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Commit 0918f09c authored by Le, Mia's avatar Le, Mia
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updated CAMI installation steps

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......@@ -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 ;;
......
......@@ -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
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