolkit 11.1.74 h6bb024c_0 nvidia
cycler 0.10.0 py39h06a4308_0 defaults
cython 0.29.24 py39hdbfa776_0 defaults
cyvcf2 0.30.14 pypi_0 pypi
dataclasses 0.8 pyhc8e2a94_3 conda-forge
datasets 2.3.2 pypi_0 pypi
dbus 1.13.18 hb2f20db_0 defaults
deepspeed 0.5.9 pypi_0 pypi
deprecation 2.1.0 pypi_0 pypi
dill 0.3.5.1 pypi_0 pypi
einops 0.4.1 pypi_0 pypi
enformer-pytorch 0.5.3 pypi_0 pypi
expat 2.4.1 h2531618_2 defaults
fairscale 0.4.4 pypi_0 pypi
fasteners 0.17.3 pypi_0 pypi
ffmpeg 4.3 hf484d3e_0 pytorch
filelock 3.7.1 pypi_0 pypi
fontconfig 2.13.1 h6c09931_0 defaults
fonttools 4.25.0 pyhd3eb1b0_0 defaults
freetype 2.11.0 h70c0345_0 defaults
fsspec 2021.11.1 pyhd8ed1ab_0 conda-forge
future 0.18.2 py39hf3d152e_4 conda-forge
gffutils 0.10.1 pypi_0 pypi
giflib 5.2.1 h7b6447c_0 defaults
glib 2.69.1 h5202010_0 defaults
gmp 6.2.1 h2531618_2 defaults
gnutls 3.6.15 he1e5248_0 defaults
google-auth 2.3.3 pyh6c4a22f_0 conda-forge
google-auth-oauthlib 0.4.6 pyhd8ed1ab_0 conda-forge
greenlet 1.1.2 pypi_0 pypi
grpcio 1.33.2 py39h0c26d4f_2 conda-forge
gst-plugins-base 1.14.0 h8213a91_2 defaults
gstreamer 1.14.0 h28cd5cc_2 defaults
h5py 3.6.0 py39ha0f2276_0 defaults
hdf5 1.10.6 hb1b8bf9_0 defaults
hjson 3.0.2 pypi_0 pypi
huggingface-hub 0.8.1 pypi_0 pypi
humanfriendly 10.0 pypi_0 pypi
icu 58.2 he6710b0_3 defaults
idna 3.1 pyhd3deb0d_0 conda-forge
importlib-metadata 4.10.0 py39hf3d152e_0 conda-forge
intel-openmp 2021.4.0 h06a4308_3561 defaults
jinja2 3.0.3 pypi_0 pypi
jinja2-time 0.2.0 pypi_0 pypi
joblib 1.1.0 pyhd3eb1b0_0 defaults
jpeg 9d h7f8727e_0 defaults
kipoi 0.7.4 pypi_0 pypi
kipoi-conda 0.2.2 pypi_0 pypi
kipoi-utils 0.7.1 pypi_0 pypi
kipoiseq 0.7.1 pypi_0 pypi
kiwisolver 1.3.1 py39h2531618_0 defaults
krb5 1.17.2 h926e7f8_0 conda-forge
lame 3.100 h7b6447c_0 defaults
lcms2 2.12 h3be6417_0 defaults
ld_impl_linux-64 2.35.1 h7274673_9 defaults
libcurl 7.76.1 hc4aaa36_1 conda-forge
libedit 3.1.20210910 h7f8727e_0 defaults
libev 4.33 h516909a_1 conda-forge
libffi 3.3 he6710b0_2 defaults
libgcc-ng 11.2.0 h1d223b6_11 conda-forge
libgfortran-ng 7.3.0 hdf63c60_0 defaults
libiconv 1.15 h63c8f33_5 defaults
libidn2 2.3.2 h7f8727e_0 defaults
libnghttp2 1.46.0 hce63b2e_0 defaults
libpng 1.6.37 hbc83047_0 defaults
libprotobuf 3.13.0.1 h8b12597_0 conda-forge
libssh2 1.10.0 ha56f1ee_2 conda-forge
libstdcxx-ng 9.1.0 hdf63c60_0 defaults
libtasn1 4.16.0 h27cfd23_0 defaults
libtiff 4.2.0 h85742a9_0 defaults
libunistring 0.9.10 h27cfd23_0 defaults
libuuid 1.0.3 h7f8727e_2 defaults
libuv 1.40.0 h7b6447c_0 defaults
libwebp 1.2.0 h89dd481_0 defaults
libwebp-base 1.2.0 h27cfd23_0 defaults
libxcb 1.14 h7b6447c_0 defaults
libxml2 2.9.10 hb55368b_3 defaults
linear-attention-transformer 0.19.1 pypi_0 pypi
linformer 0.2.1 pypi_0 pypi
llvm-openmp 12.0.1 h4bd325d_1 conda-forge
llvmlite 0.38.1 pypi_0 pypi
local-attention 1.4.3 pypi_0 pypi
lz4-c 1.9.3 h295c915_1 defaults
mako 1.2.0 pypi_0 pypi
markdown 3.3.6 pyhd8ed1ab_0 conda-forge
markupsafe 2.0.1 pypi_0 pypi
matplotlib 3.4.3 py39h06a4308_0 defaults
matplotlib-base 3.4.3 py39hbbc1b5f_0 defaults
memory-efficient-attention-pytorch 0.0.17 pypi_0 pypi
mixture-of-experts 0.2.1 pypi_0 pypi
mkl 2021.4.0 h06a4308_640 defaults
mkl-service 2.4.0 py39h7f8727e_0 defaults
mkl_fft 1.3.1 py39hd3c417c_0 defaults
mkl_random 1.2.2 py39h51133e4_0 defaults
multidict 5.2.0 py39h3811e60_1 conda-forge
multiprocess 0.70.13 pypi_0 pypi
munkres 1.1.4 py_0 defaults
natsort 7.1.1 pyhd3eb1b0_0 defaults
ncls 0.0.63 py39h38f01e4_0 bioconda
ncurses 6.3 h7f8727e_2 defaults
nettle 3.7.3 hbbd107a_1 defaults
ninja 1.10.2.3 pypi_0 pypi
numba 0.55.2 pypi_0 pypi
numcodecs 0.9.1 pypi_0 pypi
numexpr 2.7.3 py39h22e1b3c_1 defaults
numpy 1.21.2 py39h20f2e39_0 defaults
numpy-base 1.21.2 py39h79a1101_0 defaults
oauthlib 3.1.1 pyhd8ed1ab_0 conda-forge
olefile 0.46 pyhd3eb1b0_0 defaults
openh264 2.1.0 hd408876_0 defaults
openssl 1.1.1l h7f98852_0 conda-forge
optuna 2.10.0 pypi_0 pypi
packaging 21.3 pyhd8ed1ab_0 conda-forge
pandas 1.3.4 py39h8c16a72_0 defaults
pbr 5.8.1 pypi_0 pypi
pcre 8.45 h295c915_0 defaults
perceiver-pytorch 0.8.3 pypi_0 pypi
performer-pytorch 1.1.3 pypi_0 pypi
pillow 8.4.0 py39h5aabda8_0 defaults
pip 21.2.4 py39h06a4308_0 defaults
polars 0.13.55 pypi_0 pypi
poyo 0.5.0 pypi_0 pypi
prettytable 3.2.0 pypi_0 pypi
product-key-memory 0.1.10 pypi_0 pypi
protobuf 3.13.0.1 py39h41458e0_1 conda-forge
psutil 5.9.0 pypi_0 pypi
py-cpuinfo 8.0.0 pypi_0 pypi
pyarrow 8.0.0 pypi_0 pypi
pyasn1 0.4.8 py_0 conda-forge
pyasn1-modules 0.2.7 py_0 conda-forge
pybigwig 0.3.18 py39h015b436_1 bioconda
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pydeprecate 0.3.1 pyhd8ed1ab_0 conda-forge
pyfaidx 0.6.3.1 pyh5e36f6f_0 bioconda
pyfasta 0.5.2 py_1 bioconda
pyjwt 2.3.0 pyhd8ed1ab_1 conda-forge
pyopenssl 21.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.4 pyhd3eb1b0_0 defaults
pyperclip 1.8.2 pypi_0 pypi
pyqt 5.9.2 py39h2531618_6 defaults
pyranges 0.0.113 pyh5e36f6f_0 bioconda
pyrle 0.0.33 py39h38f01e4_0 bioconda
pysocks 1.7.1 py39hf3d152e_4 conda-forge
python 3.9.7 h12debd9_1 defaults
python-dateutil 2.8.2 pyhd3eb1b0_0 defaults
python-slugify 5.0.2 pypi_0 pypi
python_abi 3.9 2_cp39 conda-forge
pytorch 1.10.0 py3.9_cuda11.1_cudnn8.0.5_0 pytorch
pytorch-lightning 1.5.7 pyhd8ed1ab_0 conda-forge
pytorch-mutex 1.0 cuda pytorch
pytz 2021.3 pyhd3eb1b0_0 defaults
pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge
pyyaml 6.0 py39h7f8727e_1 defaults
qt 5.9.7 h5867ecd_1 defaults
readline 8.1 h27cfd23_0 defaults
reformer-pytorch 1.4.4 pypi_0 pypi
regex 2022.7.9 pypi_0 pypi
related 0.7.2 pypi_0 pypi
requests 2.26.0 pyhd8ed1ab_1 conda-forge
requests-oauthlib 1.3.0 pyh9f0ad1d_0 conda-forge
responses 0.18.0 pypi_0 pypi
routing-transformer 1.6.1 pypi_0 pypi
rsa 4.8 pyhd8ed1ab_0 conda-forge
scikit-learn 1.0.1 py39h51133e4_0 defaults
scipy 1.6.2 py39had2a1c9_1 defaults
seaborn 0.11.2 pyhd3eb1b0_0 defaults
setuptools 58.0.4 py39h06a4308_0 defaults
simplejson 3.17.6 pypi_0 pypi
sinkhorn-transformer 0.11.4 pypi_0 pypi
sip 4.19.13 py39h2531618_0 defaults
six 1.16.0 pyhd3eb1b0_0 defaults
sorted_nearest 0.0.33 py39hcbe4a3b_0 bioconda
sqlalchemy 1.4.35 pypi_0 pypi
sqlite 3.36.0 hc218d9a_0 defaults
stevedore 3.5.0 pypi_0 pypi
tabulate 0.8.9 py39h06a4308_0 defaults
tensorboard 2.7.0 pyhd8ed1ab_0 conda-forge
tensorboard-data-server 0.6.0 py39h95dcef6_1 conda-forge
tensorboard-plugin-wit 1.8.0 pyh44b312d_0 conda-forge
text-unidecode 1.3 pypi_0 pypi
thop 0.0.31-2005241907 pypi_0 pypi
threadpoolctl 2.2.0 pyh0d69192_0 defaults
tinydb 4.6.1 pypi_0 pypi
tk 8.6.11 h1ccaba5_0 defaults
tokenizers 0.12.1 pypi_0 pypi
torchaudio 0.10.0 py39_cu111 pytorch
torchmetrics 0.6.2 pyhd8ed1ab_0 conda-forge
torchvision 0.11.1 py39_cu111 pytorch
tornado 6.1 py39h27cfd23_0 defaults
tqdm 4.62.3 pyhd8ed1ab_0 conda-forge
transformers 4.20.1 pypi_0 pypi
triton 1.0.0 pypi_0 pypi
typing-extensions 4.3.0 pypi_0 pypi
tzdata 2021e hda174b7_0 defaults
urllib3 1.26.7 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.5 pypi_0 pypi
werkzeug 2.0.1 pyhd8ed1ab_0 conda-forge
wheel 0.37.0 pyhd3eb1b0_1 defaults
xxhash 3.0.0 pypi_0 pypi
xz 5.2.5 h7b6447c_0 defaults
yaml 0.2.5 h7b6447c_0 anaconda
yarl 1.7.2 py39h3811e60_1 conda-forge
zarr 2.11.3 pypi_0 pypi
zipp 3.6.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.11 h7b6447c_3 defaults
zstd 1.4.9 haebb681_0 defaults
from enformer-pytorch.
Related Issues (20)
- Minor typo in data.py HOT 2
- Error in fine-tuning HOT 3
- Initializing AttentionPool weights with 2 * Identity matrix. HOT 1
- Initializing AttentionPool weights with 2 * Identity matrix, again! HOT 3
- CUDA out of memory in unexpected cases HOT 2
- Reverse Complement Fails when return_seq_indices=True HOT 3
- GenomeIntervalDataset problems HOT 1
- Using transformers[torch] to limit dependencies HOT 1
- Training process HOT 22
- Fail to read .bed file
- Would using FlashAttention(2) help? HOT 4
- Rounding errors in the positional encodings HOT 6
- Hard coded input sequence length to the transformer blocks with using use_tf_gamma = True HOT 14
- Gradient checkpoint HOT 2
- Correlation Coefficient Calculation HOT 4
- Problems during fine-tuing on my own ATAC-seq data
- How to retreive the sequence of genes?
- minor question on extract sequence embeddings HOT 1
- AssertionError: if using tf gamma, only sequence length of 1536 allowed for now
- How to retrieve neular with ACTG information from the dataset
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from enformer-pytorch.