I am trying to install pysam manually as I am working on a cluster without internet connection and I do not have admin rights (thus doing it through conda is not possible, which I have tried). I have downloaded all the zipped files from the developer's repository (https://github.com/pysam-developers/pysam/archive/master.zip), then I transfer them to my directory in the cluster.
I have tried the manual installation from the unzipped repository by running (as indicated in the instructions https://github.com/pysam-developers/pysam/blob/master/INSTALL):
python path/to/pysam-master/setup.py build
But I get the following error:
# pysam: cython is available - using cythonize if necessary
Traceback (most recent call last):
File "path/to/pysam-master/setup.py", line 166, in <module>
import version
ImportError: No module named version
Line 165, 166 and 167 in the setup.py file are:
165. sys.path.insert(0, "pysam")
166. import version
167.version = version.__version__
Unfortunatelly, my knowledge has taken me only this far. Is it necessary to modify the setup.py file?
My system specs:
version.py is in path/to/pysam-master/pysam. The script uses the os-module to add the pysam directory to the working directory of the environment before importing:
sys.path.insert(0, "pysam")
So, this specific problem should be solved by replacing the "pysam" in
sys.path.insert(0, "pysam")
with the full path to the pysam-directory.