RoeiZucker
commented
1 year ago Hi! I'm currently running firm and these are the current libraries installed on my environment: Most of them are not necessary. Probably BGEN parser, geneffect, and hmmer are the most important. Feel free to contact me on roei.zucker@mail.huji.ac.il for any help needed, some of these libraries are a bit tricky to install.
Package Version
absl-py 0.15.0 aiohttp 3.7.4 aiohttp-session 2.7.0 alabaster 0.7.12 alembic 1.8.1 appdirs 1.4.4 argon2-cffi 20.1.0 astunparse 1.6.3 async-generator 1.10 async-timeout 3.0.1 asyncinit 0.2.4 attrs 20.3.0 autopage 0.5.1 Babel 2.9.1 backcall 0.2.0 bgen_parser 1.0 biopython 1.78 bleach 3.3.0 bokeh 1.4.0 boto3 1.18.21 botocore 1.21.21 cached-property 1.5.2 cachetools 4.2.2 certifi 2020.12.5 cffi 1.14.5 chardet 3.0.4 class-resolver 0.3.10 click 7.1.2 click-default-group 1.2.2 cliff 3.10.1 cloudpickle 1.6.0 cmaes 0.9.0 cmd2 2.4.2 colorlog 6.7.0 cycler 0.10.0 cykhash 1.0.2 Cython 0.29.23 dask 2021.6.2 dataclasses-json 0.5.7 decorator 4.4.2 deepTools 3.5.1 deeptoolsintervals 0.1.9 defusedxml 0.7.1 Deprecated 1.2.12 dill 0.3.4 docdata 0.0.3 docutils 0.17.1 entrypoints 0.3 et-xmlfile 1.1.0 fasta-reader 1.0.0 firm 1.3.0 flatbuffers 2.0 fsspec 0.9.0 gast 0.4.0 gcsfs 0.8.0 geneffect 1.2.4 gff-io 0.0.2 google-api-core 1.31.1 google-auth 1.34.0 google-auth-oauthlib 0.4.5 google-cloud-core 1.7.2 google-cloud-storage 1.25.0 google-pasta 0.2.0 google-resumable-media 0.5.1 googleapis-common-protos 1.53.0 greenlet 2.0.1 grpcio 1.41.1 h5py 3.5.0 hail 0.2.74 hmmer 0.1.0 humanize 1.0.0 hurry.filesize 0.9 idna 2.10 imagesize 1.2.0 importlib-metadata 4.0.1 importlib-resources 5.1.2 iniconfig 1.1.1 interval-tree 0.3.4 ipykernel 5.5.5 ipython 7.24.1 ipython-genutils 0.2.0 ipywidgets 7.6.3 isal 0.10.0 janus 0.6.1 jedi 0.18.0 Jinja2 3.0.1 jmespath 0.10.0 joblib 1.0.1 jsonschema 3.2.0 jupyter 1.0.0 jupyter-client 6.1.12 jupyter-console 6.4.0 jupyter-core 4.7.1 jupyterlab-pygments 0.1.2 jupyterlab-widgets 1.0.0 keras 2.7.0 Keras-Preprocessing 1.1.2 kiwisolver 1.3.1 libclang 12.0.0 locket 0.2.1 lxml 4.6.4 MACS3 3.0.0a6 Mako 1.2.4 Markdown 3.3.4 MarkupSafe 2.0.1 marshmallow 3.19.0 marshmallow-enum 1.5.1 matplotlib 3.4.1 matplotlib-inline 0.1.2 mistune 0.8.4 mlxtend 0.21.0 more-click 0.1.2 more-itertools 8.7.0 multidict 5.1.0 mypy-extensions 0.4.3 nbclient 0.5.3 nbconvert 6.0.7 nbformat 5.1.3 nest-asyncio 1.5.1 notebook 6.4.0 numpy 1.20.2 numpydoc 1.1.0 nvidia-cublas-cu11 11.10.3.66 nvidia-cuda-nvrtc-cu11 11.7.99 nvidia-cuda-runtime-cu11 11.7.99 nvidia-cudnn-cu11 8.5.0.96 oauthlib 3.1.1 openpyxl 3.0.7 opt-einsum 3.3.0 optuna 3.0.4 packaging 20.9 pandas 1.1.4 pandas-plink 2.2.8 pandocfilters 1.4.3 parsimonious 0.8.1 parso 0.8.2 partd 1.2.0 patsy 0.5.1 pbr 5.11.0 pexpect 4.8.0 pickle5 0.0.12 pickleshare 0.7.5 Pillow 8.2.0 pip 22.2.1 pkg_resources 0.0.0 plotly 4.14.3 pluggy 1.0.0.dev0 pooch 1.3.0 prettytable 3.5.0 prometheus-client 0.11.0 prompt-toolkit 3.0.18 protein-bert 1.0.1 protobuf 3.17.3 ptyprocess 0.7.0 pwas 1.0.2 py 1.10.0 py2bit 0.3.0 py4j 0.10.9 pyasn1 0.4.8 pyasn1-modules 0.2.8 pyBigWig 0.3.18 pycparser 2.20 pyfaidx 0.6.3.1 Pygments 2.9.0 PyJWT 2.1.0 pykeen 1.8.1 pyparsing 2.4.7 pyperclip 1.8.2 pyrsistent 0.17.3 pysam 0.16.0.1 pyspark 3.1.2 pystow 0.4.7 pytest 6.2.3 python-dateutil 2.8.1 python-json-logger 0.1.11 pytz 2021.1 PyYAML 5.4.1 pyzmq 22.1.0 qtconsole 5.1.0 QtPy 1.9.0 requests 2.25.1 requests-oauthlib 1.3.0 retrying 1.3.3 rexmex 0.1.2 rsa 4.7.2 s3transfer 0.5.0 scikit-learn 1.0.2 scipy 1.7.3 seaborn 0.11.2 Send2Trash 1.5.0 setuptools 56.0.0 six 1.15.0 sklearn 0.0.post1 snowballstemmer 2.1.0 Sphinx 4.0.2 sphinxcontrib-applehelp 1.0.2 sphinxcontrib-devhelp 1.0.2 sphinxcontrib-htmlhelp 2.0.0 sphinxcontrib-jsmath 1.0.1 sphinxcontrib-qthelp 1.0.3 sphinxcontrib-serializinghtml 1.1.5 SQLAlchemy 1.4.45 statsmodels 0.12.2 stevedore 3.5.2 tabulate 0.8.3 tensorboard 2.7.0 tensorboard-data-server 0.6.1 tensorboard-plugin-wit 1.8.0 tensorflow-addons 0.14.0 tensorflow-estimator 2.7.0 tensorflow-io-gcs-filesystem 0.21.0 termcolor 1.1.0 terminado 0.10.0 testpath 0.5.0 threadpoolctl 2.1.0 toml 0.10.2 toolz 0.11.1 torch 1.13.0 tornado 6.1 tqdm 4.42.1 traitlets 5.0.5 typeguard 2.13.0 typing-extensions 3.7.4.3 typing-inspect 0.8.0 ujson 4.0.2 ukbb-parser 1.0.2 urllib3 1.26.4 wcwidth 0.2.5 webencodings 0.5.1 Werkzeug 2.0.2 wheel 0.36.2 widgetsnbextension 3.5.1 wrapt 1.12.1 xarray 0.18.2 xlrd 2.0.1 xopen 1.1.0 yarl 1.6.3 zipp 3.4.1 zstandard 0.15.2
Hi Nadav: I tried to re-install firm software, but it still failed to solve the problem. Would it be convenient for you to tell me the version of all dependencies of your firm software? I would like to try to solve the problem based on the same environment as you run. Best wishes!