> import HTSeq > exit() # This package has binaries, they don’t work automatically scc1$ htseq-count -h -bash: htseq-count: command not found # Add the binary location to $PATH and it will be found scc1$ export PATH=/projectnb/projectname/mypython/bin:$PATH scc1$ htseq-count -h Usage: htseq-count alignment_file gff_file This script takes an alignment file in SAM/BAM format and a feature file in GFF format and calculates for each feature the number of reads mapping to it. done Stored in directory: ~/.cache/pip/wheels/cd/b4/6f/378ed9b24ccc1ced794835 Successfully built htseq Installing collected packages: htseq Successfully installed htseq-0.7.2 # Library location not automatic, export it to PYTHONPATH scc1$ export PYTHONPATH=/projectnb/projectname/mypython/lib/python2.7/site-packages:$PYTHONPATH # Test importing it scc1$ python Python 2.7.13 (default, Feb 8 2017, 12:51:33) on linux2 Type "help", "copyright", "credits" or "license" for more information. (from htseq) Building wheels for collected packages: htseq Running setup.py bdist_wheel for htseq. (from htseq) Requirement already satisfied: pysam>=0.9.0 in /share/pkg/python/2.7.13/. scc1$ module load python/2.7.13 # Install package scc1$ pip install -prefix=/projectnb/projectname/mypython/ htseq Collecting htseq Downloading HTSeq-0.7.2.tar.gz (548kB) 100% |#| 552kB 696kB/s Requirement already satisfied: numpy in /share/pkg/python/2.7.13/. We can export this as an environment variable.Įxample # Load the python module for the version you wish to use. The package cannot be used unless it is added to the library search path called $PYTHONPATH. projectnb/ projectname/ pythonlibs/lib/python X.Y/site-packages/ packagenameįor a package installed in a shared location, as above, the install location is unknown to Python. This allows libraries for different Python versions to be installed alongside one another. The Python directory structure separates packages by Python version, where X.Y are the major and minor versions. We recommend using it, but it is not required. The -no-cache-dir option disables the caching behavior of PIP. scc1$ pip install -no-cache-dir -prefix=/projectnb/ projectname/ pythonlibs packagename The library will be installed into the specified location using the standard Python directory structure. The /projectnb space is preferred to the home directory and /project space, where having many files will count against a stricter quota and where the library can be shared by members of the project. This is useful for creating a repository of shared Python packages in a project space such as /projectnb/. You can install packages in a specified location using “ pip” with the “ -prefix” option. Replace this placeholder with an actual version of the available python modules, such as “ 3.8.10“. ![]() Here we will use “ 3.X.Y” as the version of the python3 module. ![]() If you are interested in configuring entire Python environments, we suggest looking at virtual environments (virtualenv) as well.įirst, we need to load the relevant python module. The strategies laid out below will install personal versions of specific libraries. The “ pip” utility is the recommended tool for searching, downloading and installing packages from the PyPI. The Python Package Index (PyPI) contains thousands of complete Python packages and is the official repository for Python and. Install Third-Party and non-PyPI packages.Install a package to your home directory.PIP and the Python Package Index (PyPI).Always ensure software you are installing is from a credible, trusted source and that the URL or package name is correct. This advice applies to all software and repositories, but with particular current scrutiny on the PyPI repository and cupy packages. Please always double-check the name of any package before installing into your environment or on your local machine. The intention is to cause an installation of one of these packages if the package name is mistyped during installation by a user. Many of these have names which are slight misspellings of the names of other packages. Numerous packages containing malware/malicious links have been uploaded to the PyPI (Python Package Index) repository. You may request installation from RCS if you have difficulty installing or managing packages yourself. When this is the case, we provide directions below to help you install Python packages on your own. ![]() While we try to satisfy all requests for specific Python packages, we may not be able to meet your needs for various reasons. RCS maintains installations of Python for different versions and common packages for each version. ![]() There are many packages that extend Python’s standard functionality.
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