to run htseq-count on the systems server Nero so that it could be used on the nodes in jobs took a bit of doing

HTSeq is available from

http://htseq.readthedocs.io/ which links to https://pypi.python.org/pypi/HTSeq

unpack and then 'python setup.py build' and 'python setup.py install --prefix /cluster/nigeldyer/local' for a local installation avoiding the need to install in the root

the .profiles for the /home/nigeldyer and /cluster/nigeldyer need to be added to include

export PYTHONPATH=/cluster/nigeldyer/local/lib64/python2.6/site-packages/

However if the htseq-count is run to read a bam file the error

Please Install PySam to use the BAM_Reader Class (http://code.google.com/p/pysam/)Error occured when reading beginning of SAM/BAM file.
No module named pysam
[Exception type: ImportError, raised in __init__.py:937]

occurs. Intalling pysam using pip does not seem to work as pip does not support a local install and only a root install. Instead, download pysam from https://pypi.python.org/pypi/pysam, unpack and then then 'python setup.py build' and 'python setup.py install --prefix /cluster/nigeldyer/local' as before to do a local installation of pysam