azimuth_dependencies <- c("python==2.7",
"biopython==1.74",
"certifi==2019.11.28",
"cycler==0.10.0",
"futures==3.3.0",
"kiwisolver==1.1.0",
"matplotlib==2.2.3",
"mmtf-python==1.1.2",
"nose==1.3.7",
"numpy==1.11.3",
"olefile==0.46",
"pandas==0.23.4",
"Pillow==6.2.1",
"pip==20.1.1",
"pyparsing==2.4.7",
"python-dateutil==2.8.1",
"pytz==2020.1",
"reportlab==3.5.42",
"scipy==1.2.1",
"setuptools==44.0.0",
"six==1.15.0",
"subprocess32==3.5.4",
"tornado==5.1.1",
"wheel==0.36.2")
azimuth_dependencies_pip <- c("scikit-learn==0.17.1")
deephf_dependencies <- c("python==3.6",
"viennarna==2.4.5",
"absl-py==0.12.0",
"astor==0.8.1",
"biopython==1.71",
"bleach==1.5.0",
"certifi==2020.12.5",
"cycler==0.10.0",
"decorator==4.4.2",
"dotmap==1.2.20",
"gast==0.4.0",
"GPy==1.9.8",
"GPyOpt==1.2.6",
"grpcio==1.36.1",
"h5py==2.9.0",
"html5lib==0.9999999",
"importlib-metadata==3.7.2",
"Keras==2.1.6",
"kiwisolver==1.3.1",
"Mako==1.1.4",
"Markdown==3.3.4",
"MarkupSafe==1.1.1",
"matplotlib==3.1.1",
"numpy==1.14.0",
"pandas==0.25.3",
"paramz==0.9.5",
"pip==21.0.1",
"protobuf==3.15.5",
"pygpu==0.7.6",
"pyparsing==2.4.7",
"python-dateutil==2.8.1",
"pytz==2021.1",
"PyYAML==5.4.1",
"scikit-learn==0.19.1",
"scipy==1.1.0",
"setuptools==49.6.0",
"six==1.15.0",
"tensorboard==1.8.0",
"tensorflow==1.8.0",
"termcolor==1.1.0",
"Theano==1.0.5",
"tornado==6.1",
"typing-extensions==3.7.4.3",
"webencodings==0.5.1",
"Werkzeug==1.0.1",
"wheel==0.36.2",
"zipp==3.4.1")
deepcpf1_dependencies <- c("python==2.7",
"funcsigs==1.0.2",
"h5py==2.10.0",
"Keras==2.1.5",
"linecache2==1.0.0",
"Mako==1.1.4",
"MarkupSafe==1.1.1",
"mock==3.0.5",
"numpy==1.16.5",
"pip==20.1.1",
"protobuf==3.11.4",
"pygpu==0.7.6",
"PyYAML==5.3.1",
"scipy==1.2.1",
"setuptools==44.0.0",
"six==1.15.0",
"tensorflow==1.0.0",
"Theano==1.0.1",
"traceback2==1.4.0",
"unittest2==1.1.0",
"wheel==0.36.2")
enpamgb_dependencies <- c("python==3.6",
"absl-py==0.12.0",
"astunparse==1.6.3",
"biopython==1.78",
"cachetools==4.2.1",
"certifi==2020.12.5",
"chardet==4.0.0",
"flatbuffers==1.12",
"gast==0.3.3",
"google-auth==1.27.1",
"google-auth-oauthlib==0.4.3",
"google-pasta==0.2.0",
"grpcio==1.32.0",
"h5py==2.10.0",
"idna==2.10",
"importlib-metadata==3.7.2",
"joblib==1.0.1",
"Keras-Preprocessing==1.1.2",
"Markdown==3.3.4",
"numpy==1.19.5",
"oauthlib==3.1.0",
"pandas==1.1.5",
"pip==21.0.1",
"protobuf==3.15.5",
"pyasn1==0.4.8",
"pyasn1-modules==0.2.8",
"python-dateutil==2.8.1",
"pytz==2021.1",
"requests==2.25.1",
"requests-oauthlib==1.3.0",
"rsa==4.7.2",
"scikit-learn==0.21.2",
"scipy==1.5.3",
"setuptools==49.6.0",
"six==1.15.0",
"termcolor==1.1.0",
"typing-extensions==3.7.4.3",
"urllib3==1.26.3",
"Werkzeug==1.0.1",
"wheel==0.36.2",
"wrapt==1.12.1",
"zipp==3.4.1")
enpamgb_dependencies_pip <- c("tensorflow==2.4.1")
lindel_dependencies <- c("python==3.6",
"certifi==2020.12.5",
"numpy==1.19.5",
"pip==21.0.1",
"scipy==1.5.3",
"setuptools==49.6.0",
"wheel==0.36.2")
crisprai_dependencies <- c("python==2.7.18",
"biopython==1.68",
"bx-python==0.7.3",
"pysam==0.15.3",
"scikit-learn==0.17.1",
"scipy==0.18.1",
"viennarna==2.4.18",
"wheel==0.36.2")
crisprai_dependencies_pip <- c("pandas==0.15.0")
deepspcas9_dependencies <- c("python==2.7",
"scipy==1.1.0",
"numpy==1.14.5")
deepspcas9_dependencies_pip <- c("tensorflow==1.4.1")
rs3_dependencies <- c("python==3.7.7",
"joblib==1.0.1",
"pandas==1.3.5",
"scikit-learn==1.0.2",
"biopython==1.78",
"lightgbm==3.2.1",
"tqdm==4.64.0",
"requests==2.27.1")
rs3_dependencies_pip <- c("sglearn==1.2.5")
#' @importFrom basilisk BasiliskEnvironment
env_azimuth <- BasiliskEnvironment(envname="azimuth_basilisk",
pkgname="crisprScore",
paths="python/azimuth",
packages=azimuth_dependencies,
channels = c("bioconda", "conda-forge"),
pip=azimuth_dependencies_pip)
env_lindel <- BasiliskEnvironment(envname="lindel_basilisk",
pkgname="crisprScore",
paths="python/lindel",
packages=lindel_dependencies,
channels=c("conda-forge", "bioconda"))
env_crisprai <- BasiliskEnvironment(envname="crisprai_basilisk",
pkgname="crisprScore",
packages=crisprai_dependencies,
channels = c("main",
"anaconda",
"bioconda",
"conda-forge"),
pip=crisprai_dependencies_pip)
env_deepspcas9 <- BasiliskEnvironment(envname="deepspcas9__basilisk",
pkgname="crisprScore",
packages=deepspcas9_dependencies,
channels = c("bioconda", "conda-forge"),
pip=deepspcas9_dependencies_pip)
env_rs3 <- BasiliskEnvironment(envname="rs3__basilisk",
pkgname="crisprScore",
packages=rs3_dependencies,
channels = c("bioconda", "conda-forge"),
pip=rs3_dependencies_pip)
if (.Platform$OS.type!="windows"){
env_deephf <- BasiliskEnvironment(envname="deephf_basilisk",
pkgname="crisprScore",
paths="python/deephf",
packages=deephf_dependencies,
channels=c("conda-forge", "bioconda"))
env_enpamgb <- BasiliskEnvironment(envname="enpamgb_basilisk",
pkgname="crisprScore",
paths="python/enpamgb",
packages=enpamgb_dependencies,
channels=c("conda-forge", "bioconda"),
pip=enpamgb_dependencies_pip)
env_deepcpf1 <- BasiliskEnvironment(envname="deepcpf1_basilisk",
pkgname="crisprScore",
paths="python/deepcpf1",
packages=deepcpf1_dependencies,
channels=c("conda-forge", "bioconda"))
} else {
env_deephf <- NULL
env_enpamgb <- NULL
env_deepcpf1 <- NULL
}