merged cami37 from cami_restructured

cami_37.sh

+# ====================================================
+# FileName: cami_37.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_37.sh
+                    OR
+                    ./cami_37.sh
+
+  If you can't run the script you have to give it the execution permissions:
+  Try:
+                    chmod +x cami_37.sh
+  And finally run:
+                   0) Create cami environment:
+                      sh cami_37.sh
+                      option: y    create cami env
+                   1) Initialize cami:
+                      conda activate cami
+                   2) Update cami:
+                      sh cami_37.sh
+                      option: u    update env cami
+                   3) Install cami certificate:
+                      sh cami_37.sh
+                      option: ce fix drugstone certificates
+                   4) Execute an example:
+                      sh cami_37.sh
+                      option: ex   execute an example
+                   5) Remove tmp file:
+                      sh cami_37.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_37.sh                        |"
+  echo "|   opt: u    update env cami         |"
+  echo "| Install cami certificate:           |"
+  echo "|   sh cami_37.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_37_env.yaml; pip install domino-python; pip install pcst_fast;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
+
+# vim: set sw=2 ts=2 sts=2 et ft=sh fdm=indent:

cami_37_env.yaml

+name: cami
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.7
+  - graph-tool
+  - networkx
+  - pandas
+  - numpy
+  - jupyter
+  - pip
+  - matplotlib
+  - statsmodels