From 61cbd1baf3ea2c5e93ea0d4f0d005fef365ef16f Mon Sep 17 00:00:00 2001
From: bay9355 <mia.le@studium.uni-hamburg.de>
Date: Wed, 26 Apr 2023 17:32:41 +0200
Subject: [PATCH] merged cami37 from cami_restructured
---
cami_37.sh | 190 +++++++++++++++++++++++++++++++++++++++++++++++
cami_37_env.yaml | 15 ++++
2 files changed, 205 insertions(+)
create mode 100755 cami_37.sh
create mode 100644 cami_37_env.yaml
diff --git a/cami_37.sh b/cami_37.sh
new file mode 100755
index 0000000..cf563a8
--- /dev/null
+++ b/cami_37.sh
@@ -0,0 +1,190 @@
+# ====================================================
+# 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:
diff --git a/cami_37_env.yaml b/cami_37_env.yaml
new file mode 100644
index 0000000..32f5a6d
--- /dev/null
+++ b/cami_37_env.yaml
@@ -0,0 +1,15 @@
+name: cami
+channels:
+ - bioconda
+ - conda-forge
+ - defaults
+dependencies:
+ - python=3.7
+ - graph-tool
+ - networkx
+ - pandas
+ - numpy
+ - jupyter
+ - pip
+ - matplotlib
+ - statsmodels
--
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