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cami.sh 6.62 KiB
# ====================================================
# FileName: cami.sh
# Author: Marcos Chow Castro <mctechnology170318@gmail.com>
# GitHub: https://github.com/mctechnology17
# Date: 22.11.2021 20:30
# ====================================================
which conda > /dev/null
if test $? -ne 0
then
echo "$0: conda is not installed. Please first install it"
exit 1
fi
copyright() {
cat <<END
Copyright (c) 2021 Marcos Chow Castro
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
END
exit 1
}
usage(){
cat <<END
Usage:
sh cami.sh
OR
./cami.sh
If you can't run the script you have to give it the execution permissions:
Try:
chmod +x cami.sh
And finally run:
0) Create cami environment:
sh cami.sh
option: y create cami env
1) Initialize cami:
conda activate cami
2) Update cami:
sh cami.sh
option: u update env cami
3) Install cami certificate:
sh cami.sh
option: ce fix drugstone certificates
4) Execute an example:
sh cami.sh
option: ex execute an example
5) Remove tmp file:
sh cami.sh
option: cl remove tmp file
END
exit 1
}
menu() {
echo "===================================="
echo "| CAMI ENVIRONMENT INSTALLER |"
echo "|----------------------------------|"
echo "| h help/usage |"
echo "| y create cami env |"
echo "| a cami activate |"
echo "| u update env cami |"
echo "| ce install cami certificate |"
echo "| ex execute an example |"
echo "| cl remove tmp file |"
echo "| d cami deactivate |"
echo "| s show env |"
echo "| r remove cami env |"
echo "| c copyright/permission |"
echo "|----------------------------------|"
echo "| Press ENTER or CTRL+C to EXIT |"
echo "===================================="
echo "Continue?"
}
install_cami() {
echo "cami: adding channels"
conda config --add channels defaults
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
echo "======================================="
echo "| CAMI ENV SUCCESSFULLY CREATED |"
echo "|-------------------------------------|"
echo "| For a complete installation |"
echo "| you must follow the following steps |"
echo "| Initialize cami: |"
echo "| conda activate cami |"
echo "| Update cami: |"
echo "| sh cami.sh |"
echo "| opt: u update env cami |"
echo "| Install cami certificate: |"
echo "| sh cami.sh |"
echo "| opt: ce fix drugstone certificate |"
echo "|-------------------------------------|"
}
darwin_certificate() {
if [ -d $HOME/opt/anaconda3/envs/cami/lib/python3.7/site-packages/certifi/ ]; then
cat drugstone_certificates.txt >> $HOME/opt/anaconda3/envs/cami/lib/python3.7/site-packages/certifi/cacert.pem
echo "cami: certificate updated successfully"
elif [ -d /opt/anaconda3/envs/cami/lib/python3.7/site-packages/certifi/ ]; then
cat drugstone_certificates.txt >> /opt/anaconda3/envs/cami/lib/python3.7/site-packages/certifi/cacert.pem
echo "cami: certificate updated successfully"
else
echo "cami: the directory certifi in cami_env NOT EXIST"
fi
}
linux_certificate() {
if [ -d $HOME/anaconda3/envs/cami/lib/python3.7/site-packages/certifi/ ]; then
cat drugstone_certificates.txt >> $HOME/anaconda3/envs/cami/lib/python3.7/site-packages/certifi/cacert.pem
echo "cami: certificate updated successfully"
elif [ -d /anaconda3/envs/cami/lib/python3.7/site-packages/certifi/ ]; then
cat drugstone_certificates.txt >> /anaconda3/envs/cami/lib/python3.7/site-packages/certifi/cacert.pem
echo "cami: certificate updated successfully"
else
echo "cami: the directory certifi in cami_env NOT EXIST"
fi
}
install_certificate() {
case `uname -s` in
Darwin) echo "Darwin" && darwin_certificate ;;
Linux) echo "Linux" && linux_certificate ;;
esac
}
if [ "$1" = "example" ] ; then
./cami/example_run.py
exit 0
elif [ "$1" = "clean" ] ; then
rm -r cami/__pycache__
rm -r data/tmp
exit 0
fi
remove_cami() {
clear
echo "|-------------------------|"
echo "| Are you sure you want to|"
echo "| delete cami env [y/n]?|"
echo "+-------------------------+"
echo "| Press CTRL+C to exit |"
echo "+-------------------------+"
read -r cami_del
if [ "$cami_del" = "y" ]; then
conda env remove -n cami
else
echo "No change made!"
exit 1
fi
}
menu
read -r cami_tmp
case $cami_tmp in
y|Y) install_cami ;;
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 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 ;;
ce|CE) install_certificate ;;
ex|EX) ./cami/example_run.py ;;
cl|CL) rm -r cami/__pycache__; rm -r data/tmp ;;
*) echo No change made ;;
esac
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