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My program needs Python 3 in order to run. How do I install it?


yum search cm-python3

(the prefix “cm-” is important) should turn up the Bright Cluster Manager Python 3 package for more recent Bright Cluster Manager software.

A yum install of the package will then place it.

The guide below is a guide for older versions of Bright, and is only useful as a kind of overview now.

(A version that worked with Bright Cluster Manager 6.1 is at https://kb.brightcomputing.com/knowledge-base/how-can-i-install-the-latest-python-in-bright/)
You can install Python 3.x in /cm/shared/apps and create an
environment module file to select when you want to use it:

Step 1 – Download the source code:

- wget http://python.org/ftp/python/3.3.4/Python-3.3.4.tar.xz

Step 2 – Build Python:
-  tar xf Python-3.3.4.tar.xz
- cd Python-3.3.4
- ./configure --prefix=/cm/shared/apps/python/3.3.4 --enable-shared
-  make && make altinstall
- cd /cm/shared/apps/python/3.3.4/bin  && ln -s python3.3 python

Step 3 – Create an environment module file:
- mkdir -p /cm/shared/modulefiles/python
- cd /cm/shared/modulefiles/python
– Create a text file e.g. vim  3.3.4 with the following contents:

#%Module -*- tcl -*-
## modulefile
proc ModulesHelp { } {

  puts stderr "\tAdds Python 3.3.4  to your environment variables,"

module-whatis "adds Adds Pyhton 3.3.4  to your environment variables"

set               root              /cm/shared/apps/python/3.3.4
prepend-path      PATH              $root/bin
prepend-path      LD_LIBRARY_PATH   $root/lib:$root/lib64

Example: Installing a python module (snakemake):
module load python/3.3.4
wget https://bitbucket.org/pypa/setuptools/raw/bootstrap/ez_setup.py

python3.3 ez_setup.py
curl https://raw.github.com/pypa/pip/master/contrib/get-pip.py  | python3.3 -

And install snakemake:

easy_install-3.3 snakemake

Updated on December 9, 2020

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