Deploy Camoco in a separate conda environment

camoco.yml

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

deploy-camoco.sh

#!/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