Created
March 29, 2022 09:00
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Deploy Camoco in a separate conda environment
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name: camoco | |
channels: | |
- conda-forge | |
- defaults | |
dependencies: | |
- _libgcc_mutex=0.1=conda_forge | |
- _openmp_mutex=4.5=1_gnu | |
- bzip2=1.0.8=h7f98852_4 | |
- ca-certificates=2021.10.8=ha878542_0 | |
- cython=0.29.28=py38h709712a_0 | |
- ld_impl_linux-64=2.36.1=hea4e1c9_2 | |
- libffi=3.4.2=h7f98852_5 | |
- libgcc-ng=11.2.0=h1d223b6_14 | |
- libgomp=11.2.0=h1d223b6_14 | |
- libnsl=2.0.0=h7f98852_0 | |
- libstdcxx-ng=11.2.0=he4da1e4_14 | |
- libuuid=2.32.1=h7f98852_1000 | |
- libzlib=1.2.11=h166bdaf_1014 | |
- ncurses=6.3=h9c3ff4c_0 | |
- openssl=3.0.2=h166bdaf_1 | |
- pip=22.0.4=pyhd8ed1ab_0 | |
- python=3.8.13=ha86cf86_0_cpython | |
- python_abi=3.8=2_cp38 | |
- readline=8.1=h46c0cb4_0 | |
- setuptools=61.1.1=py38h578d9bd_0 | |
- sqlite=3.37.1=h4ff8645_0 | |
- tk=8.6.12=h27826a3_0 | |
- wheel=0.37.1=pyhd8ed1ab_0 | |
- xz=5.2.5=h516909a_1 | |
- zlib=1.2.11=h166bdaf_1014 | |
- git | |
- pip: | |
- aiofiles==0.8.0 | |
- aiohttp==4.0.0a1 | |
- aiosqlite==0.17.0 | |
- async-timeout==3.0.1 | |
- asyncssh==2.10.0 | |
- attrs==21.4.0 | |
- backoff==1.11.1 | |
- boto3==1.21.27 | |
- botocore==1.24.27 | |
- cachetools==5.0.0 | |
- certifi==2021.10.8 | |
- cffi==1.15.0 | |
- chardet==3.0.4 | |
- charset-normalizer==2.0.12 | |
- click==8.0.4 | |
- cryptography==36.0.2 | |
- cycler==0.11.0 | |
- decorator==5.1.1 | |
- deprecated==1.2.13 | |
- fastcluster==1.2.6 | |
- fonttools==4.31.2 | |
- fuzzywuzzy==0.18.0 | |
- gcloud==0.18.3 | |
- google-api-core==2.7.1 | |
- google-auth==2.6.2 | |
- google-cloud==0.34.0 | |
- google-cloud-core==2.2.3 | |
- google-cloud-kms==2.11.1 | |
- google-cloud-storage==2.2.1 | |
- google-crc32c==1.3.0 | |
- google-resumable-media==2.3.2 | |
- googleapis-common-protos==1.56.0 | |
- grpcio==1.45.0 | |
- grpcio-status==1.45.0 | |
- h5py==3.6.0 | |
- httplib2==0.20.4 | |
- idna==3.3 | |
- jmespath==1.0.0 | |
- joblib==1.1.0 | |
- jwcrypto==1.0 | |
- kiwisolver==1.4.1 | |
- markov-clustering==0.0.6.dev0 | |
- matplotlib==3.5.1 | |
- multidict==4.7.6 | |
- networkx==1.11 | |
- numexpr==2.8.1 | |
- numpy==1.22.3 | |
- oauth2client==4.1.3 | |
- packaging==21.3 | |
- pandas==1.4.1 | |
- patsy==0.5.2 | |
- pillow==9.0.1 | |
- proto-plus==1.20.3 | |
- protobuf==4.0.0rc2 | |
- psutil==5.9.0 | |
- pyasn1==0.4.8 | |
- pyasn1-modules==0.2.8 | |
- pycparser==2.21 | |
- pycryptodome==3.14.1 | |
- pyparsing==3.0.7 | |
- pyrebase4==4.5.0 | |
- python-dateutil==2.8.2 | |
- python-jwt==3.3.2 | |
- python-levenshtein==0.12.2 | |
- pytz==2022.1 | |
- pyyaml==6.0 | |
- requests==2.27.1 | |
- requests-toolbelt==0.9.1 | |
- rsa==4.8 | |
- s3transfer==0.5.2 | |
- scikit-learn==1.0.2 | |
- scipy==1.8.0 | |
- six==1.16.0 | |
- statsmodels==0.13.2 | |
- tables==3.7.0 | |
- threadpoolctl==3.1.0 | |
- tinydb==4.7.0 | |
- tinydb-serialization==2.1.0 | |
- tqdm==4.63.1 | |
- typing-extensions==4.1.1 | |
- urllib3==1.26.9 | |
- wrapt==1.14.0 | |
- yarl==1.7.2 | |
prefix: /opt/anaconda3/envs/camoco |
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#!/bin/bash | |
# be sure that development libraries for sqlite3 are installed! | |
# E.g., for debian run: | |
# apt install libsqlite3-dev | |
conda env create -f camoco.yml -n camoco | |
wget https://github.com/rogerbinns/apsw/releases/download/3.27.2-r1/apsw-3.27.2-r1.zip | |
unzip apsw-3.27.2-r1.zip | |
cd apsw-3.27.2-rg | |
eval "$(conda shell.bash hook)" | |
conda activate camoco | |
python setup.py install | |
cd .. | |
pip install git+https://github.com/LinkageIO/Minus80 | |
pip install git+https://github.com/LinkageIO/LocusPocus | |
pip install git+https://github.com/LinkageIO/Camoco@v1.0.0 |
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