How to compile and install wndchrm / WND-CHARM using bash script in Ubuntu 14.04 LTS 64-bit

Posted: 2015/04/01 in Data Science, Ubuntu
Tags: , , , , , , , , , , , ,
# hardware requirements: see https://github.com/wnd-charm/wnd-charm
# Wndchrm - an open source utility for biological image analysis
# WND-CHARM is an acronym that stands for "Weighted Neighbor Distance using Compound Hierarchy of Algorithms Representing Morphology."
cd
rm -rf wnd-charm
# install prerequisites:
sudo apt-get update
sudo apt-get install build-essential libtiff4-dev libfftw3-dev libX11-dev libxt-dev libxaw7-dev phylip
sudo apt-get install python-networkx python-skimage python-sklearn checkinstall
sudo apt-get install python-matplotlib python-numpy python-pandas
sudo apt-get install python-jsonschema openbox ipython python-scipy
sudo apt-get install spyder unp python-pip build-essential python-dev swig
sudo pip install --upgrade beautifulsoup4 numpy scipy matplotlib argparse
sudo pip install --upgrade ipython mistune networkx pandas py4j runipy
sudo pip install --upgrade scikit-image scikit-learn scipy-data_fitting
sudo pip install --upgrade statsmodels jsonschema
# install wnd-charm
git clone https://github.com/wnd-charm/wnd-charm.git
cd wnd-charm
sudo ./configure
sudo make
sudo make check
# change version from 'charm' to 1 when running sudo checkinstall to avoid errors!
# so checkinstall build values should be as follows:
# 0 - Maintainer: [ root ]
# 1 - Summary: [ Package created with checkinstall 1.6.2 ]
# 2 - Name: [ wnd ]
# 3 - Version: [ 1 ] -> instead of invalid Version: [ charm ]
# 4 - Release: [ 1 ]
# 5 - License: [ GPL ]
# 6 - Group: [ checkinstall ]
# 7 - Architecture: [ amd64 ]
# 8 - Source location: [ wnd-charm ]
# 9 - Alternate source location: [ ]
# 10 - Requires: [ ]
# 11 - Provides: [ wnd ]
# 12 - Conflicts: [ ]
# 13 - Replaces: [ ]
sudo checkinstall
apt-cache show wnd
# output of apt-cache show wnd should similar to this:
# Package: wnd
# Status: install ok installed
# Priority: extra
# Section: checkinstall
# Installed-Size: 1076
# Maintainer: root
# Architecture: amd64
# Version: 1-1
# Provides: wnd
# Description: Package created with checkinstall 1.6.2
# Description-md5: 556b8d22567101c7733f37ce6557412e
wndchrm
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