Exporting and Distributing Environments # Load the python module for the python version you wish to use. scc1$ virtualenv -system-site-packages /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. This allows your virtual environment to access the Python packages that are available as part of our Python modules. To give your virtual environment access to the system site-packages directory you can use the –system-site-packages flag. > import HTSeq > exit() (mynewenv) scc1$ which htseq-count /projectnb/yourprojectname/venvs/mynewenv/bin/htseq-count # Exit/Deactivate the virtual environment (mynewenv) scc1$ deactivate scc1$ Using the –system-site-packages flag Type "help", "copyright", "credits" or "license" for more information. 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. 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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