The virtualenvwrapper package is a set of extensions to the virtualenv tool. > import HTSeq > Virtual Environment Wrapper (virtualenvwrapper) Type "help", "copyright", "credits" or "license" for more information. (mysecondenv) scc1$ which htseq-count /projectnb/yourprojectname/venvs/mysecondenv/bin/htseq-count (mysecondenv) scc1$ python Python 3.7.7 (default, May 21 2020, 14:57:43) (mysecondenv) scc1$ pip install -r requirements.txt Collecting htseq scc1$ source /projectnb/yourprojectname/venvs/mysecondenv/bin/activate (mysecondenv) scc1$ # Install everything in the requirements file. scc1$ virtualenv /projectnb/yourprojectname/venvs/mysecondenv New python executable in /projectnb/yourprojectname/venvs/mysecondenv/bin/python Installing setuptools, pip, wheel.done. (mynewenv) scc1$ deactivate scc1$ # Build new virtualenv. # Exit/Deactivate current virtual environment. (mynewenv) scc1$ pip freeze -local > requirements.txt (mynewenv) scc1$ cat requirements.txt HTSeq=0.12.4 # Export list of packages in pip “requirements” format (you can give this to someone). scc1$ module load python3/3.7.7 scc1$ source /projectnb/yourprojectname/venvs/mynewenv/bin/activate (mynewenv) scc1$ # See what is installed in this virtualenv. > import HTSeq > exit() (mynewenv) scc1$ which htseq-count /projectnb/yourprojectname/venvs/mynewenv/bin/htseq-count # Exit/Deactivate the virtual environment (mynewenv) scc1$ deactivate scc1$ Exporting and Distributing Environments # Load the python module for the python version you wish to use. Successfully installed htseq-0.12.4 numpy-1.19.1 pysam-0.16.0.1 # Make sure it works (mynewenv) scc1$ which python /projectnb/yourprojectname/venvs/mynewenv/bin/python (mynewenv) scc1$ python Python 3.7.7 (default, May 21 2020, 14:57:43) Installing collected packages: numpy, pysam, htseq
"htseq") (mynewenv) scc1$ pip install htseq Collecting htseq # Activate it scc1$ source /projectnb/yourprojectname/venvs/mynewenv/bin/activate (mynewenv) scc1$ # Install packages into this virtualenv (e.g. scc1$ virtualenv /projectnb/yourprojectname/venvs/mynewenv New python executable in /projectnb/yourprojectname/venvs/mynewenv/bin/python Installing setuptools, pip, wheel.done.
scc1$ module load python3/3.8.10 # Create a virtual environment in your /projectnb/ space. # Load the python module for the python version you wish to use. The home directory is a not recommended due to strict space and file number quotas. Note: The recommended location for virtualenvs is in the /projectnb space of any project.
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