diff --git a/cami.sh b/cami.sh index f4ff74be129e2066b28ae8a436fcc60ebfe32ffd..98aafcd83a2cc1a7e6f9a6689d34c14479e493cb 100755 --- a/cami.sh +++ b/cami.sh @@ -70,7 +70,6 @@ END } menu() { - clear echo "====================================" echo "| CAMI ENVIRONMENT INSTALLER |" echo "|----------------------------------|" @@ -97,7 +96,7 @@ install_cami() { conda config --add channels conda-forge conda config --add channels bioconda echo "cami: creating environment variable with python 3.7" - conda create --name cami -c conda-forge graph-tool python=3.7 + conda env create -f cami_env.yaml echo "=======================================" echo "| CAMI ENV SUCCESSFULLY CREATED |" echo "|-------------------------------------|" @@ -178,7 +177,7 @@ case $cami_tmp in h|H) usage ;; c|C) copyright ;; a|A) conda activate cami || echo "cami: If it was not activated successfully, please try manually: conda activate cami" ;; - u|U) conda install numpy matplotlib pandas networkx pip jupyter requests; pip install pcst_fast; conda env update cami --file=cami_env.yaml ;; + u|U) conda env update cami --file=cami_env.yaml; pip install domino-python; pip install requests_html; pip install biodigest ;; d|D) conda deactivate ;; s|S) conda info --envs ;; r|R) remove_cami ;; diff --git a/cami_env.yaml b/cami_env.yaml index 94ef0d21d14e1f3d4f885cef3a63cba5341a9ed4..41c7ad32d157929e79e719271677fd3e30d474cf 100644 --- a/cami_env.yaml +++ b/cami_env.yaml @@ -4,258 +4,13 @@ channels: - conda-forge - defaults dependencies: - - appnope=0.1.2 - - argcomplete=1.12.3 - - argon2-cffi=21.1.0 - - argon2-cffi-bindings=21.2.0 - - async_generator=1.10 - - atk-1.0=2.36.0 - - attrs=21.2.0 - - backcall=0.2.0 - - backports=1.0 - - backports.functools_lru_cache=1.6.4 - - bleach=4.1.0 - - boost=1.72.0 - - boost-cpp=1.72.0 - - bottleneck=1.3.4 - - brotli=1.0.9 - - brotli-bin=1.0.9 - - brotlipy=0.7.0 - - bzip2=1.0.8 - - c-ares=1.18.1 - - ca-certificates=2021.10.8 - - cached-property=1.5.2 - - cached_property=1.5.2 - - cairo=1.16.0 - - cairomm=1.12.2 - - cairomm-1.0=1.12.2 - - certifi=2021.10.8 - - cffi=1.15.0 - - charset-normalizer=2.0.10 - - cryptography=36.0.0 - - cycler=0.11.0 - - dbus=1.13.6 - - debugpy=1.5.1 - - decorator=5.1.0 - - defusedxml=0.7.1 - - entrypoints=0.3 - - epoxy=1.5.9 - - expat=2.4.1 - - fancycompleter=0.9.1 - - flit-core=3.7.1 - - font-ttf-dejavu-sans-mono=2.37 - - font-ttf-inconsolata=3.000 - - font-ttf-source-code-pro=2.038 - - font-ttf-ubuntu=0.83 - - fontconfig=2.13.1 - - fonts-conda-ecosystem=1 - - fonts-conda-forge=1 - - fonttools=4.28.1 - - freetype=2.10.4 - - fribidi=1.0.10 - - gdk-pixbuf=2.42.6 - - gettext=0.19.8.1 - - giflib=5.2.1 - - glib=2.70.1 - - glib-tools=2.70.1 - - gmp=6.2.1 - - graph-tool=2.35 - - graphite2=1.3.13 - - gtk3=3.24.22 - - h5py=3.6.0 - - harfbuzz=2.4.0 - - hdf5=1.12.1 - - hicolor-icon-theme=0.17 - - icu=64.2 - - idna=3.3 - - importlib-metadata=4.8.2 - - importlib_metadata=4.8.2 - - importlib_resources=5.4.0 - - ipykernel=6.5.0 - - ipython=7.29.0 - - ipython_genutils=0.2.0 - - ipywidgets=7.6.5 - - jbig=2.1 - - jedi=0.18.1 - - jinja2=3.0.3 - - jpeg=9d - - jsonschema=4.2.1 - - jupyter=1.0.0 - - jupyter_client=7.0.6 - - jupyter_console=6.4.0 - - jupyter_core=4.9.1 - - jupyterlab_pygments=0.1.2 - - jupyterlab_widgets=1.0.2 - - kiwisolver=1.3.2 - - krb5=1.19.2 - - lcms2=2.12 - - lerc=3.0 - - libblas=3.9.0 - - libbrotlicommon=1.0.9 - - libbrotlidec=1.0.9 - - libbrotlienc=1.0.9 - - libcblas=3.9.0 - - libclang=13.0.1 - - libcurl=7.81.0 - - libcxx=12.0.1 - - libdeflate=1.8 - - libedit=3.1.20191231 - - libev=4.33 - - libffi=3.4.2 - - libgfortran=5.0.0 - - libgfortran5=9.3.0 - - libgirepository=1.70.0 - - libglib=2.70.1 - - libiconv=1.16 - - liblapack=3.9.0 - - libllvm13=13.0.1 - - libnghttp2=1.46.0 - - libopenblas=0.3.18 - - libpng=1.6.37 - - librsvg=2.50.3 - - libsodium=1.0.18 - - libssh2=1.10.0 - - libtiff=4.3.0 - - libwebp-base=1.2.1 - - libxcb=1.13 - - libxml2=2.9.10 - - libzlib=1.2.11 - - llvm-openmp=12.0.1 - - lz4-c=1.9.3 - - markupsafe=2.0.1 - - matplotlib=3.5.0 - - matplotlib-base=3.5.0 - - matplotlib-inline=0.1.3 - - mistune=0.8.4 - - munkres=1.0.7 - - mysql-common=8.0.28 - - nbclient=0.5.9 - - nbconvert=6.3.0 - - nbformat=5.1.3 - - ncurses=6.2 - - nest-asyncio=1.5.1 - - notebook=6.4.6 - - nspr=4.32 - - numexpr=2.8.0 - - olefile=0.46 - - openjpeg=2.4.0 - - openssl=3.0.0 - - packaging=21.3 - - pandoc=2.16.1 - - pandocfilters=1.5.0 - - pango=1.42.4 - - parso=0.8.2 - - pcre=8.45 - - pdbpp=0.10.3 - - pexpect=4.8.0 - - pickleshare=0.7.5 - - pillow=8.4.0 - - pip=21.3.1 - - pixman=0.38.0 - - prometheus_client=0.12.0 - - prompt-toolkit=3.0.22 - - prompt_toolkit=3.0.22 - - pthread-stubs=0.4 - - ptyprocess=0.7.0 - - pycairo=1.20.1 - - pycparser=2.21 - - pygments=2.10.0 - - pygobject=3.42.0 - - pyopenssl=22.0.0 - - pyparsing=3.0.6 - - pyqt=5.9.2 - - pyqt5-sip=4.19.18 - - pyrepl=0.9.0 - - pyrsistent=0.18.0 - - pysocks=1.7.1 - - python=3.7.12 - - python-dateutil=2.8.2 - - python_abi=3.7 - - pytz=2021.3 - - pyzmq=22.3.0 - - qt=5.9.7 - - qtconsole=5.2.0 - - qtconsole-base=5.2.2 - - qtpy=1.11.2 - - readline=8.1 - - requests=2.27.1 - - send2trash=1.8.0 - - setuptools=59.2.0 - - sigcpp-2.0=2.10.7 - - sip=4.19.8 - - six=1.16.0 - - sparsehash=2.0.4 - - sqlite=3.36.0 - - terminado=0.12.1 - - testpath=0.5.0 - - tk=8.6.11 - - tornado=6.1 - - traitlets=5.1.1 - - typing_extensions=4.0.0 - - unicodedata2=13.0.0.post2 - - urllib3=1.26.8 - - wcwidth=0.2.5 - - webencodings=0.5.1 - - wheel=0.37.0 - - widgetsnbextension=3.5.2 - - wmctrl=0.4 - - xorg-libxau=1.0.9 - - xorg-libxdmcp=1.1.3 - - xz=5.2.5 - - zeromq=4.3.4 - - zipp=3.6.0 - - zlib=1.2.11 - - zstandard=0.16.0 - - zstd=1.5.0 - - pip: - - appdirs==1.4.4 - - beautifulsoup4==4.10.0 - - biodigest==0.2.4 - - bioservices==1.10.1 - - biothings-client==0.2.6 - - bs4==0.0.1 - - cattrs==22.1.0 - - colorama==0.4.5 - - colorlog==6.7.0 - - cssselect==1.1.0 - - domino-python==0.1.1 - - easydev==0.12.0 - - exceptiongroup==1.0.0rc9 - - fake-useragent==0.1.11 - - gevent==21.12.0 - - graph-tools==1.5 - - greenlet==1.1.3 - - grequests==0.6.0 - - gseapy==0.10.5 - - joblib==1.2.0 - - lxml==4.7.1 - - networkx==2.4 - - numpy==1.18.1 - - pandas==1.0.1 - - parse==1.19.0 - - patsy==0.5.2 - - pcst-fast==1.0.7 - - perlcompat==1.1 - - psutil==5.9.0 - - pybind11==2.8.1 - - pyee==8.2.2 - - pyppeteer==1.0.2 - - pyquery==1.4.3 - - pytess==1.0.0 - - python-louvain==0.14 - - requests-cache==0.9.6 - - requests-html==0.10.0 - - scipy==1.4.1 - - seaborn==0.11.2 - - soupsieve==2.3.1 - - statsmodels==0.11.0 - - suds-community==1.1.2 - - tqdm==4.62.3 - - url-normalize==1.4.3 - - w3lib==1.22.0 - - websockets==10.1 - - wrapt==1.14.1 - - xmltodict==0.13.0 - - zope-event==4.5.0 - - zope-interface==5.4.0 -prefix: /Users/Mia/opt/anaconda3/envs/cami + - python=3.7 + - graph-tool=2.45 + - networkx + - pandas + - numpy + - jupyter + - pip + - matplotlib + - statsmodels +prefix: /Users/Mia/opt/anaconda3/envs/cami_env